WorldWideScience

Sample records for bioinformatically detectable group

  1. Bioinformatics

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren

    , and medicine will be particularly affected by the new results and the increased understanding of life at the molecular level. Bioinformatics is the development and application of computer methods for analysis, interpretation, and prediction, as well as for the design of experiments. It has emerged...

  2. The web server of IBM's Bioinformatics and Pattern Discovery group.

    Science.gov (United States)

    Huynh, Tien; Rigoutsos, Isidore; Parida, Laxmi; Platt, Daniel; Shibuya, Tetsuo

    2003-07-01

    We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences and the interactive annotation of amino acid sequences. Additionally, annotations for more than 70 archaeal, bacterial, eukaryotic and viral genomes are available on-line and can be searched interactively. The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

  3. Application of bioinformatics on the detection of pathogens by Pcr

    International Nuclear Information System (INIS)

    Rezig, Slim; Sakhri, Saber

    2007-01-01

    Salmonellas are the main responsible agent for the frequent food-borne gastrointestinal diseases. Their detection using classical methods are laborious and their results take a lot of time to be revealed. In this context, we tried to set up a revealing technique of the invA virulence gene, found in the majority of Salmonella species. After amplification with PCR using specific primers created and verified by bioinformatics programs, two couples of primers were set up and they appeared to be very specific and sensitive for the detection of invA gene. (Author)

  4. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

    Science.gov (United States)

    Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd.; Ayob, Mohd. Khan; Bakar, Mohd. Faizal Abu; Isa, Mohd Noor Mat

    2016-11-01

    In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE_71_length_93919_cov_158.931839_21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE_23_length_52851_cov_190.061386_17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE_106_length_32943_cov_169.147919_8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

  5. A Virtual Bioinformatics Knowledge Environment for Early Cancer Detection

    Science.gov (United States)

    Crichton, Daniel; Srivastava, Sudhir; Johnsey, Donald

    2003-01-01

    Discovery of disease biomarkers for cancer is a leading focus of early detection. The National Cancer Institute created a network of collaborating institutions focused on the discovery and validation of cancer biomarkers called the Early Detection Research Network (EDRN). Informatics plays a key role in enabling a virtual knowledge environment that provides scientists real time access to distributed data sets located at research institutions across the nation. The distributed and heterogeneous nature of the collaboration makes data sharing across institutions very difficult. EDRN has developed a comprehensive informatics effort focused on developing a national infrastructure enabling seamless access, sharing and discovery of science data resources across all EDRN sites. This paper will discuss the EDRN knowledge system architecture, its objectives and its accomplishments.

  6. Detecting the genetic link between Alzheimer's disease and obesity using bioinformatics analysis of GWAS data

    OpenAIRE

    Zhuang, Qi-Shuai; Zheng, Hao; Gu, Xiao-Dan; Shen, Liang; Ji, Hong-Fang

    2017-01-01

    Alzheimer's disease (AD) represents the major form of dementia in the elderly. In recent years, accumulating evidence indicate that obesity may act as a risk factor for AD, while the genetic link between the two conditions remains unclear. This bioinformatics analysis aimed to detect the genetic link between AD and obesity on single nucleotide polymorphisms (SNPs), gene, and pathway levels based on genome-wide association studies data. A total of 31 SNPs were found to be shared by AD and obes...

  7. The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update.

    Science.gov (United States)

    Huynh, Tien; Rigoutsos, Isidore

    2004-07-01

    In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. There is an increasing number of problems that these tools can help tackle; these problems range from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences, the identification--directly from sequence--of structural deviations from alpha-helicity and the annotation of amino acid sequences for antimicrobial activity. Additionally, annotations for more than 130 archaeal, bacterial, eukaryotic and viral genomes are now available on-line and can be searched interactively. The tools and code bundles continue to be accessible from http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

  8. Detecting Microsatellites in Genome Data: Variance in Definitions and Bioinformatic Approaches Cause Systematic Bias

    Directory of Open Access Journals (Sweden)

    Angelika Merkel

    2008-01-01

    Full Text Available Microsatellites are currently one of the most commonly used genetic markers. The application of bioinformatic tools has become common practice in the study of these short tandem repeats (STR. However, in silico studies can suffer from study bias. Using a meta-analysis on microsatellite distribution in yeast we show that estimates of numbers of repeats reported by different studies can differ in the order of several magnitudes, even within a single genome. These differences arise because varying definitions of microsatellites, spanning repeat size, array length and array composition, are used in different search paradigms, with minimum array length being the main influencing factor. Structural differences in the implemented search algorithm additionally contribute to variation in the number of repeats detected. We suggest that for future studies a consistent approach to STR searches is adopted in order to improve the power of intra- and interspecific comparisons

  9. Group discussion improves lie detection.

    Science.gov (United States)

    Klein, Nadav; Epley, Nicholas

    2015-06-16

    Groups of individuals can sometimes make more accurate judgments than the average individual could make alone. We tested whether this group advantage extends to lie detection, an exceptionally challenging judgment with accuracy rates rarely exceeding chance. In four experiments, we find that groups are consistently more accurate than individuals in distinguishing truths from lies, an effect that comes primarily from an increased ability to correctly identify when a person is lying. These experiments demonstrate that the group advantage in lie detection comes through the process of group discussion, and is not a product of aggregating individual opinions (a "wisdom-of-crowds" effect) or of altering response biases (such as reducing the "truth bias"). Interventions to improve lie detection typically focus on improving individual judgment, a costly and generally ineffective endeavor. Our findings suggest a cheap and simple synergistic approach of enabling group discussion before rendering a judgment.

  10. Using Informatics-, Bioinformatics- and Genomics-Based Approaches for the Molecular Surveillance and Detection of Biothreat Agents

    Science.gov (United States)

    Seto, Donald

    The convergence and wealth of informatics, bioinformatics and genomics methods and associated resources allow a comprehensive and rapid approach for the surveillance and detection of bacterial and viral organisms. Coupled with the continuing race for the fastest, most cost-efficient and highest-quality DNA sequencing technology, that is, "next generation sequencing", the detection of biological threat agents by `cheaper and faster' means is possible. With the application of improved bioinformatic tools for the understanding of these genomes and for parsing unique pathogen genome signatures, along with `state-of-the-art' informatics which include faster computational methods, equipment and databases, it is feasible to apply new algorithms to biothreat agent detection. Two such methods are high-throughput DNA sequencing-based and resequencing microarray-based identification. These are illustrated and validated by two examples involving human adenoviruses, both from real-world test beds.

  11. A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.

    Science.gov (United States)

    Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike; Khan, Arifa S

    2018-01-01

    Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have

  12. Aptamer Bioinformatics

    Directory of Open Access Journals (Sweden)

    Andrew B. Kinghorn

    2017-11-01

    Full Text Available Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment, an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. As aptamers are genetic in nature, bioinformatic approaches have been used to improve both aptamers and their selection. This review will discuss the advancements made in several enclaves of aptamer bioinformatics, including simulation of aptamer selection, fragment-based aptamer design, patterning of libraries, identification of lead aptamers from high-throughput sequencing (HTS data and in silico aptamer optimization.

  13. Applications in Bioastronautics and Bioinformatics: Early Radiation Cataracts Detected by Noninvasive, Quantitative, and Remote Means

    Science.gov (United States)

    Ansari, Rafat R.; King, James F.; Giblin, Frank J.

    2000-01-01

    Human exploration of Mars is a key goal in NASA's exploration planning in the next 20 years. Maintaining crew health and good vision is certainly an important aspect of achieving a successful mission. Continuous radiation exposure is a risk factor for radiation-induced cataracts in astronauts because radiation exposure in space travel has the potential of accelerating the aging process (ref. 1). A patented compact device (ref. 2) based on the technique of dynamic light scattering (DLS) was designed for monitoring an astronaut's ocular health during long-duration space travel. This capability of early diagnosis, unmatched by any other clinical technique in use today, may enable prompt initiation of preventive/curative therapy. An Internet web-based system integrating photon correlation data and controlling the hardware to monitor cataract development in vivo at a remote site in real time (teleophthalmology) is currently being developed. The new technology detects cataracts very early (at the molecular level). Cataract studies onboard the International Space Station will be helpful in quantifying any adverse effect of radiation to ocular health. The normal lens in a human eye, situated behind the cornea, is a transparent tissue. It contains 35 wt % protein and 65 wt % water. Aging, disease (e.g., diabetes), smoking, dehydration, malnutrition, and exposure to ultraviolet light and ionizing radiation can cause agglomeration of the lens proteins. Protein aggregation can take place anywhere in the lens, causing lens opacity. The aggregation and opacification could produce nuclear (central portion of the lens) or cortical (peripheral) cataracts. Nuclear and posterior subcapsular (the membrane's capsule surrounds the whole lens) cataracts, being on the visual optical axis of the eye, cause visual impairment that can finally lead to blindness. The lens proteins, in their native state, are small in size. As a cataract develops, this size grows from a few nanometers

  14. A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for Membrane Proteins

    Directory of Open Access Journals (Sweden)

    Teresa Milano

    2016-01-01

    Full Text Available The MocR bacterial transcriptional regulators are characterized by an N-terminal domain, 60 residues long on average, possessing the winged-helix-turn-helix (wHTH architecture responsible for DNA recognition and binding, linked to a large C-terminal domain (350 residues on average that is homologous to fold type-I pyridoxal 5′-phosphate (PLP dependent enzymes like aspartate aminotransferase (AAT. These regulators are involved in the expression of genes taking part in several metabolic pathways directly or indirectly connected to PLP chemistry, many of which are still uncharacterized. A bioinformatics analysis is here reported that studied the features of a distinct group of MocR regulators predicted to be functionally linked to a family of homologous genes coding for integral membrane proteins of unknown function. This group occurs mainly in the Actinobacteria and Gammaproteobacteria phyla. An analysis of the multiple sequence alignments of their wHTH and AAT domains suggested the presence of specificity-determining positions (SDPs. Mapping of SDPs onto a homology model of the AAT domain hinted at possible structural/functional roles in effector recognition. Likewise, SDPs in wHTH domain suggested the basis of specificity of Transcription Factor Binding Site recognition. The results reported represent a framework for rational design of experiments and for bioinformatics analysis of other MocR subgroups.

  15. Genome Exploitation and Bioinformatics Tools

    Science.gov (United States)

    de Jong, Anne; van Heel, Auke J.; Kuipers, Oscar P.

    Bioinformatic tools can greatly improve the efficiency of bacteriocin screening efforts by limiting the amount of strains. Different classes of bacteriocins can be detected in genomes by looking at different features. Finding small bacteriocins can be especially challenging due to low homology and because small open reading frames (ORFs) are often omitted from annotations. In this chapter, several bioinformatic tools/strategies to identify bacteriocins in genomes are discussed.

  16. Grouping by proximity in haptic contour detection

    OpenAIRE

    Overvliet, Krista; Krampe, Ralf; Wagemans, Johan

    2013-01-01

    We investigated the applicability of the Gestalt principle of perceptual grouping by proximity in the haptic modality. To do so, we investigated the influence of element proximity on haptic contour detection. In the course of four sessions ten participants performed a haptic contour detection task in which they freely explored a haptic random dot display that contained a contour in 50% of the trials. A contour was defined by a higher density of elements (raised dots), relative to the backgrou...

  17. Grouping by proximity in haptic contour detection.

    Science.gov (United States)

    Overvliet, Krista E; Krampe, Ralf Th; Wagemans, Johan

    2013-01-01

    We investigated the applicability of the Gestalt principle of perceptual grouping by proximity in the haptic modality. To do so, we investigated the influence of element proximity on haptic contour detection. In the course of four sessions ten participants performed a haptic contour detection task in which they freely explored a haptic random dot display that contained a contour in 50% of the trials. A contour was defined by a higher density of elements (raised dots), relative to the background surface. Proximity of the contour elements as well as the average proximity of background elements was systematically varied. We hypothesized that if proximity of contour elements influences haptic contour detection, detection will be more likely when contour elements are in closer proximity. This should be irrespective of the ratio with the proximity of the background elements. Results showed indeed that the closer the contour elements were, the higher the detection rates. Moreover, this was the case independent of the contour/background ratio. We conclude that the Gestalt law of proximity applies to haptic contour detection.

  18. Bioinformatics Approaches for Human Gut Microbiome Research

    Directory of Open Access Journals (Sweden)

    Zhijun Zheng

    2016-07-01

    Full Text Available The human microbiome has received much attention because many studies have reported that the human gut microbiome is associated with several diseases. The very large datasets that are produced by these kinds of studies means that bioinformatics approaches are crucial for their analysis. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also summarized the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our understanding of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and monitoring.

  19. Emerging strengths in Asia Pacific bioinformatics.

    Science.gov (United States)

    Ranganathan, Shoba; Hsu, Wen-Lian; Yang, Ueng-Cheng; Tan, Tin Wee

    2008-12-12

    The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.

  20. Possible Biomarkers for the Early Detection of HIV-associated Heart Diseases: A Proteomics and Bioinformatics Prediction

    Directory of Open Access Journals (Sweden)

    Suraiya Rasheed

    2015-01-01

    Full Text Available The frequency of cardiovascular disorders is increasing in HIV-infected individuals despite a significant reduction in the viral load by antiretroviral therapies (ART. Since the CD4+ T-cells are responsible for the viral load as well as immunological responses, we hypothesized that chronic HIV-infection of T-cells produces novel proteins/enzymes that cause cardiac dysfunctions. To identify specific factors that might cause cardiac disorders without the influence of numerous cofactors produced by other pathogenic microorganisms that co-inhabit most HIV-infected individuals, we analyzed genome-wide proteomes of a CD4+ T-cell line at different stages of HIV replication and cell growth over >6 months. Subtractive analyses of several hundred differentially regulated proteins from HIV-infected and uninfected counterpart cells and comparisons with proteins expressed from the same cells after treating with the antiviral drug Zidovudine/AZT and inhibiting virus replication, identified a well-coordinated network of 12 soluble/diffusible proteins in HIV-infected cells. Functional categorization, bioinformatics and statistical analyses of each protein predicted that the expression of cardiac-specific Ca2+ kinase together with multiple Ca2+ release channels causes a sustained overload of Ca2+ in the heart which induces fetal/cardiac myosin heavy chains (MYH6 and MYH7 and a myosin light-chain kinase. Each of these proteins has been shown to cause cardiac stress, arrhythmia, hypertrophic signaling, cardiomyopathy and heart failure (p = 8 × 10−11. Translational studies using the newly discovered proteins produced by HIV infection alone would provide additional biomarkers that could be added to the conventional markers for an early diagnosis and/or development of specific therapeutic interventions for heart diseases in HIV-infected individuals.

  1. Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data

    Directory of Open Access Journals (Sweden)

    Nathan D. Olson

    2017-09-01

    Full Text Available High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures are not sensitive enough and require either a known or culturable contaminant. Whole genome sequencing (WGS is a promising approach for detecting contaminants due to its sensitivity and lack of need for a priori assumptions about the contaminant. Prior to applying WGS, we must first understand its limitations for detecting contaminants and potential for false positives. Herein we demonstrate and characterize a WGS-based approach to detect organismal contaminants using an existing metagenomic taxonomic classification algorithm. Simulated WGS datasets from ten genera as individuals and binary mixtures of eight organisms at varying ratios were analyzed to evaluate the role of contaminant concentration and taxonomy on detection. For the individual genomes the false positive contaminants reported depended on the genus, with Staphylococcus, Escherichia, and Shigella having the highest proportion of false positives. For nearly all binary mixtures the contaminant was detected in the in-silico datasets at the equivalent of 1 in 1,000 cells, though F. tularensis was not detected in any of the simulated contaminant mixtures and Y. pestis was only detected at the equivalent of one in 10 cells. Once a WGS method for detecting contaminants is characterized, it can be applied to evaluate microbial material purity, in efforts to ensure that contaminants are characterized in microbial materials used to validate pathogen detection assays, generate genome assemblies for database submission, and benchmark sequencing methods.

  2. The 2016 Bioinformatics Open Source Conference (BOSC).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

    2016-01-01

    Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

  3. Rising Strengths Hong Kong SAR in Bioinformatics.

    Science.gov (United States)

    Chakraborty, Chiranjib; George Priya Doss, C; Zhu, Hailong; Agoramoorthy, Govindasamy

    2017-06-01

    Hong Kong's bioinformatics sector is attaining new heights in combination with its economic boom and the predominance of the working-age group in its population. Factors such as a knowledge-based and free-market economy have contributed towards a prominent position on the world map of bioinformatics. In this review, we have considered the educational measures, landmark research activities and the achievements of bioinformatics companies and the role of the Hong Kong government in the establishment of bioinformatics as strength. However, several hurdles remain. New government policies will assist computational biologists to overcome these hurdles and further raise the profile of the field. There is a high expectation that bioinformatics in Hong Kong will be a promising area for the next generation.

  4. Biggest challenges in bioinformatics.

    Science.gov (United States)

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-04-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the 'Biggest Challenges in Bioinformatics' in a 'World Café' style event.

  5. Biggest challenges in bioinformatics

    OpenAIRE

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-01-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held in October at Heidelberg University in Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the ‘Biggest Challenges in Bioinformatics' in a ‘World Café' style event.

  6. Working Group 3: Greenhouse signal detection

    International Nuclear Information System (INIS)

    Barnett, T.; Ellsaesser, H.; Groisman, P.Ya.; Grotch, S.; Jenkins, G.; Karoly, D.; Riches, M.; Santer, B.; Schoenwiese, C.; Vinnikov, K.; Zwiers, F.

    1990-01-01

    Quantitative efforts to detect the greenhouse-gas signal (GHG) in nature are in their infancy. The reasons for this state of affairs are numerous. It is only in the last few years that GCMs have advanced to the point where their simulations of GHG signals might be marginally believable. Without reasonably good a priori predictions of expected GHG signals from the models, the detection problem is moot. The observational data sets describing changes in the global climate system over the last 50-100 years needed for adequate detection studies have also only come into existence in the last five years. Finally, no coherent, generally-agreed-on detection strategy has been developed by the scientific community interested in the GHG problem. The lack of adequate model predictions and observational sets are largely responsible for this latter condition. The rudimentary detection efforts that have been conducted have generally been based on recognizing the fingerprint of GHG signals in the oceans and atmosphere. GCM results for 1 x 2 x CO 2 equilibrium runs have been used to search for GHG effects induced in tropospheric air and ocean surface temperature fields since the early 1900s. No significant effect has been found

  7. Bioinformatics and Cancer

    Science.gov (United States)

    Researchers take on challenges and opportunities to mine "Big Data" for answers to complex biological questions. Learn how bioinformatics uses advanced computing, mathematics, and technological platforms to store, manage, analyze, and understand data.

  8. Deep learning in bioinformatics.

    Science.gov (United States)

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2017-09-01

    In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Computational Biology and Bioinformatics in Nigeria

    Science.gov (United States)

    Fatumo, Segun A.; Adoga, Moses P.; Ojo, Opeolu O.; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

    2014-01-01

    Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries. PMID:24763310

  10. Computational biology and bioinformatics in Nigeria.

    Directory of Open Access Journals (Sweden)

    Segun A Fatumo

    2014-04-01

    Full Text Available Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  11. Computational biology and bioinformatics in Nigeria.

    Science.gov (United States)

    Fatumo, Segun A; Adoga, Moses P; Ojo, Opeolu O; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

    2014-04-01

    Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  12. Bioinformatics in the information age

    Energy Technology Data Exchange (ETDEWEB)

    Spengler, Sylvia J.

    2000-02-01

    There is a well-known story about the blind man examining the elephant: the part of the elephant examined determines his perception of the whole beast. Perhaps bioinformatics--the shotgun marriage between biology and mathematics, computer science, and engineering--is like an elephant that occupies a large chair in the scientific living room. Given the demand for and shortage of researchers with the computer skills to handle large volumes of biological data, where exactly does the bioinformatics elephant sit? There are probably many biologists who feel that a major product of this bioinformatics elephant is large piles of waste material. If you have tried to plow through Web sites and software packages in search of a specific tool for analyzing and collating large amounts of research data, you may well feel the same way. But there has been progress with major initiatives to develop more computing power, educate biologists about computers, increase funding, and set standards. For our purposes, bioinformatics is not simply a biologically inclined rehash of information theory (1) nor is it a hodgepodge of computer science techniques for building, updating, and accessing biological data. Rather bioinformatics incorporates both of these capabilities into a broad interdisciplinary science that involves both conceptual and practical tools for the understanding, generation, processing, and propagation of biological information. As such, bioinformatics is the sine qua non of 21st-century biology. Analyzing gene expression using cDNA microarrays immobilized on slides or other solid supports (gene chips) is set to revolutionize biology and medicine and, in so doing, generate vast quantities of data that have to be accurately interpreted (Fig. 1). As discussed at a meeting a few months ago (Microarray Algorithms and Statistical Analysis: Methods and Standards; Tahoe City, California; 9-12 November 1999), experiments with cDNA arrays must be subjected to quality control

  13. Towards Detecting Group Identities in Complex Artificial Societies

    DEFF Research Database (Denmark)

    Grappiolo, Corrado; Yannakakis, Georgios N.

    2012-01-01

    This paper presents a framework for modelling group struc- tures and dynamics in both artificial societies and human-populated vir- tual environments such as computer games. The group modelling (GM) framework proposed focuses on the detection of existing, pre-defined group structures and is compo......This paper presents a framework for modelling group struc- tures and dynamics in both artificial societies and human-populated vir- tual environments such as computer games. The group modelling (GM) framework proposed focuses on the detection of existing, pre-defined group structures...

  14. Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information.

    Science.gov (United States)

    Tang, Zaixiang; Shen, Yueping; Li, Yan; Zhang, Xinyan; Wen, Jia; Qian, Chen'ao; Zhuang, Wenzhuo; Shi, Xinghua; Yi, Nengjun

    2018-03-15

    Large-scale molecular data have been increasingly used as an important resource for prognostic prediction of diseases and detection of associated genes. However, standard approaches for omics data analysis ignore the group structure among genes encoded in functional relationships or pathway information. We propose new Bayesian hierarchical generalized linear models, called group spike-and-slab lasso GLMs, for predicting disease outcomes and detecting associated genes by incorporating large-scale molecular data and group structures. The proposed model employs a mixture double-exponential prior for coefficients that induces self-adaptive shrinkage amount on different coefficients. The group information is incorporated into the model by setting group-specific parameters. We have developed a fast and stable deterministic algorithm to fit the proposed hierarchal GLMs, which can perform variable selection within groups. We assess the performance of the proposed method on several simulated scenarios, by varying the overlap among groups, group size, number of non-null groups, and the correlation within group. Compared with existing methods, the proposed method provides not only more accurate estimates of the parameters but also better prediction. We further demonstrate the application of the proposed procedure on three cancer datasets by utilizing pathway structures of genes. Our results show that the proposed method generates powerful models for predicting disease outcomes and detecting associated genes. The methods have been implemented in a freely available R package BhGLM (http://www.ssg.uab.edu/bhglm/). nyi@uab.edu. Supplementary data are available at Bioinformatics online.

  15. Teaching bioinformatics to engineers.

    Science.gov (United States)

    Mihalas, George I; Tudor, Anca; Paralescu, Sorin; Andor, Minodora; Stoicu-Tivadar, Lacramioara

    2014-01-01

    The paper refers to our methodology and experience in establishing the content of the course in bioinformatics introduced to the school of "Information Systems in Healthcare" (SIIS), master level. The syllabi of both lectures and laboratory works are presented and discussed.

  16. Abnormality degree detection method using negative potential field group detectors

    Science.gov (United States)

    Zhang, Hongli; Liu, Shulin; Li, Dong; Shi, Kunju; Wang, Bo; Cui, Jiqiang

    2015-09-01

    Online monitoring methods have been widely used in many major devices, however the normal and abnormal states of equipment are estimated mainly based on the monitoring results whether monitored parameters exceed the setting thresholds. Using these monitoring methods may cause serious false positive or false negative results. In order to precisely monitor the state of equipment, the problem of abnormality degree detection without fault sample is studied with a new detection method called negative potential field group detectors(NPFG-detectors). This method achieves the quantitative expression of abnormality degree and provides the better detection results compared with other methods. In the process of Iris data set simulation, the new algorithm obtains the successful results in abnormal detection. The detection rates for 3 types of Iris data set respectively reach 100%, 91.6%, and 95.24% with 50% training samples. The problem of Bearing abnormality degree detection via an abnormality degree curve is successfully solved.

  17. Bioinformatics for Exploration

    Science.gov (United States)

    Johnson, Kathy A.

    2006-01-01

    For the purpose of this paper, bioinformatics is defined as the application of computer technology to the management of biological information. It can be thought of as the science of developing computer databases and algorithms to facilitate and expedite biological research. This is a crosscutting capability that supports nearly all human health areas ranging from computational modeling, to pharmacodynamics research projects, to decision support systems within autonomous medical care. Bioinformatics serves to increase the efficiency and effectiveness of the life sciences research program. It provides data, information, and knowledge capture which further supports management of the bioastronautics research roadmap - identifying gaps that still remain and enabling the determination of which risks have been addressed.

  18. Advance in structural bioinformatics

    CERN Document Server

    Wei, Dongqing; Zhao, Tangzhen; Dai, Hao

    2014-01-01

    This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conform

  19. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  20. Crowdsourcing for bioinformatics.

    Science.gov (United States)

    Good, Benjamin M; Su, Andrew I

    2013-08-15

    Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base population and protein structure determination all benefit from human input. In some cases, people are needed in vast quantities, whereas in others, we need just a few with rare abilities. Crowdsourcing encompasses an emerging collection of approaches for harnessing such distributed human intelligence. Recently, the bioinformatics community has begun to apply crowdsourcing in a variety of contexts, yet few resources are available that describe how these human-powered systems work and how to use them effectively in scientific domains. Here, we provide a framework for understanding and applying several different types of crowdsourcing. The framework considers two broad classes: systems for solving large-volume 'microtasks' and systems for solving high-difficulty 'megatasks'. Within these classes, we discuss system types, including volunteer labor, games with a purpose, microtask markets and open innovation contests. We illustrate each system type with successful examples in bioinformatics and conclude with a guide for matching problems to crowdsourcing solutions that highlights the positives and negatives of different approaches.

  1. Complex Event Detection in Pedestrian Groups from Uavs

    Science.gov (United States)

    Burkert, F.; Butenuth, M.

    2012-07-01

    We present a new hierarchical event detection approach for highly complex scenarios in pedestrian groups on the basis of airborne image sequences from UAVs. Related work on event detection for pedestrians is capable of learning and analyzing recurring motion paths to detect abnormal paths and of analyzing the type of motion interaction between pairs of pedestrians. However, these approaches can only describe basic motion and fail at the analysis of pedestrian groups with complex behavior. We overcome the limitations of the related work by using a dynamic pedestrian graph of a scene which contains basic pairwise pedestrian motion interaction labels in the first layer. In the second layer, pedestrian groups are analyzed based on the dynamic pedestrian graph in order to get higher-level information about group behavior. This is done by a heuristic assignment of predefined scenarios out of a model library to the data. The assignment is based on the motion interaction labels, on dynamic group motion parameters and on a set of subgraph features. Experimental results are shown based on a new UAV dataset which contains group motion of different complexity levels.

  2. COMPLEX EVENT DETECTION IN PEDESTRIAN GROUPS FROM UAVS

    Directory of Open Access Journals (Sweden)

    F. Burkert

    2012-07-01

    Full Text Available We present a new hierarchical event detection approach for highly complex scenarios in pedestrian groups on the basis of airborne image sequences from UAVs. Related work on event detection for pedestrians is capable of learning and analyzing recurring motion paths to detect abnormal paths and of analyzing the type of motion interaction between pairs of pedestrians. However, these approaches can only describe basic motion and fail at the analysis of pedestrian groups with complex behavior. We overcome the limitations of the related work by using a dynamic pedestrian graph of a scene which contains basic pairwise pedestrian motion interaction labels in the first layer. In the second layer, pedestrian groups are analyzed based on the dynamic pedestrian graph in order to get higher-level information about group behavior. This is done by a heuristic assignment of predefined scenarios out of a model library to the data. The assignment is based on the motion interaction labels, on dynamic group motion parameters and on a set of subgraph features. Experimental results are shown based on a new UAV dataset which contains group motion of different complexity levels.

  3. Bioinformatics: A History of Evolution "In Silico"

    Science.gov (United States)

    Ondrej, Vladan; Dvorak, Petr

    2012-01-01

    Bioinformatics, biological databases, and the worldwide use of computers have accelerated biological research in many fields, such as evolutionary biology. Here, we describe a primer of nucleotide sequence management and the construction of a phylogenetic tree with two examples; the two selected are from completely different groups of organisms:…

  4. Heme detection in parasitic protists of the group Trypanosomatidae

    OpenAIRE

    KOVÁŘOVÁ, Julie

    2010-01-01

    This study deals with detection of heme in three different species of the group Trypanosomatidae: Trypanosoma brucei, Leishmania tarentolae and Phytomonas serpens. The main goal was to improve the current knowledge about heme metabolism in Phytomonas serpens. It was found that P. serpens does not require heme for growth, though it does ingest it if available.

  5. Flow cytometry bioinformatics.

    Directory of Open Access Journals (Sweden)

    Kieran O'Neill

    Full Text Available Flow cytometry bioinformatics is the application of bioinformatics to flow cytometry data, which involves storing, retrieving, organizing, and analyzing flow cytometry data using extensive computational resources and tools. Flow cytometry bioinformatics requires extensive use of and contributes to the development of techniques from computational statistics and machine learning. Flow cytometry and related methods allow the quantification of multiple independent biomarkers on large numbers of single cells. The rapid growth in the multidimensionality and throughput of flow cytometry data, particularly in the 2000s, has led to the creation of a variety of computational analysis methods, data standards, and public databases for the sharing of results. Computational methods exist to assist in the preprocessing of flow cytometry data, identifying cell populations within it, matching those cell populations across samples, and performing diagnosis and discovery using the results of previous steps. For preprocessing, this includes compensating for spectral overlap, transforming data onto scales conducive to visualization and analysis, assessing data for quality, and normalizing data across samples and experiments. For population identification, tools are available to aid traditional manual identification of populations in two-dimensional scatter plots (gating, to use dimensionality reduction to aid gating, and to find populations automatically in higher dimensional space in a variety of ways. It is also possible to characterize data in more comprehensive ways, such as the density-guided binary space partitioning technique known as probability binning, or by combinatorial gating. Finally, diagnosis using flow cytometry data can be aided by supervised learning techniques, and discovery of new cell types of biological importance by high-throughput statistical methods, as part of pipelines incorporating all of the aforementioned methods. Open standards, data

  6. The 2015 Bioinformatics Open Source Conference (BOSC 2015.

    Directory of Open Access Journals (Sweden)

    Nomi L Harris

    2016-02-01

    Full Text Available The Bioinformatics Open Source Conference (BOSC is organized by the Open Bioinformatics Foundation (OBF, a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG before the annual Intelligent Systems in Molecular Biology (ISMB conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

  7. The 2015 Bioinformatics Open Source Conference (BOSC 2015).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

    2016-02-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

  8. Emergent Computation Emphasizing Bioinformatics

    CERN Document Server

    Simon, Matthew

    2005-01-01

    Emergent Computation is concerned with recent applications of Mathematical Linguistics or Automata Theory. This subject has a primary focus upon "Bioinformatics" (the Genome and arising interest in the Proteome), but the closing chapter also examines applications in Biology, Medicine, Anthropology, etc. The book is composed of an organized examination of DNA, RNA, and the assembly of amino acids into proteins. Rather than examine these areas from a purely mathematical viewpoint (that excludes much of the biochemical reality), the author uses scientific papers written mostly by biochemists based upon their laboratory observations. Thus while DNA may exist in its double stranded form, triple stranded forms are not excluded. Similarly, while bases exist in Watson-Crick complements, mismatched bases and abasic pairs are not excluded, nor are Hoogsteen bonds. Just as there are four bases naturally found in DNA, the existence of additional bases is not ignored, nor amino acids in addition to the usual complement of...

  9. Bioinformatics meets parasitology.

    Science.gov (United States)

    Cantacessi, C; Campbell, B E; Jex, A R; Young, N D; Hall, R S; Ranganathan, S; Gasser, R B

    2012-05-01

    The advent and integration of high-throughput '-omics' technologies (e.g. genomics, transcriptomics, proteomics, metabolomics, glycomics and lipidomics) are revolutionizing the way biology is done, allowing the systems biology of organisms to be explored. These technologies are now providing unique opportunities for global, molecular investigations of parasites. For example, studies of a transcriptome (all transcripts in an organism, tissue or cell) have become instrumental in providing insights into aspects of gene expression, regulation and function in a parasite, which is a major step to understanding its biology. The purpose of this article was to review recent applications of next-generation sequencing technologies and bioinformatic tools to large-scale investigations of the transcriptomes of parasitic nematodes of socio-economic significance (particularly key species of the order Strongylida) and to indicate the prospects and implications of these explorations for developing novel methods of parasite intervention. © 2011 Blackwell Publishing Ltd.

  10. LXtoo: an integrated live Linux distribution for the bioinformatics community.

    Science.gov (United States)

    Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

    2012-07-19

    Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

  11. Virtual Bioinformatics Distance Learning Suite

    Science.gov (United States)

    Tolvanen, Martti; Vihinen, Mauno

    2004-01-01

    Distance learning as a computer-aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material…

  12. Interdisciplinary Introductory Course in Bioinformatics

    Science.gov (United States)

    Kortsarts, Yana; Morris, Robert W.; Utell, Janine M.

    2010-01-01

    Bioinformatics is a relatively new interdisciplinary field that integrates computer science, mathematics, biology, and information technology to manage, analyze, and understand biological, biochemical and biophysical information. We present our experience in teaching an interdisciplinary course, Introduction to Bioinformatics, which was developed…

  13. Extending Abdominal Aortic Aneurysm Detection to Older Age Groups

    DEFF Research Database (Denmark)

    Makrygiannis, Georgios; Labalue, Philippe; Erpicum, Marie

    2016-01-01

    . Current screening policies (e.g., men aged 65-74 years), however, do not account for aging and increased life expectancy of Western populations. This study investigated AAA detection by extending the target population to older age groups (75-85 years). METHODS: AAA screening was conducted in the County......-74 age group but rose to 7.3% in the age-extended group (75-85 years). Further in addition to age, height, current smoking, history of coronary artery disease, hypercholesterolemia, peripheral artery disease of the lower limbs, and varicose veins were significantly associated with the presence of AAA......BACKGROUND: There is evident benefit in terms of reduced aneurysm-related mortality from screening programs of abdominal aortic aneurysm (AAA) in men aged 65 years and more. Recent studies in the United Kingdom and Sweden have shown a decline of the prevalence of AAA in the general population...

  14. Leak detection in turbo group condensers using helium

    International Nuclear Information System (INIS)

    Gomez Cores, C.; Lloret, J.

    1997-01-01

    This method allows a rapid location of leaks (small or not) in the pipelines of a turbo group condenser, before opening the condenser boxes and no need of stooping the turbo group operation. This operation can last two hours maximum depending on the volume of the box or semi box. The technique consists of injecting helium into the water side and detecting it in the steam side, in the outlet of not condensable gases of the ejector. In the same way, probable air inlet to the condenser can be proved (auxiliary systems, turbo group joints to the condenser, etc.) in order to improve the vacuum and/or reduce the quantity of oxygen dissolved in the water of the steam side. (author) [es

  15. VLSI Microsystem for Rapid Bioinformatic Pattern Recognition

    Science.gov (United States)

    Fang, Wai-Chi; Lue, Jaw-Chyng

    2009-01-01

    A system comprising very-large-scale integrated (VLSI) circuits is being developed as a means of bioinformatics-oriented analysis and recognition of patterns of fluorescence generated in a microarray in an advanced, highly miniaturized, portable genetic-expression-assay instrument. Such an instrument implements an on-chip combination of polymerase chain reactions and electrochemical transduction for amplification and detection of deoxyribonucleic acid (DNA).

  16. Group-based Motion Detection for Energy-Efficient Localisation

    Directory of Open Access Journals (Sweden)

    Alban Cotillon

    2012-10-01

    Full Text Available Long-term outdoor localization remains challenging due to the high energy profiles of GPS modules. Duty cycling the GPS module combined with inertial sensors can improve energy consumption. However, inertial sensors that are kept active all the time can also drain mobile node batteries. This paper proposes duty cycling strategies for inertial sensors to maintain a target position accuracy and node lifetime. We present a method for duty cycling motion sensors according to features of movement events, and evaluate its energy and accuracy profile for an empirical data trace of cattle movement. We further introduce the concept of group-based duty cycling, where nodes that cluster together can share the burden of motion detection to reduce their duty cycles. Our evaluation shows that both variants of motion sensor duty cycling yield up to 78% improvement in overall node power consumption, and that the group-based method yields an additional 20% power reduction during periods of low mobility.

  17. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  18. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software.

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians.

  19. Detection of Electronic Anklet Wearers’ Groupings throughout Telematics Monitoring

    Directory of Open Access Journals (Sweden)

    Paulo Lima Machado

    2017-01-01

    Full Text Available Ankle bracelets (anklets imposed by law to track convicted individuals are being used in many countries as an alternative to overloaded prisons. There are many different systems for monitoring individuals wearing such devices, and these electronic anklet monitoring systems commonly detect violations of circulation areas permitted to holders. In spite of being able to monitor individual localization, such systems do not identify grouping activities of the monitored individuals, although this kind of event could represent a real risk of further offenses planned by those individuals. In order to address such a problem and to help monitoring systems to be able to have a proactive approach, this paper proposes sensor data fusion algorithms that are able to identify such groups based on data provided by anklet positioning devices. The results from the proposed algorithms can be applied to support risk assessment in the context of monitoring systems. The processing is performed using geographic points collected by a monitoring center, and as result, it produces a history of groups with their members, timestamps, locations and frequency of meetings. The proposed algorithms are validated in various serial and parallel computing scenarios, and the correspondent results are presented and discussed. The information produced by the proposed algorithms yields to a better characterization of the monitored individuals and can be adapted to support decision-making systems used by authorities that are responsible for planning decisions regarding actions affecting public security.

  20. How to test bioinformatics software?

    Science.gov (United States)

    Kamali, Amir Hossein; Giannoulatou, Eleni; Chen, Tsong Yueh; Charleston, Michael A; McEwan, Alistair L; Ho, Joshua W K

    2015-09-01

    Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Bioinformatics programs developed for computational simulation and large-scale data analysis are widely used in almost all areas of biophysics. The appropriate choice of algorithms and correct implementation of these algorithms are critical for obtaining reliable computational results. Nonetheless, it is often very difficult to systematically test these programs as it is often hard to verify the correctness of the output, and to effectively generate failure-revealing test cases. Software testing is an important process of verification and validation of scientific software, but very few studies have directly dealt with the issues of bioinformatics software testing. In this work, we review important concepts and state-of-the-art methods in the field of software testing. We also discuss recent reports on adapting and implementing software testing methodologies in the bioinformatics field, with specific examples drawn from systems biology and genomic medicine.

  1. Designing XML schemas for bioinformatics.

    Science.gov (United States)

    Bruhn, Russel Elton; Burton, Philip John

    2003-06-01

    Data interchange bioinformatics databases will, in the future, most likely take place using extensible markup language (XML). The document structure will be described by an XML Schema rather than a document type definition (DTD). To ensure flexibility, the XML Schema must incorporate aspects of Object-Oriented Modeling. This impinges on the choice of the data model, which, in turn, is based on the organization of bioinformatics data by biologists. Thus, there is a need for the general bioinformatics community to be aware of the design issues relating to XML Schema. This paper, which is aimed at a general bioinformatics audience, uses examples to describe the differences between a DTD and an XML Schema and indicates how Unified Modeling Language diagrams may be used to incorporate Object-Oriented Modeling in the design of schema.

  2. CirComPara: A Multi‐Method Comparative  Bioinformatics Pipeline to Detect and Study circRNAs from RNA‐seq Data

    Directory of Open Access Journals (Sweden)

    Enrico Gaffo

    2017-02-01

    Full Text Available Circular RNAs (circRNAs are generated by backsplicing of immature RNA forming covalently closed loops of intron/exon RNA molecules. Pervasiveness, evolutionary conservation, massive and regulated expression, and posttranscriptional regulatory roles of circRNAs in eukaryotes have been appreciated and described only recently. Moreover, being easily detectable disease markers, circRNAs undoubtedly represent a molecular class with high bearing on molecular pathobiology. CircRNAs can be detected from RNAseq data using appropriate computational methods to identify the sequence reads spanning backsplice junctions that do not colinearly map to the reference genome. To this end, several programs were developed and critical assessment of various strategies and tools suggested the combination of at least two methods as good practice to guarantee robust circRNA detection. Here,we present CirComPara (http://github.com/egaffo/CirComPara, an automated bioinformatics pipeline, to detect, quantify and annotate circRNAs from RNAseq data using in parallel four different methods for backsplice identification. CirComPara also provides quantification of linear RNAs and gene expression, ultimately comparing and correlating circRNA and gene/transcript expression level. We applied our method to RNAseqdata of monocyte and macrophage samples in relation to haploinsufficiency of the RNAbinding splicing factor Quaking (QKI. The biological relevance of the results, in terms of number, types and variations of circRNAs expressed, illustrates CirComPara potential to enlarge the knowledge of the transcriptome, adding details on the circRNAome, and facilitating further computational and experimental studies.

  3. Emerging strengths in Asia Pacific bioinformatics

    OpenAIRE

    Ranganathan, Shoba; Hsu, Wen-Lian; Yang, Ueng-Cheng; Tan, Tin Wee

    2008-01-01

    The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20?23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology,...

  4. Taking Bioinformatics to Systems Medicine.

    Science.gov (United States)

    van Kampen, Antoine H C; Moerland, Perry D

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically contributes to systems medicine. First, we explain the role of bioinformatics in the management and analysis of data. In particular we show the importance of publicly available biological and clinical repositories to support systems medicine studies. Second, we discuss how the integration and analysis of multiple types of omics data through integrative bioinformatics may facilitate the determination of more predictive and robust disease signatures, lead to a better understanding of (patho)physiological molecular mechanisms, and facilitate personalized medicine. Third, we focus on network analysis and discuss how gene networks can be constructed from omics data and how these networks can be decomposed into smaller modules. We discuss how the resulting modules can be used to generate experimentally testable hypotheses, provide insight into disease mechanisms, and lead to predictive models. Throughout, we provide several examples demonstrating how bioinformatics contributes to systems medicine and discuss future challenges in bioinformatics that need to be addressed to enable the advancement of systems medicine.

  5. Generalized Centroid Estimators in Bioinformatics

    Science.gov (United States)

    Hamada, Michiaki; Kiryu, Hisanori; Iwasaki, Wataru; Asai, Kiyoshi

    2011-01-01

    In a number of estimation problems in bioinformatics, accuracy measures of the target problem are usually given, and it is important to design estimators that are suitable to those accuracy measures. However, there is often a discrepancy between an employed estimator and a given accuracy measure of the problem. In this study, we introduce a general class of efficient estimators for estimation problems on high-dimensional binary spaces, which represent many fundamental problems in bioinformatics. Theoretical analysis reveals that the proposed estimators generally fit with commonly-used accuracy measures (e.g. sensitivity, PPV, MCC and F-score) as well as it can be computed efficiently in many cases, and cover a wide range of problems in bioinformatics from the viewpoint of the principle of maximum expected accuracy (MEA). It is also shown that some important algorithms in bioinformatics can be interpreted in a unified manner. Not only the concept presented in this paper gives a useful framework to design MEA-based estimators but also it is highly extendable and sheds new light on many problems in bioinformatics. PMID:21365017

  6. Bioinformatics in translational drug discovery.

    Science.gov (United States)

    Wooller, Sarah K; Benstead-Hume, Graeme; Chen, Xiangrong; Ali, Yusuf; Pearl, Frances M G

    2017-08-31

    Bioinformatics approaches are becoming ever more essential in translational drug discovery both in academia and within the pharmaceutical industry. Computational exploitation of the increasing volumes of data generated during all phases of drug discovery is enabling key challenges of the process to be addressed. Here, we highlight some of the areas in which bioinformatics resources and methods are being developed to support the drug discovery pipeline. These include the creation of large data warehouses, bioinformatics algorithms to analyse 'big data' that identify novel drug targets and/or biomarkers, programs to assess the tractability of targets, and prediction of repositioning opportunities that use licensed drugs to treat additional indications. © 2017 The Author(s).

  7. An innovative approach for testing bioinformatics programs using metamorphic testing

    Directory of Open Access Journals (Sweden)

    Liu Huai

    2009-01-01

    Full Text Available Abstract Background Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered. Results We propose to use a novel software testing technique, metamorphic testing (MT, to test a range of bioinformatics programs. Instead of requiring a mechanism to verify whether an individual test output is correct, the MT technique verifies whether a pair of test outputs conform to a set of domain specific properties, called metamorphic relations (MRs, thus greatly increases the number and variety of test cases that can be applied. To demonstrate how MT is used in practice, we applied MT to test two open-source bioinformatics programs, namely GNLab and SeqMap. In particular we show that MT is simple to implement, and is effective in detecting faults in a real-life program and some artificially fault-seeded programs. Further, we discuss how MT can be applied to test programs from various domains of bioinformatics. Conclusion This paper describes the application of a simple, effective and automated technique to systematically test a range of bioinformatics programs. We show how MT can be implemented in practice through two real-life case studies. Since many bioinformatics programs, particularly those for large scale simulation and data analysis, are hard to test systematically, their developers may benefit from using MT as part of the testing strategy. Therefore our work

  8. The secondary metabolite bioinformatics portal

    DEFF Research Database (Denmark)

    Weber, Tilmann; Kim, Hyun Uk

    2016-01-01

    . In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http......://www.secondarymetabolites.org) is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field....

  9. Bioinformatics analysis of circulating cell-free DNA sequencing data.

    Science.gov (United States)

    Chan, Landon L; Jiang, Peiyong

    2015-10-01

    The discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis. Cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases. The advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cell-free DNA molecules in plasma in a genome-wide fashion and at single-base resolution. Consequently, clinical applications of circulating cell-free DNA analysis have not only revolutionized noninvasive prenatal diagnosis but also facilitated cancer detection and monitoring toward an era of blood-based personalized medicine. With the remarkably increasing throughput and lowering cost of next generation sequencing, bioinformatics analysis becomes increasingly demanding to understand the large amount of data generated by these sequencing platforms. In this Review, we highlight the major bioinformatics algorithms involved in the analysis of cell-free DNA sequencing data. Firstly, we briefly describe the biological properties of these molecules and provide an overview of the general bioinformatics approach for the analysis of cell-free DNA. Then, we discuss the specific upstream bioinformatics considerations concerning the analysis of sequencing data of circulating cell-free DNA, followed by further detailed elaboration on each key clinical situation in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved. We also discuss bioinformatics analysis as well as clinical applications of the newly developed massively parallel bisulfite sequencing of cell-free DNA. Finally, we offer our perspectives on the future development of bioinformatics in noninvasive diagnosis. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  10. Taking Bioinformatics to Systems Medicine

    NARCIS (Netherlands)

    van Kampen, Antoine H. C.; Moerland, Perry D.

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically

  11. Bioinformatics and the Undergraduate Curriculum

    Science.gov (United States)

    Maloney, Mark; Parker, Jeffrey; LeBlanc, Mark; Woodard, Craig T.; Glackin, Mary; Hanrahan, Michael

    2010-01-01

    Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of…

  12. Reproducible Bioinformatics Research for Biologists

    Science.gov (United States)

    This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

  13. The Aspergillus Mine - publishing bioinformatics

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla; Rasmussen, Jane Lind Nybo; Theobald, Sebastian

    with the Joint Genome Institute. The Aspergillus Mine is not intended as a genomic data sharing service but instead focuses on creating an environment where the results of bioinformatic analysis is made available for inspection. The data and code is public upon request and figures can be obtained directly from...

  14. Bioinformatics of genomic association mapping

    NARCIS (Netherlands)

    Vaez Barzani, Ahmad

    2015-01-01

    In this thesis we present an overview of bioinformatics-based approaches for genomic association mapping, with emphasis on human quantitative traits and their contribution to complex diseases. We aim to provide a comprehensive walk-through of the classic steps of genomic association mapping

  15. Computational intelligence techniques in bioinformatics.

    Science.gov (United States)

    Hassanien, Aboul Ella; Al-Shammari, Eiman Tamah; Ghali, Neveen I

    2013-12-01

    Computational intelligence (CI) is a well-established paradigm with current systems having many of the characteristics of biological computers and capable of performing a variety of tasks that are difficult to do using conventional techniques. It is a methodology involving adaptive mechanisms and/or an ability to learn that facilitate intelligent behavior in complex and changing environments, such that the system is perceived to possess one or more attributes of reason, such as generalization, discovery, association and abstraction. The objective of this article is to present to the CI and bioinformatics research communities some of the state-of-the-art in CI applications to bioinformatics and motivate research in new trend-setting directions. In this article, we present an overview of the CI techniques in bioinformatics. We will show how CI techniques including neural networks, restricted Boltzmann machine, deep belief network, fuzzy logic, rough sets, evolutionary algorithms (EA), genetic algorithms (GA), swarm intelligence, artificial immune systems and support vector machines, could be successfully employed to tackle various problems such as gene expression clustering and classification, protein sequence classification, gene selection, DNA fragment assembly, multiple sequence alignment, and protein function prediction and its structure. We discuss some representative methods to provide inspiring examples to illustrate how CI can be utilized to address these problems and how bioinformatics data can be characterized by CI. Challenges to be addressed and future directions of research are also presented and an extensive bibliography is included. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  17. Working Group Report: WIMP Dark Matter Direct Detection

    Energy Technology Data Exchange (ETDEWEB)

    Cushman, P.; Galbiati, C.; McKinsey, D. N.; Robertson, H.; Tait, T. M.P.

    2013-10-30

    As part of the Snowmass process, the Cosmic Frontier WIMP Direct Detection subgroup (CF1) has drawn on input from the Cosmic Frontier and the broader Particle Physics community to produce this document. The charge to CF1 was (a) to summarize the current status and projected sensitivity of WIMP direct detection experiments worldwide, (b) motivate WIMP dark matter searches over a broad parameter space by examining a spectrum of WIMP models, (c) establish a community consensus on the type of experimental program required to explore that parameter space, and (d) identify the common infrastructure required to practically meet those goals.

  18. Cultural diversity and work-group performance : Detecting the rules

    NARCIS (Netherlands)

    Girndt, T.

    2000-01-01

    With greater levels of international cooperation, work-groups are increasingly composed of members from different cultures. These groups often suffer from communication problems; however, research suggests that they also benefit from their members cultural diversity and generate higher ranges of

  19. Detection and application of influence rankings in small group meetings

    NARCIS (Netherlands)

    Rienks, R.; Zhang, D.; Gatica-Perez, D.; Post, W.

    2006-01-01

    We address the problem of automatically detecting participant's influence levels in meetings. The impact and social psychological background are discussed. The more influential a participant is, the more he or she influences the outcome of a meeting. Experiments on 40 meetings show that application

  20. Adaptive Pseudo Dilation for Gestalt Edge Grouping and Contour Detection

    NARCIS (Netherlands)

    Papari, Giuseppe; Petkov, Nicolai

    2008-01-01

    We consider the problem of detecting object contours in natural images. In many cases, local luminance changes turn out to be stronger in textured areas than on object contours. Therefore, local edge features, which only look at a small neighborhood of each pixel, cannot be reliable indicators of

  1. Preface to Introduction to Structural Bioinformatics

    NARCIS (Netherlands)

    Feenstra, K. Anton; Abeln, Sanne

    2018-01-01

    While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which

  2. Detection of dengue group viruses by fluorescence in situ hybridization

    Directory of Open Access Journals (Sweden)

    Raquin Vincent

    2012-10-01

    Full Text Available Abstract Background Dengue fever (DF and dengue hemorrhagic fever (DHF represent a global challenge in public health. It is estimated that 50 to 100 million infections occur each year causing approximately 20,000 deaths that are usually linked to severe cases like DHF and dengue shock syndrome. The causative agent of DF is dengue virus (genus Flavivirus that comprises four distinct serotypes (DENV-1 to DENV-4. Fluorescence in situ hybridization (FISH has been used successfully to detect pathogenic agents, but has not been implemented in detecting DENV. To improve our understanding of DENV infection and dissemination in host tissues, we designed specific probes to detect DENV in FISH assays. Methods Oligonucleotide probes were designed to hybridize with RNA from the broadest range of DENV isolates belonging to the four serotypes, but not to the closest Flavivirus genomes. Three probes that fit the criteria defined for FISH experiments were selected, targeting both coding and non-coding regions of the DENV genome. These probes were tested in FISH assays against the dengue vector Aedes albopictus (Diptera: Culicidae. The FISH experiments were led in vitro using the C6/36 cell line, and in vivo against dissected salivary glands, with epifluorescence and confocal microscopy. Results The three 60-nt oligonucleotides probes DENV-Probe A, B and C cover a broad range of DENV isolates from the four serotypes. When the three probes were used together, specific fluorescent signals were observed in C6/36 infected with each DENV serotypes. No signal was detected in either cells infected with close Flavivirus members West Nile virus or yellow fever virus. The same protocol was used on salivary glands of Ae. albopictus fed with a DENV-2 infectious blood-meal which showed positive signals in the lateral lobes of infected samples, with no significant signal in uninfected mosquitoes. Conclusion Based on the FISH technique, we propose a way to design and use

  3. Foraging in groups allows collective predator detection in a mammal species without alarm calls

    OpenAIRE

    Olivier Pays; Guy Beauchamp; Alecia J. Carter; Anne W. Goldizen

    2013-01-01

    Although collective detection plays a key role in determining individual survival, few studies have carefully examined the collective process of detection. We investigated collective detection in the eastern grey kangaroo (Macropus giganteus), a species that forages in temporary groups and rarely produces auditory alarm signals on detection. In experimental trials, we exposed one group member to a predation threat (a python, Morelia spilota) that its companions could only detect indirectly by...

  4. Utility library for structural bioinformatics.

    Science.gov (United States)

    Gront, Dominik; Kolinski, Andrzej

    2008-02-15

    In this Note we present a new software library for structural bioinformatics. The library contains programs, computing sequence- and profile-based alignments and a variety of structural calculations with user-friendly handling of various data formats. The software organization is very flexible. Algorithms are written in Java language and may be used by Java programs. Moreover the modules can be accessed from Jython (Python scripting language implemented in Java) scripts. Finally, the new version of BioShell delivers several utility programs that can do typical bioinformatics task from a command-line level. Availability The software is available for download free of charge from its website: http://bioshell.chem.uw.edu.pl. This website provides also numerous examples, code snippets and API documentation.

  5. A Bioinformatics Facility for NASA

    Science.gov (United States)

    Schweighofer, Karl; Pohorille, Andrew

    2006-01-01

    Building on an existing prototype, we have fielded a facility with bioinformatics technologies that will help NASA meet its unique requirements for biological research. This facility consists of a cluster of computers capable of performing computationally intensive tasks, software tools, databases and knowledge management systems. Novel computational technologies for analyzing and integrating new biological data and already existing knowledge have been developed. With continued development and support, the facility will fulfill strategic NASA s bioinformatics needs in astrobiology and space exploration. . As a demonstration of these capabilities, we will present a detailed analysis of how spaceflight factors impact gene expression in the liver and kidney for mice flown aboard shuttle flight STS-108. We have found that many genes involved in signal transduction, cell cycle, and development respond to changes in microgravity, but that most metabolic pathways appear unchanged.

  6. Image Science and Analysis Group Spacecraft Damage Detection/Characterization

    Science.gov (United States)

    Wheaton, Ira M., Jr.

    2010-01-01

    This project consisted of several tasks that could be served by an intern to assist the ISAG in detecting damage to spacecrafts during missions. First, this project focused on supporting the Micrometeoroid Orbital Debris (MMOD) damage detection and assessment for the Hubble Space Telescope (HST) using imagery from the last two HST Shuttle servicing missions. In this project, we used coordinates of two windows on the Shuttle Aft flight deck from where images were taken and the coordinates of three ID points in order to calculate the distance from each window to the three points. Then, using the specifications from the camera used, we calculated the image scale in pixels per inch for planes parallel to and planes in the z-direction to the image plane (shown in Table 1). This will help in the future for calculating measurements of objects in the images. Next, tabulation and statistical analysis were conducted for screening results (shown in Table 2) of imagery with Orion Thermal Protection System (TPS) damage. Using the Microsoft Excel CRITBINOM function and Goal Seek, the probabilities of detection of damage to different shuttle tiles were calculated as shown in Table 3. Using developed measuring tools, volume and area measurements will be created from 3D models of Orion TPS damage. Last, mathematical expertise was provided to the Photogrammetry Team. These mathematical tasks consisted of developing elegant image space error equations for observations along 3D lines, circles, planes, etc. and checking proofs for minimal sets of sufficient multi-linear constraints. Some of the processes and resulting equations are displayed in Figure 1.

  7. [Detection and analysis of anti-Rh blood group antibodies].

    Science.gov (United States)

    Wu, Yuan-jun; Wu, Yong; Chen, Bao-chan; Liu, Yan

    2008-06-01

    To study the prevalence and distribution of anti-Rh blood group antibodies in Chinese population and its clinical significance. Irregular antibodies were screened and identified by Microcolum Gel Coomb's test. For those identified as positive anti-Rh samples, monoclonal antibodies (anti-D, -C, -c, -E and -e) were used to identify the specific antigen and confirm the accuracy of the irregular antibody tests. The titers, Ig-types and 37 Degrees Celsius-reactivity were tested to confirm its clinical significance. For evaluation of the origin of irregular antibodies, histories of pregnancy and transfusion were reviewed. For the newborns who had positive antibodies, their mothers were tested simultaneously to confirm the origin of the antibodies. 47 out of 54 000 (0.087%) patients were identified as positive with Rh blood group antibodies.Of them, 27 cases had history of pregnancy, 13 had transfusion and 1 had the histories of both. 6 newborns had antibodies derived form their mothers. The specificity of the antibody was as follows: 29 with anti-E (61.70%), 8 with anti-D (17.02%), anti-cE 5(10.64%), 4 with anti-c (8.51%) and 1 with anti-C (2.13%). All the 47 Rh blood group antibodies were IgG or IgG+IgM, and were reactive to red blood cells with corresponding antigens at 37 Degrees Celsius, with a highest titer of 1:4 096. The prevalence of Rh antibodies is lower in Chinese population as compared with that in White population.Of all the antibodies, anti-E is most frequently identified and anti-D was declining. Alloimmunization by pregnancy and transfusion is the major cause of Rh antibody production. Rh blood group antibodies derived from mothers are the major cause of Non-ABO-HDN.

  8. Maritime Group Motion Analysis: Representation, Learning, Recognition, and Deviation Detection

    Science.gov (United States)

    2017-02-01

    represent behaviors. Keywords: Group tracks, motion analysis, behavior pattern 1 Introduction Motion activity analysis of single and multiple...its decomposition into anti-symmetric, and symmetric (both with and without trace) elements of the velocity gradient tensor is attributed to Cauchy...orientation of the deformation axis (see Fig.1). These geometric invariants are simply the eigenvalues of the decomposed velocity gradient tensor , and

  9. Inconsistencies in DIF Detection for Sub-Groups in Heterogeneous Language Groups

    Science.gov (United States)

    Ercikan, Kadriye; Roth, Wolff-Michael; Simon, Marielle; Sandilands, Debra; Lyons-Thomas, Juliette

    2014-01-01

    Diversity and heterogeneity among language groups have been well documented. Yet most fairness research that focuses on measurement comparability considers linguistic minority students such as English language learners (ELLs) or Francophone students living in minority contexts in Canada as a single group. Our focus in this research is to examine…

  10. Accounting for imperfect detection of groups and individuals when estimating abundance.

    Science.gov (United States)

    Clement, Matthew J; Converse, Sarah J; Royle, J Andrew

    2017-09-01

    If animals are independently detected during surveys, many methods exist for estimating animal abundance despite detection probabilities account for imperfect detection of groups, while assuming that individuals within groups are detected perfectly. However, this assumption is often unsupported. We introduce an abundance estimator for grouped animals when detection of groups is imperfect and group size may be under-counted, but not over-counted. The estimator combines an MRDS model with an N-mixture model to account for imperfect detection of individuals. The new MRDS-Nmix model requires the same data as an MRDS model (independent detection histories, an estimate of distance to transect, and an estimate of group size), plus a second estimate of group size provided by the second observer. We extend the model to situations in which detection of individuals within groups declines with distance. We simulated 12 data sets and used Bayesian methods to compare the performance of the new MRDS-Nmix model to an MRDS model. Abundance estimates generated by the MRDS-Nmix model exhibited minimal bias and nominal coverage levels. In contrast, MRDS abundance estimates were biased low and exhibited poor coverage. Many species of conservation interest reside in groups and could benefit from an estimator that better accounts for imperfect detection. Furthermore, the ability to relax the assumption of perfect detection of individuals within detected groups may allow surveyors to re-allocate resources toward detection of new groups instead of extensive surveys of known groups. We believe the proposed estimator is feasible because the only additional field data required are a second estimate of group size.

  11. Charged Particle Tracking and Vertex Detection Group summary report

    International Nuclear Information System (INIS)

    Hanson, G.; Meyer, D.

    1984-09-01

    Charged particle tracking is essential in order to investigate the new physics expected at the SSC. The Tracking Group studied radiation damage and rate limitations to tracking devices, vertex detectors, and central tracking. The Group concluded that silicon strips and large wire tracking chambers with small cells can probably survive at the design luminosity of 10 33 cm -2 sec -1 ; however, the presently designed electronics for silicon strip vertex detectors can withstand a luminosity of only 10 31 cm -2 sec -1 . Wire chambers at a radius of less than about 25 cm can withstand a luminosity of less than or equal to 10 32 cm -2 sec -1 only. Actual tracking and pattern recognition in central tracking chambers at a luminosity of 10 33 cm -2 sec -1 will be very difficult because of multiple interactions within the resolving time of the chambers; detailed simulations are needed in order to decide whether tracking is indeed possible at this luminosity. Scintillating glass fibers are an interesting possibility both for vertex detectors and for central trackers, but much research and development is still needed both on the fibers themselves and on the readout

  12. Experiment of monopole detection by Osaka City University Group

    International Nuclear Information System (INIS)

    Suwada, Tsuyoshi; Cho, Akiteru; Takahashi, Tamotsu; Azuma, Shigeru; Ozaki, Masanosuke

    1984-01-01

    The observation on the ground to find the slow monopoles in cosmic ray has been performed by using a five-layer proportional counter system. To improve the detection efficiency, He-filled proportional counters were developed. The characteristics of the He counters are described in this paper. The stability of characteristics of the counters with He-CH 4 , Ar-He-CH 4 or He-iso C 4 H 10 was examined. The counters worked stably with the quenching gas of 10 percent CH 4 concentration and with the gas of 5percent iso C 4 H 10 . The features of the pulse height distribution of the He-i so C 4 H 10 counter was better than that of the He-CH 4 counter. The drift velocity of the He counters was slower than that of Ar counters. Two layers were added to the system to observe the pulse height of the particles passing through the counters and the position along the wire. The total number of the counter layers is now seven. (Kato, T.)

  13. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

    Science.gov (United States)

    Attwood, Teresa K; Atwood, Teresa K; Bongcam-Rudloff, Erik; Brazas, Michelle E; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M; Schneider, Maria Victoria; van Gelder, Celia W G

    2015-04-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.

  14. BioStar: an online question & answer resource for the bioinformatics community

    Science.gov (United States)

    Although the era of big data has produced many bioinformatics tools and databases, using them effectively often requires specialized knowledge. Many groups lack bioinformatics expertise, and frequently find that software documentation is inadequate and local colleagues may be overburdened or unfamil...

  15. Academic Training - Bioinformatics: Decoding the Genome

    CERN Multimedia

    Chris Jones

    2006-01-01

    ACADEMIC TRAINING LECTURE SERIES 27, 28 February 1, 2, 3 March 2006 from 11:00 to 12:00 - Auditorium, bldg. 500 Decoding the Genome A special series of 5 lectures on: Recent extraordinary advances in the life sciences arising through new detection technologies and bioinformatics The past five years have seen an extraordinary change in the information and tools available in the life sciences. The sequencing of the human genome, the discovery that we possess far fewer genes than foreseen, the measurement of the tiny changes in the genomes that differentiate us, the sequencing of the genomes of many pathogens that lead to diseases such as malaria are all examples of completely new information that is now available in the quest for improved healthcare. New tools have allowed similar strides in the discovery of the associated protein structures, providing invaluable information for those searching for new drugs. New DNA microarray chips permit simultaneous measurement of the state of expression of tens...

  16. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.

    Science.gov (United States)

    Schneider, Maria V; Walter, Peter; Blatter, Marie-Claude; Watson, James; Brazas, Michelle D; Rother, Kristian; Budd, Aidan; Via, Allegra; van Gelder, Celia W G; Jacob, Joachim; Fernandes, Pedro; Nyrönen, Tommi H; De Las Rivas, Javier; Blicher, Thomas; Jimenez, Rafael C; Loveland, Jane; McDowall, Jennifer; Jones, Phil; Vaughan, Brendan W; Lopez, Rodrigo; Attwood, Teresa K; Brooksbank, Catherine

    2012-05-01

    Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.

  17. The importance of early detection of lip cancer risk groups

    Science.gov (United States)

    Fratila, M.; Rosu, S.

    2014-03-01

    in frequency as well as in the therapeutic problems raised. In the face and oral cavity cancer catagory, lip represents 2% of all cases and 19-25% of the total facial cancer area. Lip cancer is one of the localizations that, when detected early, can benefit from an effective therapy with high chances of healing. In order to achieve a complex treatment, interdisciplinary collaboration is required, only thus being able to determine both the therapeutic methods as well as their association.

  18. Bioinformatics in Africa: The Rise of Ghana?

    Directory of Open Access Journals (Sweden)

    Thomas K Karikari

    2015-09-01

    Full Text Available Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics.

  19. Bioinformatics in Africa: The Rise of Ghana?

    Science.gov (United States)

    Karikari, Thomas K

    2015-09-01

    Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics.

  20. Search strategies in structural bioinformatics.

    Science.gov (United States)

    Oakley, Mark T; Barthel, Daniel; Bykov, Yuri; Garibaldi, Jonathan M; Burke, Edmund K; Krasnogor, Natalio; Hirst, Jonathan D

    2008-06-01

    Optimisation problems pervade structural bioinformatics. In this review, we describe recent work addressing a selection of bioinformatics challenges. We begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity. We then turn to research into de novo protein structure prediction, in which structures are generated from first principles. In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled. We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm. One strategy to reduce the size of the search space is to restrict the protein chain to sites on a regular lattice. In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.

  1. A conceptual basis to encode and detect organic functional groups in XML.

    Science.gov (United States)

    Sankar, Punnaivanam; Krief, Alain; Vijayasarathi, Durairaj

    2013-06-01

    A conceptual basis to define and detect organic functional groups is developed. The basic model of a functional group is termed as a primary functional group and is characterized by a group center composed of one or more group center atoms bonded to terminal atoms and skeletal carbon atoms. The generic group center patterns are identified from the structures of known functional groups. Accordingly, a chemical ontology 'Font' is developed to organize the existing functional groups as well as the new ones to be defined by the chemists. The basic model is extended to accommodate various combinations of primary functional groups as functional group assemblies. A concept of skeletal group is proposed to define the characteristic groups composed of only carbon atoms to be regarded as equivalent to functional groups. The combination of primary functional groups with skeletal groups is categorized as skeletal group assembly. In order to make the model suitable for reaction modeling purpose, a Graphical User Interface (GUI) is developed to define the functional groups and to encode in XML format appropriate to detect them in chemical structures. The system is capable of detecting multiple instances of primary functional groups as well as the overlapping poly-functional groups as the respective assemblies. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

    DEFF Research Database (Denmark)

    Schneider, Maria V.; Walter, Peter; Blatter, Marie-Claude

    2012-01-01

    Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response...... to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes...... to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials...

  3. Fuzzy Logic in Medicine and Bioinformatics

    Directory of Open Access Journals (Sweden)

    Angela Torres

    2006-01-01

    Full Text Available The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions and in bioinformatics (comparison of genomes.

  4. Online Bioinformatics Tutorials | Office of Cancer Genomics

    Science.gov (United States)

    Bioinformatics is a scientific discipline that applies computer science and information technology to help understand biological processes. The NIH provides a list of free online bioinformatics tutorials, either generated by the NIH Library or other institutes, which includes introductory lectures and "how to" videos on using various tools.

  5. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  6. A Mathematical Optimization Problem in Bioinformatics

    Science.gov (United States)

    Heyer, Laurie J.

    2008-01-01

    This article describes the sequence alignment problem in bioinformatics. Through examples, we formulate sequence alignment as an optimization problem and show how to compute the optimal alignment with dynamic programming. The examples and sample exercises have been used by the author in a specialized course in bioinformatics, but could be adapted…

  7. Bioinformatics clouds for big data manipulation.

    Science.gov (United States)

    Dai, Lin; Gao, Xin; Guo, Yan; Xiao, Jingfa; Zhang, Zhang

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics. This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  8. Bioinformatics clouds for big data manipulation

    Directory of Open Access Journals (Sweden)

    Dai Lin

    2012-11-01

    Full Text Available Abstract As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS, Software as a Service (SaaS, Platform as a Service (PaaS, and Infrastructure as a Service (IaaS, and present our perspectives on the adoption of cloud computing in bioinformatics. Reviewers This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  9. Bioinformatics clouds for big data manipulation

    Science.gov (United States)

    2012-01-01

    Abstract As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics. Reviewers This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor. PMID:23190475

  10. Bioinformatics clouds for big data manipulation

    KAUST Repository

    Dai, Lin

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics.This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor. 2012 Dai et al.; licensee BioMed Central Ltd.

  11. Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

    Science.gov (United States)

    Ranganathan, Shoba; Eisenhaber, Frank; Tong, Joo Chuan; Tan, Tin Wee

    2009-12-03

    The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 7-11, 2009 at Biopolis, Singapore. Besides bringing together scientists from the field of bioinformatics in this region, InCoB has actively engaged clinicians and researchers from the area of systems biology, to facilitate greater synergy between these two groups. InCoB2009 followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India), Hong Kong and Taipei (Taiwan), with InCoB2010 scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. The Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and symposia on Clinical Bioinformatics (CBAS), the Singapore Symposium on Computational Biology (SYMBIO) and training tutorials were scheduled prior to the scientific meeting, and provided ample opportunity for in-depth learning and special interest meetings for educators, clinicians and students. We provide a brief overview of the peer-reviewed bioinformatics manuscripts accepted for publication in this supplement, grouped into thematic areas. In order to facilitate scientific reproducibility and accountability, we have, for the first time, introduced minimum information criteria for our pubilcations, including compliance to a Minimum Information about a Bioinformatics Investigation (MIABi). As the regional research expertise in bioinformatics matures, we have delineated a minimum set of bioinformatics skills required for addressing the computational challenges of the "-omics" era.

  12. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

  13. A quick guide for building a successful bioinformatics community.

    Science.gov (United States)

    Budd, Aidan; Corpas, Manuel; Brazas, Michelle D; Fuller, Jonathan C; Goecks, Jeremy; Mulder, Nicola J; Michaut, Magali; Ouellette, B F Francis; Pawlik, Aleksandra; Blomberg, Niklas

    2015-02-01

    "Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop "The 'How To Guide' for Establishing a Successful Bioinformatics Network" at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).

  14. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

  15. Detection of group D and viridans streptococci in blood by radiometric methods

    Energy Technology Data Exchange (ETDEWEB)

    Beckwith, D.G.

    1979-01-01

    A prospective study was conducted to evaluate the radiometric detection of group D and viridans streptococci in blood, using three media preparations, Bactec 6A and 6B isotonic media and 8B hypertonic medium. All enterococci tested were detected by the 6A and 6B media. However, the 6A medium failed to detect 76% of the Streptococcus bovis isolates and 57% of the viridans streptococci, whereas all S. bovis isolates and 95% of the viridans streptococci were detected with the 6B formulation. No improvement in detection was noted in comparing the 6B and the 8B hypertonic media. The importance of adequate detection of this group of organisms, especially in patients with endocarditis, is discussed.

  16. Detection rates of trichomonas vaginalis, in different age groups, using real-time polymerase chain reaction.

    Science.gov (United States)

    Stemmer, Shlomo M; Adelson, Martin E; Trama, Jason P; Dorak, M Tevfik; Mordechai, Eli

    2012-10-01

    The study aimed to compare the overall detection rate of Trichomonas vaginalis to Chlamydia trachomatis and Neiserria gonorrhea and report detection rates by age groups. Real-time polymerase chain reaction was used to detect the presence of T. vaginalis, C. trachomatis, and N. gonorrhea in cervical samples obtained from patients during gynecological examinations. A total of 78,428, 119,451, and 117,494 samples from women age 12 to 75 years were retrospectively analyzed for the presence of T. vaginalis, C. trachomatis, and N. gonorrhea, respectively. T. vaginalis and C. trachomatis detection rates in Florida, New Jersey, and Texas were calculated in different age groups. The overall detection rate was 4.3% for T. vaginalis, 3.8% for C. trachomatis, and 0.6% for N. gonorrhea. The overall detection rate of T. vaginalis in Florida was 4.7% (n = 22,504), in New Jersey was 3.6% (n = 22,249), and in Texas was 4.5% (n = 33,675). Calculation of infection rates with T. vaginalis revealed differences between selected age groups with the highest detection rates in all 3 states found in age group 46 to 55 years (6.2%), which was higher than the overall detection rates in other age groups (p rate was found in age group 12 to 25 years (7.3%). The overall infection rates of T. vaginalis were higher compared with those of C. trachomatis and N. gonorrhea. Detection rates of T. vaginalis were found to be highest among women age 46 to 55 years and may be due to T. vaginalis infiltrating the subepithelial glands and being detected only during hormone-induced or antibiotic-induced changes in the vaginal flora.

  17. Bioinformatics study of the mangrove actin genes

    Science.gov (United States)

    Basyuni, M.; Wasilah, M.; Sumardi

    2017-01-01

    This study describes the bioinformatics methods to analyze eight actin genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, subcellular localization, similarity, and phylogenetic. The physical and chemical properties of eight mangroves showed variation among the genes. The percentage of the secondary structure of eight mangrove actin genes followed the order of a helix > random coil > extended chain structure for BgActl, KcActl, RsActl, and A. corniculatum Act. In contrast to this observation, the remaining actin genes were random coil > extended chain structure > a helix. This study, therefore, shown the prediction of secondary structure was performed for necessary structural information. The values of chloroplast or signal peptide or mitochondrial target were too small, indicated that no chloroplast or mitochondrial transit peptide or signal peptide of secretion pathway in mangrove actin genes. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove actin genes. To clarify the relationship among the mangrove actin gene, a phylogenetic tree was constructed. Three groups of mangrove actin genes were formed, the first group contains B. gymnorrhiza BgAct and R. stylosa RsActl. The second cluster which consists of 5 actin genes the largest group, and the last branch consist of one gene, B. sexagula Act. The present study, therefore, supported the previous results that plant actin genes form distinct clusters in the tree.

  18. A novel reduced-complexity group detection structure in MIMO frequency selective fading channels

    KAUST Repository

    Qaraqe, Khalid A.

    2010-09-01

    In this paper a novel reduced complexity detection method named modified symbol flipping method is introduced and its advantages on reducing the burden of the calculations at the receiver compared to the optimum maximum likelihood detection method on multiple input- multiple output frequency selective fading channels are explained. The initial concept of the symbol flipping method is derived from a preliminary detection scheme named bit flipping which was introduced in [1]. The detection structure employed in this paper is ing, detection, and cancellation. On the detection stage, the proposed method is employed and the results are compared to the group maximum likelihood detection scheme proposed in [2]. Simulation results show that a 6 dB performance gain can be achieved at the expense of a slight increase in complexity in comparison with the conventional symbol flipping scheme. © 2010 Crown.

  19. Serological and molecular detection of spotted fever group Rickettsia in a group of pet dogs from Luanda, Angola.

    Science.gov (United States)

    Barradas, Patrícia F; Vilhena, Hugo; Oliveira, Ana Cristina; Granada, Sara; Amorim, Irina; Ferreira, Paula; Cardoso, Luís; Gärtner, Fátima; de Sousa, Rita

    2017-05-31

    Infections with tick-borne rickettsiae can cause diseases well known in humans but still not so well characterized in dogs. Susceptibility to infection depends on the virulence of Rickettsia spp. and only a few of them have been described to cause disease in dogs. The aim of this study was to investigate the exposure to Rickettsia spp. among a group of pet dogs from Luanda, Angola. Out of 103 dogs included in the study, 62 (60.2%) were infested with ticks. Plasma specimens tested for serology by an immunofluorescence assay (IFA) revealed that six (5.8%) dogs had detectable immunoglobulin G (IgG) antibodies to spotted fever group Rickettsia (SFGR), with endpoint titers of 64 for two dogs, 128 for three dogs and 1024 for one dog. From the seropositive group of dogs, five (83%) of them were males, with their age ranging from 1 to 8 years old. Among the seropositive dogs, four (66.7%) were parasitized with ticks and no breed (or cross) was found to be associated with specific antibodies. Rickettsia spp. DNA was detected by nested-polymerase chain reaction (PCR) in two (1.9%) dogs that were found to be seronegative. Seroprevalence and molecular detection of Rickettsia spp. infection in this group of pet dogs from Luanda is low compared with other studies performed in the same type of hosts in other areas. Although many dogs were parasitized with ticks, a low prevalence of Rickettsia spp. could be related with the hypothesis of a low rickettsial prevalence in the infesting ticks. This study provides evidence that dogs in Luanda are exposed to Rickettsia spp., but further studies are needed to better characterize the bacterial infections in dogs and in their ectoparasites.

  20. Meeting review: 2002 O'Reilly Bioinformatics Technology Conference.

    Science.gov (United States)

    Counsell, Damian

    2002-01-01

    At the end of January I travelled to the States to speak at and attend the first O'Reilly Bioinformatics Technology Conference. It was a large, well-organized and diverse meeting with an interesting history. Although the meeting was not a typical academic conference, its style will, I am sure, become more typical of meetings in both biological and computational sciences.Speakers at the event included prominent bioinformatics researchers such as Ewan Birney, Terry Gaasterland and Lincoln Stein; authors and leaders in the open source programming community like Damian Conway and Nat Torkington; and representatives from several publishing companies including the Nature Publishing Group, Current Science Group and the President of O'Reilly himself, Tim O'Reilly. There were presentations, tutorials, debates, quizzes and even a 'jam session' for musical bioinformaticists.

  1. When cloud computing meets bioinformatics: a review.

    Science.gov (United States)

    Zhou, Shuigeng; Liao, Ruiqi; Guan, Jihong

    2013-10-01

    In the past decades, with the rapid development of high-throughput technologies, biology research has generated an unprecedented amount of data. In order to store and process such a great amount of data, cloud computing and MapReduce were applied to many fields of bioinformatics. In this paper, we first introduce the basic concepts of cloud computing and MapReduce, and their applications in bioinformatics. We then highlight some problems challenging the applications of cloud computing and MapReduce to bioinformatics. Finally, we give a brief guideline for using cloud computing in biology research.

  2. Polymerase chain reaction assay for the detection of Bacillus cereus group cells

    DEFF Research Database (Denmark)

    Hansen, Bjarne Munk; Leser, Thomas D.; Hendriksen, Niels Bohse

    2001-01-01

    Recent investigations have shown that members of the Bacillus cereus group carry genes which have the potential to cause gastrointestinal and somatic diseases. Although most cases of diseases caused by the B. cereus group bacteria are relatively mild, it is desirable to be able to detect members ...

  3. Coronavirus Genomics and Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Kwok-Yung Yuen

    2010-08-01

    Full Text Available The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999-2002, with estimated substitution rate of 4´10-4 to 2´10-2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV, between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1. Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses.

  4. Deciphering psoriasis. A bioinformatic approach.

    Science.gov (United States)

    Melero, Juan L; Andrades, Sergi; Arola, Lluís; Romeu, Antoni

    2018-02-01

    Psoriasis is an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. The cause of psoriasis is still unknown. The fundamental feature of the disease is the hyperproliferation of keratinocytes and the recruitment of cells from the immune system in the region of the affected skin, which leads to deregulation of many well-known gene expressions. Based on data mining and bioinformatic scripting, here we show a new dimension of the effect of psoriasis at the genomic level. Using our own pipeline of scripts in Perl and MySql and based on the freely available NCBI Gene Expression Omnibus (GEO) database: DataSet Record GDS4602 (Series GSE13355), we explore the extent of the effect of psoriasis on gene expression in the affected tissue. We give greater insight into the effects of psoriasis on the up-regulation of some genes in the cell cycle (CCNB1, CCNA2, CCNE2, CDK1) or the dynamin system (GBPs, MXs, MFN1), as well as the down-regulation of typical antioxidant genes (catalase, CAT; superoxide dismutases, SOD1-3; and glutathione reductase, GSR). We also provide a complete list of the human genes and how they respond in a state of psoriasis. Our results show that psoriasis affects all chromosomes and many biological functions. If we further consider the stable and mitotically inheritable character of the psoriasis phenotype, and the influence of environmental factors, then it seems that psoriasis has an epigenetic origin. This fit well with the strong hereditary character of the disease as well as its complex genetic background. Copyright © 2017 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

  5. [Pharmacogenetics II. Research molecular methods, bioinformatics and ethical concerns].

    Science.gov (United States)

    Daudén, E

    2007-01-01

    Pharmacogenetics refers to the study of the individual pharmacological response based on the genotype. Its objective is to optimize treatment in an individual basis, thereby creating a more efficient and safe personalized therapy. In the second part of this review, the molecular methods of study in pharmacogenetics, including microarray technology or DNA chips, are discussed. Among them we highlight the microarrays used to determine the gene expression that detect specific RNA sequences, and the microarrays employed to determine the genotype that detect specific DNA sequences, including polymorphisms, particularly single nucleotide polymorphisms (SNPs). The relationship between pharmacogenetics, bioinformatics and ethical concerns is reviewed.

  6. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Campos, Benito; Barnkob, Mike Stein

    2014-01-01

    cancer immunotherapies has yet to be fulfilled. The insufficient efficacy of existing treatments can be attributed to a number of biological and technical issues. In this review, we detail the current limitations of immunotherapy target selection and design, and review computational methods to streamline...... therapy target discovery in a bioinformatics analysis pipeline. We describe specialized bioinformatics tools and databases for three main bottlenecks in immunotherapy target discovery: the cataloging of potentially antigenic proteins, the identification of potential HLA binders, and the selection epitopes...

  7. Text string detection from natural scenes by structure-based partition and grouping.

    Science.gov (United States)

    Yi, Chucai; Tian, YingLi

    2011-09-01

    Text information in natural scene images serves as important clues for many image-based applications such as scene understanding, content-based image retrieval, assistive navigation, and automatic geocoding. However, locating text from a complex background with multiple colors is a challenging task. In this paper, we explore a new framework to detect text strings with arbitrary orientations in complex natural scene images. Our proposed framework of text string detection consists of two steps: 1) image partition to find text character candidates based on local gradient features and color uniformity of character components and 2) character candidate grouping to detect text strings based on joint structural features of text characters in each text string such as character size differences, distances between neighboring characters, and character alignment. By assuming that a text string has at least three characters, we propose two algorithms of text string detection: 1) adjacent character grouping method and 2) text line grouping method. The adjacent character grouping method calculates the sibling groups of each character candidate as string segments and then merges the intersecting sibling groups into text string. The text line grouping method performs Hough transform to fit text line among the centroids of text candidates. Each fitted text line describes the orientation of a potential text string. The detected text string is presented by a rectangle region covering all characters whose centroids are cascaded in its text line. To improve efficiency and accuracy, our algorithms are carried out in multi-scales. The proposed methods outperform the state-of-the-art results on the public Robust Reading Dataset, which contains text only in horizontal orientation. Furthermore, the effectiveness of our methods to detect text strings with arbitrary orientations is evaluated on the Oriented Scene Text Dataset collected by ourselves containing text strings in nonhorizontal

  8. Artificial Evolution for the Detection of Group Identities in Complex Artificial Societies

    DEFF Research Database (Denmark)

    Grappiolo, Corrado; Togelius, Julian; Yannakakis, Georgios N.

    2013-01-01

    This paper aims at detecting the presence of group structures in complex artificial societies by solely observing and analysing the interactions occurring among the artificial agents. Our approach combines: (1) an unsupervised method for clustering interactions into two possible classes, namely in......- group and out-group, (2) reinforcement learning for deriving the existing levels of collaboration within the society, and (3) an evolutionary algorithm for the detection of group structures and the assignment of group identities to the agents. Under a case study of static societies — i.e. the agents do...... not evolve their social preferences — where agents interact with each other by means of the Ultimatum Game, our approach proves to be successful for small-sized social networks independently on the underlying social structure of the society; promising results are also registered for mid-size societies....

  9. Collective detection in escape responses of temporary groups of Iberian green frogs

    OpenAIRE

    José Martín; Juan José Luque-Larena; Pilar López

    2006-01-01

    When confronted with a predator, prey are often in close proximity to conspecifics. This situation has generated several hypotheses regarding antipredator strategies adopted by individuals within groups of gregarious species, such as the "risk dilution," "early detection," or "collective detection" effects. However, whether short-term temporary aggregations of nongregarious animals are also influenced in their escape decisions by nearby conspecifics remains little explored. We simulated preda...

  10. Detection of genetically diverse human immunodeficiency virus type 1 group M and O isolates by PCR.

    OpenAIRE

    Respess, R A; Butcher, A; Wang, H; Chaowanachan, T; Young, N; Shaffer, N; Mastro, T D; Biryahwaho, B; Downing, R; Tanuri, A; Schechter, M; Pascu, R; Zekeng, L; Kaptué, L; Gürtler, L

    1997-01-01

    A panel of 136 genetically diverse group M and 5 group O adult isolates from outside the United States and Europe were evaluated by PCR with the Roche AMPLICOR HIV-1 test, a modified version of the AMPLICOR HIV-1 test, and a new primer pair/probe system. Detection of some of these isolates was less efficient with the AMPLICOR HIV-1 test; however, the assay was significantly improved by reducing the sample input and lowering the annealing temperature. The new primer pair/probe set detected 140...

  11. F-formation detection: individuating free-standing conversational groups in images.

    Directory of Open Access Journals (Sweden)

    Francesco Setti

    Full Text Available Detection of groups of interacting people is a very interesting and useful task in many modern technologies, with application fields spanning from video-surveillance to social robotics. In this paper we first furnish a rigorous definition of group considering the background of the social sciences: this allows us to specify many kinds of group, so far neglected in the Computer Vision literature. On top of this taxonomy we present a detailed state of the art on the group detection algorithms. Then, as a main contribution, we present a brand new method for the automatic detection of groups in still images, which is based on a graph-cuts framework for clustering individuals; in particular, we are able to codify in a computational sense the sociological definition of F-formation, that is very useful to encode a group having only proxemic information: position and orientation of people. We call the proposed method Graph-Cuts for F-formation (GCFF. We show how GCFF definitely outperforms all the state of the art methods in terms of different accuracy measures (some of them are brand new, demonstrating also a strong robustness to noise and versatility in recognizing groups of various cardinality.

  12. Group localisation and unsupervised detection and classification of basic crowd behaviour events for surveillance applications

    Science.gov (United States)

    Roubtsova, Nadejda S.; de With, Peter H. N.

    2013-02-01

    Technology for monitoring crowd behaviour is in demand for surveillance and security applications. The trend in research is to tackle detection of complex crowd behaviour events (panic, ght, evacuation etc.) directly using machine learning techniques. In this paper, we present a contrary, bottom-up approach seeking basic group information: (1) instantaneous location and (2) the merge, split and lateral slide-by events - the three basic motion patterns comprising any crowd behaviour. The focus on such generic group information makes our algorithm suitable as a building block in a variety of surveillance systems, possibly integrated with static content analysis solutions. Our feature extraction framework has optical ow in its core. The framework is universal being motion-based, rather than object-detection-based and generates a large variety of motion-blob- characterising features useful for an array of classi cation problems. Motion-based characterisation is performed on a group as an atomic whole and not by means of superposition of individual human motions. Within that feature space, our classi cation system makes decisions based on heuristic rules and thresholds, without machine learning. Our system performs well on group localisation, consistently generating contours around both moving and halted groups. The visual output of our periodical group localisation is equivalent to tracking and the group contour accuracy ranges from adequate to exceptionally good. The system successfully detects and classi es within our merge/split/slide-by event space in surveillance-type video sequences, di ering in resolution, scale, quality and motion content. Quantitatively, its performance is characterised by a good recall: 83% on detection and 71% on combined detection and classi cation.

  13. Navigating the changing learning landscape: perspective from bioinformatics.ca

    OpenAIRE

    Brazas, Michelle D.; Ouellette, B. F. Francis

    2013-01-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable...

  14. Development of Bioinformatics Infrastructure for Genomics Research.

    Science.gov (United States)

    Mulder, Nicola J; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Ahmed, Azza; Ahmed, Rehab; Akanle, Bola; Alibi, Mohamed; Armstrong, Don L; Aron, Shaun; Ashano, Efejiro; Baichoo, Shakuntala; Benkahla, Alia; Brown, David K; Chimusa, Emile R; Fadlelmola, Faisal M; Falola, Dare; Fatumo, Segun; Ghedira, Kais; Ghouila, Amel; Hazelhurst, Scott; Isewon, Itunuoluwa; Jung, Segun; Kassim, Samar Kamal; Kayondo, Jonathan K; Mbiyavanga, Mamana; Meintjes, Ayton; Mohammed, Somia; Mosaku, Abayomi; Moussa, Ahmed; Muhammd, Mustafa; Mungloo-Dilmohamud, Zahra; Nashiru, Oyekanmi; Odia, Trust; Okafor, Adaobi; Oladipo, Olaleye; Osamor, Victor; Oyelade, Jellili; Sadki, Khalid; Salifu, Samson Pandam; Soyemi, Jumoke; Panji, Sumir; Radouani, Fouzia; Souiai, Oussama; Tastan Bishop, Özlem

    2017-06-01

    Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community. H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for

  15. Preliminary Study of Bioinformatics Patents and Their Classifications Registered in the KIPRIS Database.

    Science.gov (United States)

    Park, Hyun-Seok

    2012-12-01

    Whereas a vast amount of new information on bioinformatics is made available to the public through patents, only a small set of patents are cited in academic papers. A detailed analysis of registered bioinformatics patents, using the existing patent search system, can provide valuable information links between science and technology. However, it is extremely difficult to select keywords to capture bioinformatics patents, reflecting the convergence of several underlying technologies. No single word or even several words are sufficient to identify such patents. The analysis of patent subclasses can provide valuable information. In this paper, I did a preliminary study of the current status of bioinformatics patents and their International Patent Classification (IPC) groups registered in the Korea Intellectual Property Rights Information Service (KIPRIS) database.

  16. Detecting Emotional Expression in Face-to-Face and Online Breast Cancer Support Groups

    Science.gov (United States)

    Liess, Anna; Simon, Wendy; Yutsis, Maya; Owen, Jason E.; Piemme, Karen Altree; Golant, Mitch; Giese-Davis, Janine

    2008-01-01

    Accurately detecting emotional expression in women with primary breast cancer participating in support groups may be important for therapists and researchers. In 2 small studies (N = 20 and N = 16), the authors examined whether video coding, human text coding, and automated text analysis provided consistent estimates of the level of emotional…

  17. DIF Detection Using Multiple-Group Categorical CFA with Minimum Free Baseline Approach

    Science.gov (United States)

    Chang, Yu-Wei; Huang, Wei-Kang; Tsai, Rung-Ching

    2015-01-01

    The aim of this study is to assess the efficiency of using the multiple-group categorical confirmatory factor analysis (MCCFA) and the robust chi-square difference test in differential item functioning (DIF) detection for polytomous items under the minimum free baseline strategy. While testing for DIF items, despite the strong assumption that all…

  18. Update in research and methods in proteomics and bioinformatics.

    Science.gov (United States)

    Bencharit, Sompop; Border, Michael B; Edelmann, Alex; Byrd, Warren C

    2013-10-01

    The 3rd International Conference on Proteomics & Bioinformatics (Proteomics 2013) Philadelphia, PA, USA, 15-17 July 2013 The Third International Conference on Proteomics & Bioinformatics (Proteomics 2013) was sponsored by the OMICS group and was organized in order to strengthen the future of proteomics science by bringing together professionals, researchers and scholars from leading universities across the globe. The main topics of this conference included the integration of novel platforms in data analysis, the use of a systems biology approach, different novel mass spectrometry platforms and biomarker discovery methods. The conference was divided into proteomic methods and research interests. Among these two categories, interactions between methods in proteomics and bioinformatics, as well as other research methodologies, were discussed. Exceptional topics from the keynote forum, oral presentations and the poster session have been highlighted. The topics range from new techniques for analyzing proteomics data, to new models designed to help better understand genetic variations to the differences in the salivary proteomes of HIV-infected patients.

  19. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

    Directory of Open Access Journals (Sweden)

    Teresa K Attwood

    2015-04-01

    Full Text Available In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.

  20. GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

    Science.gov (United States)

    Atwood, Teresa K.; Bongcam-Rudloff, Erik; Brazas, Michelle E.; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M.; Schneider, Maria Victoria; van Gelder, Celia W. G.

    2015-01-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all. PMID:25856076

  1. A quick guide for building a successful bioinformatics community.

    Directory of Open Access Journals (Sweden)

    Aidan Budd

    2015-02-01

    Full Text Available "Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i the exchange and development of ideas and expertise; (ii career development; (iii coordinated funding activities; (iv interactions and engagement with professionals from other fields; and (v other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop "The 'How To Guide' for Establishing a Successful Bioinformatics Network" at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB and the 12th European Conference on Computational Biology (ECCB.

  2. BIRCH: A user-oriented, locally-customizable, bioinformatics system

    Directory of Open Access Journals (Sweden)

    Fristensky Brian

    2007-02-01

    Full Text Available Abstract Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere.

  3. BIRCH: a user-oriented, locally-customizable, bioinformatics system.

    Science.gov (United States)

    Fristensky, Brian

    2007-02-09

    Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere.

  4. A Quick Guide for Building a Successful Bioinformatics Community

    Science.gov (United States)

    Budd, Aidan; Corpas, Manuel; Brazas, Michelle D.; Fuller, Jonathan C.; Goecks, Jeremy; Mulder, Nicola J.; Michaut, Magali; Ouellette, B. F. Francis; Pawlik, Aleksandra; Blomberg, Niklas

    2015-01-01

    “Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB). PMID:25654371

  5. Detection of shielded radionuclides from weak and poorly resolved spectra using group positive RIVAL

    International Nuclear Information System (INIS)

    Kump, Paul; Bai, Er-Wei; Chan, Kung-Sik; Eichinger, William

    2013-01-01

    This paper is concerned with the identification of nuclides from weak and poorly resolved spectra in the presence of unknown radiation shielding materials such as carbon, water, concrete and lead. Since a shield will attenuate lower energies more so than higher ones, isotope sub-spectra must be introduced into models and into detection algorithms. We propose a new algorithm for detection, called group positive RIVAL, that encourages the selection of groups of sub-spectra rather than the selection of individual sub-spectra that may be from the same parent isotope. Indeed, the proposed algorithm incorporates group positive LASSO, and, as such, we supply the consistency results of group positive LASSO and adaptive group positive LASSO. In an example employing various shielding materials and material thicknesses, group positive RIVAL is shown to perform well in all scenarios with the exception of ones in which the shielding material is lead. - Highlights: ► Identification of nuclides from weak and poorly resolved spectra. ► Shielding materials such as carbon, water, concrete, and lead are considered. ► Isotope spectra are decomposed into their sub-spectra. ► A variable selection algorithm is proposed that encourages group selection. ► Simulations demonstrate the proposed method's performance when nuclides have been shielded

  6. MicroRNA from tuberculosis RNA: A bioinformatics study

    OpenAIRE

    Wiwanitkit, Somsri; Wiwanitkit, Viroj

    2012-01-01

    The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...

  7. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    Science.gov (United States)

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2015-06-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Planning bioinformatics workflows using an expert system.

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T

    2017-04-15

    Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. https://github.com/jefftc/changlab. jeffrey.t.chang@uth.tmc.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  9. Planning bioinformatics workflows using an expert system

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T.

    2017-01-01

    Abstract Motivation: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. Results: To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. Availability and Implementation: https://github.com/jefftc/changlab Contact: jeffrey.t.chang@uth.tmc.edu PMID:28052928

  10. Joint digital signal processing of Nyquist-wavelength division multiplexing superchannel with group detection

    Science.gov (United States)

    Zhang, Tianyun; Yao, Shuchang; Fu, Songnian; Tang, Ming; Liu, Deming

    2014-12-01

    To relax the limited sampling rate of an analog-to-digital converter (ADC) and to reduce the complexity of conventional fiber-optical superchannel coherent detection, we propose and demonstrate a joint digital signal processing (DSP) technique of Nyquist-wavelength division multiplexing superchannel with group detection. At the receiver side, three Nyquist-spaced channels with 12.5 Gbaud polarization multiplexing-quadrature phase shift keying signals are group detected with a sampling rate per channel of 1.33 times over the normal sampling rate. A modified carrier separation technique is then put forward to retrieve the high-frequency interference component of both the designated channel and its adjacent channels, which can subsequently be used to recover the designated channel with new constant modulus algorithm-based joint multiinput-multioutput equalizers. The results show that the proposed group detection and joint DSP algorithm can simultaneously improve the transmission performance and reduce the complexity of both the transmitter and receiver, regardless of bandwidth restrictions from the waveshaper, ADC module, and coherent receiver.

  11. A New M Dwarf Debris Disk Candidate in a Young Moving Group Discovered with Disk Detective

    Science.gov (United States)

    Silverberg, Steven M.; Kuchner, Marc J.; Wisniewski, John P.; Gagne, Jonathan; Bans, Alissa S.; Bhattacharjee, Shambo; Currie, Thayne R.; Debes, John R.; Biggs, Joseph R; Bosch, Milton

    2016-01-01

    We used the Disk Detective citizen science project and the BANYAN II Bayesian analysis tool to identify a new candidate member of a nearby young association with infrared excess. WISE J080822.18-644357.3, an M5.5-type debris disk system with significant excess at both 12 and 22 microns, is a likely member (approx.90% BANYAN II probability) of the approx.45 Myr old Carina association. Since this would be the oldest M dwarf debris disk detected in a moving group, this discovery could be an important constraint on our understanding of M dwarf debris disk evolution.

  12. Infusing Bioinformatics and Research-Like Experience into a Molecular Biology Laboratory Course

    Science.gov (United States)

    Nogaj, Luiza A.

    2014-01-01

    A nine-week laboratory project designed for a sophomore level molecular biology course is described. Small groups of students (3-4 per group) choose a tumor suppressor gene (TSG) or an oncogene for this project. Each group researches the role of their TSG/oncogene from primary literature articles and uses bioinformatics engines to find the gene…

  13. Divide and Conquer: Sub-Grouping of ASD Improves ASD Detection Based on Brain Morphometry.

    Science.gov (United States)

    Katuwal, Gajendra J; Baum, Stefi A; Cahill, Nathan D; Michael, Andrew M

    2016-01-01

    Low success (ASD) classification using brain morphometry from the large multi-site ABIDE dataset and inconsistent findings on brain morphometric abnormalities in ASD can be attributed to the ASD heterogeneity. In this study, we show that ASD brain morphometry is highly heterogeneous, and demonstrate that the heterogeneity can be mitigated and classification improved if autism severity (AS), verbal IQ (VIQ) and age are used with morphometric features. Morphometric features from structural MRIs (sMRIs) of 734 males (ASD: 361, controls: 373) of ABIDE were derived using FreeSurfer. Applying the Random Forest classifier, an AUC of 0.61 was achieved. Adding VIQ and age to morphometric features, AUC improved to 0.68. Sub-grouping the subjects by AS, VIQ and age improved the classification with the highest AUC of 0.8 in the moderate-AS sub-group (AS = 7-8). Matching subjects on age and/or VIQ in each sub-group further improved the classification with the highest AUC of 0.92 in the low AS sub-group (AS = 4-5). AUC decreased with AS and VIQ, and was the lowest in the mid-age sub-group (13-18 years). The important features were mainly from the frontal, temporal, ventricular, right hippocampal and left amygdala regions. However, they highly varied with AS, VIQ and age. The curvature and folding index features from frontal, temporal, lingual and insular regions were dominant in younger subjects suggesting their importance for early detection. When the experiments were repeated using the Gradient Boosting classifier similar results were obtained. Our findings suggest that identifying brain biomarkers in sub-groups of ASD can yield more robust and insightful results than searching across the whole spectrum. Further, it may allow identification of sub-group specific brain biomarkers that are optimized for early detection and monitoring, increasing the utility of sMRI as an important tool for early detection of ASD.

  14. Polymerase chain reaction assay for the detection of Bacillus cereus group cells

    DEFF Research Database (Denmark)

    Hansen, Bjarne Munk; Leser, Thomas D.; Hendriksen, Niels Bohse

    2001-01-01

    of the B. cereus group in food and in the environment. Using 16S rDNA as target, a PCR assay for the detection of B. cereus group cells has been developed. Primers specific for the 16S rDNA of the B. cereus group bacteria were selected and used in combination with consensus primers for 165 rDNA as internal...... PCR procedure control. The PCR procedure was optimized with respect to annealing temperature. When DNA from the B. cereus group bacteria was present, the PCR assay yielded a B. cereus specific fragment, while when non-B. cereus prokaryotic DNA was present, the consensus 165 rDNA primers directed...

  15. Rhesus monkeys (Macaca mulatta) detect rhythmic groups in music, but not the beat.

    Science.gov (United States)

    Honing, Henkjan; Merchant, Hugo; Háden, Gábor P; Prado, Luis; Bartolo, Ramón

    2012-01-01

    It was recently shown that rhythmic entrainment, long considered a human-specific mechanism, can be demonstrated in a selected group of bird species, and, somewhat surprisingly, not in more closely related species such as nonhuman primates. This observation supports the vocal learning hypothesis that suggests rhythmic entrainment to be a by-product of the vocal learning mechanisms that are shared by several bird and mammal species, including humans, but that are only weakly developed, or missing entirely, in nonhuman primates. To test this hypothesis we measured auditory event-related potentials (ERPs) in two rhesus monkeys (Macaca mulatta), probing a well-documented component in humans, the mismatch negativity (MMN) to study rhythmic expectation. We demonstrate for the first time in rhesus monkeys that, in response to infrequent deviants in pitch that were presented in a continuous sound stream using an oddball paradigm, a comparable ERP component can be detected with negative deflections in early latencies (Experiment 1). Subsequently we tested whether rhesus monkeys can detect gaps (omissions at random positions in the sound stream; Experiment 2) and, using more complex stimuli, also the beat (omissions at the first position of a musical unit, i.e. the 'downbeat'; Experiment 3). In contrast to what has been shown in human adults and newborns (using identical stimuli and experimental paradigm), the results suggest that rhesus monkeys are not able to detect the beat in music. These findings are in support of the hypothesis that beat induction (the cognitive mechanism that supports the perception of a regular pulse from a varying rhythm) is species-specific and absent in nonhuman primates. In addition, the findings support the auditory timing dissociation hypothesis, with rhesus monkeys being sensitive to rhythmic grouping (detecting the start of a rhythmic group), but not to the induced beat (detecting a regularity from a varying rhythm).

  16. Rhesus monkeys (Macaca mulatta detect rhythmic groups in music, but not the beat.

    Directory of Open Access Journals (Sweden)

    Henkjan Honing

    Full Text Available It was recently shown that rhythmic entrainment, long considered a human-specific mechanism, can be demonstrated in a selected group of bird species, and, somewhat surprisingly, not in more closely related species such as nonhuman primates. This observation supports the vocal learning hypothesis that suggests rhythmic entrainment to be a by-product of the vocal learning mechanisms that are shared by several bird and mammal species, including humans, but that are only weakly developed, or missing entirely, in nonhuman primates. To test this hypothesis we measured auditory event-related potentials (ERPs in two rhesus monkeys (Macaca mulatta, probing a well-documented component in humans, the mismatch negativity (MMN to study rhythmic expectation. We demonstrate for the first time in rhesus monkeys that, in response to infrequent deviants in pitch that were presented in a continuous sound stream using an oddball paradigm, a comparable ERP component can be detected with negative deflections in early latencies (Experiment 1. Subsequently we tested whether rhesus monkeys can detect gaps (omissions at random positions in the sound stream; Experiment 2 and, using more complex stimuli, also the beat (omissions at the first position of a musical unit, i.e. the 'downbeat'; Experiment 3. In contrast to what has been shown in human adults and newborns (using identical stimuli and experimental paradigm, the results suggest that rhesus monkeys are not able to detect the beat in music. These findings are in support of the hypothesis that beat induction (the cognitive mechanism that supports the perception of a regular pulse from a varying rhythm is species-specific and absent in nonhuman primates. In addition, the findings support the auditory timing dissociation hypothesis, with rhesus monkeys being sensitive to rhythmic grouping (detecting the start of a rhythmic group, but not to the induced beat (detecting a regularity from a varying rhythm.

  17. Detection of Hot Gas in Galaxy Groups via the Sunyaev-Zel'dovich Effect

    OpenAIRE

    Moodley, K.; Warne, R.; Goheer, N.; Trac, H.

    2008-01-01

    Motivated by the observed shortfall of baryons in the local universe, we investigate the ability of high resolution cosmic microwave background (CMB) experiments to detect hot gas in the outer regions of nearby group halos. We construct hot gas models with the gas in hydrostatic equilibrium with the dark matter and described by a polytropic equation of state. We also consider models that add entropy to the gas in line with constraints from X-ray observations. We calculate the thermal Sunyaev-...

  18. A bioinformatics approach to marker development

    NARCIS (Netherlands)

    Tang, J.

    2008-01-01

    The thesis focuses on two bioinformatics research topics: the development of tools for an efficient and reliable identification of single nucleotides polymorphisms (SNPs) and polymorphic simple sequence repeats (SSRs) from expressed sequence tags (ESTs) (Chapter 2, 3 and 4), and the subsequent

  19. SPECIES DATABASES AND THE BIOINFORMATICS REVOLUTION.

    Science.gov (United States)

    Biological databases are having a growth spurt. Much of this results from research in genetics and biodiversity, coupled with fast-paced developments in information technology. The revolution in bioinformatics, defined by Sugden and Pennisi (2000) as the "tools and techniques for...

  20. An integrative bioinformatics pipeline for the genomewide ...

    Indian Academy of Sciences (India)

    An integrative bioinformatics pipeline for the genomewide identification of novel porcine microRNA genes. Wei Fang, Na Zhou, Dengyun Li, Zhigang Chen, Pengfei Jiang and Deli Zhang. J. Genet. 92,587 593. Figure 1. Primary sequence of the predicted SSc-mir-2053 precursor and locations of some terms in the secondary ...

  1. Novel bioinformatic developments for exome sequencing

    NARCIS (Netherlands)

    Lelieveld, S.H.; Veltman, J.A.; Gilissen, C.F.

    2016-01-01

    With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers

  2. An integrative bioinformatics pipeline for the genomewide ...

    Indian Academy of Sciences (India)

    2013-12-06

    Dec 6, 2013 ... The majority of miRNAs in pig (Sus scrofa), an impor- tant domestic animal, remain unknown. From this perspec- tive, we attempted the genomewide identification of novel porcine miRNAs. Here, we propose a novel integrative bioinformatics pipeline to identify conservative and non- conservative novel ...

  3. Development and implementation of a bioinformatics online ...

    African Journals Online (AJOL)

    Thus, there is the need for appropriate strategies of introducing the basic components of this emerging scientific field to part of the African populace through the development of an online distance education learning tool. This study involved the design of a bioinformatics online distance educative tool an implementation of ...

  4. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    reaction (PCR), oligo hybridization and DNA sequencing. Proper primer design is actually one of the most important factors/steps in successful DNA sequencing. Various bioinformatics programs are available for selection of primer pairs from a template sequence. The plethora programs for PCR primer design reflects the.

  5. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

  6. "Extreme Programming" in a Bioinformatics Class

    Science.gov (United States)

    Kelley, Scott; Alger, Christianna; Deutschman, Douglas

    2009-01-01

    The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP).…

  7. Protein raftophilicity. How bioinformatics can help membranologists

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Sperotto, Maria Maddalena

    )-based bioinformatics approach. The ANN was trained to recognize feature-based patterns in proteins that are considered to be associated with lipid rafts. The trained ANN was then used to predict protein raftophilicity. We found that, in the case of α-helical membrane proteins, their hydrophobic length does not affect...

  8. Privacy Preserving PCA on Distributed Bioinformatics Datasets

    Science.gov (United States)

    Li, Xin

    2011-01-01

    In recent years, new bioinformatics technologies, such as gene expression microarray, genome-wide association study, proteomics, and metabolomics, have been widely used to simultaneously identify a huge number of human genomic/genetic biomarkers, generate a tremendously large amount of data, and dramatically increase the knowledge on human…

  9. Bioinformatics in Undergraduate Education: Practical Examples

    Science.gov (United States)

    Boyle, John A.

    2004-01-01

    Bioinformatics has emerged as an important research tool in recent years. The ability to mine large databases for relevant information has become increasingly central to many different aspects of biochemistry and molecular biology. It is important that undergraduates be introduced to the available information and methodologies. We present a…

  10. Bioinformatics applications in proteomics data analysis

    NARCIS (Netherlands)

    Peng, M.

    2015-01-01

    In this thesis, I detail my 4-year efforts in developing bioinformatics tools and algorithms to address the growing demands of current proteomics endeavors, covering a range of facets such as large-scale protein expression profiling, charting post-translation modifications as well as

  11. Insect E-probe Diagnostic Nucleic acid Analysis (EDNA): the application of a novel bioinformatic tool to detection of vectors and pathogens in individual insect and simulated insect trap metagenomes

    Science.gov (United States)

    Plant pathogen detection takes many forms. In simple cases, researchers are attempting to detect a known pathogen from a known host utilizing targeted nucleic acid or antigenic assays. However, in more complex scenarios researchers may not know the identity of a pathogen, or they may need to screen ...

  12. Grouped fuzzy SVM with EM-based partition of sample space for clustered microcalcification detection.

    Science.gov (United States)

    Wang, Huiya; Feng, Jun; Wang, Hongyu

    2017-07-20

    Detection of clustered microcalcification (MC) from mammograms plays essential roles in computer-aided diagnosis for early stage breast cancer. To tackle problems associated with the diversity of data structures of MC lesions and the variability of normal breast tissues, multi-pattern sample space learning is required. In this paper, a novel grouped fuzzy Support Vector Machine (SVM) algorithm with sample space partition based on Expectation-Maximization (EM) (called G-FSVM) is proposed for clustered MC detection. The diversified pattern of training data is partitioned into several groups based on EM algorithm. Then a series of fuzzy SVM are integrated for classification with each group of samples from the MC lesions and normal breast tissues. From DDSM database, a total of 1,064 suspicious regions are selected from 239 mammography, and the measurement of Accuracy, True Positive Rate (TPR), False Positive Rate (FPR) and EVL = TPR* 1-FPR are 0.82, 0.78, 0.14 and 0.72, respectively. The proposed method incorporates the merits of fuzzy SVM and multi-pattern sample space learning, decomposing the MC detection problem into serial simple two-class classification. Experimental results from synthetic data and DDSM database demonstrate that our integrated classification framework reduces the false positive rate significantly while maintaining the true positive rate.

  13. A New Strategy to Reduce Influenza Escape: Detecting Therapeutic Targets Constituted of Invariance Groups

    Directory of Open Access Journals (Sweden)

    Julie Lao

    2017-03-01

    Full Text Available The pathogenicity of the different flu species is a real public health problem worldwide. To combat this scourge, we established a method to detect drug targets, reducing the possibility of escape. Besides being able to attach a drug candidate, these targets should have the main characteristic of being part of an essential viral function. The invariance groups that are sets of residues bearing an essential function can be detected genetically. They consist of invariant and synthetic lethal residues (interdependent residues not varying or slightly varying when together. We analyzed an alignment of more than 10,000 hemagglutinin sequences of influenza to detect six invariance groups, close in space, and on the protein surface. In parallel we identified five potential pockets on the surface of hemagglutinin. By combining these results, three potential binding sites were determined that are composed of invariance groups located respectively in the vestigial esterase domain, in the bottom of the stem and in the fusion area. The latter target is constituted of residues involved in the spring-loaded mechanism, an essential step in the fusion process. We propose a model describing how this potential target could block the reorganization of the hemagglutinin HA2 secondary structure and prevent viral entry into the host cell.

  14. Agile parallel bioinformatics workflow management using Pwrake.

    Science.gov (United States)

    Mishima, Hiroyuki; Sasaki, Kensaku; Tanaka, Masahiro; Tatebe, Osamu; Yoshiura, Koh-Ichiro

    2011-09-08

    In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error.Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles

  15. Agile parallel bioinformatics workflow management using Pwrake

    Science.gov (United States)

    2011-01-01

    Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

  16. Detection of Group B Streptococcus in Brazilian pregnant women and antimicrobial susceptibility patterns

    Directory of Open Access Journals (Sweden)

    Didier Silveira Castellano-Filho

    2010-12-01

    Full Text Available Group B Streptococcus (GBS is still not routinely screened during pregnancy in Brazil, being prophylaxis and empirical treatment based on identification of risk groups. This study aimed to investigate GBS prevalence in Brazilian pregnant women by culture or polymerase chain reaction (PCR associated to the enrichment culture, and to determine the antimicrobial susceptibility patterns of isolated bacteria, so as to support public health policies and empirical prophylaxis. After an epidemiological survey, vaginal and anorectal specimens were collected from 221 consenting laboring women. Each sample was submitted to enrichment culture and sheep blood agar was used to isolate suggestive GBS. Alternatively, specific PCR was performed from enrichment cultures. Antimicrobial susceptibility patterns were determined for isolated bacteria by agar diffusion method. No risk groups were identified. Considering the culture-based methodology, GBS was detected in 9.5% of the donors. Twenty five bacterial strains were isolated and identified. Through the culture-PCR methodology, GBS was detected in 32.6% specimens. Bacterial resistance was not detected against ampicillin, cephazolin, vancomycin and ciprofloxacin, whereas 22.7% were resistant to erythromycin and 50% were resistant to clindamycin. GBS detection may be improved by the association of PCR and enrichment culture. Considering that colony selection in agar plates may be laboring and technician-dependent, it may not reflect the real prevalence of streptococci. As in Brazil prevention strategies to reduce the GBS associated diseases have not been adopted, prospective studies are needed to anchor public health policies especially considering the regional GBS antimicrobial susceptibility patterns.

  17. Navigating the changing learning landscape: perspective from bioinformatics.ca.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2013-09-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs.

  18. Evaluation of Simplexa Group A Strep Direct Kit Compared to Hologic Group A Streptococcal Direct Assay for Detection of Group A Streptococcus in Throat Swabs.

    Science.gov (United States)

    Church, Deirdre L; Lloyd, Tracie; Larios, Oscar; Gregson, Daniel B

    2018-03-01

    Diagnosis of bacterial pharyngitis is confirmed by detection of group A Streptococcus (GAS) in patient throat samples. Testing of throat samples has historically relied on culture, but new molecular methods allow much faster test turnaround time (i.e., same day versus 48 to 72 h for culture). Our laboratory uses the Hologic GAS Direct (GASD) assay for screening more than 125,000 throat samples per year. Simplexa GAS Direct is a new real-time quantitative PCR (qPCR) assay that does not require initial DNA extraction. Performance of Simplexa qPCR was compared to GASD. A total of 289 throat swabs were collected from patients attending ambulatory clinics in Calgary, Alberta, Canada. A total of 60 (20.8%) of the samples were initially GAS positive by either method: 54 by both methods, 4 by Simplex qPCR alone, and 2 by GASD alone. An in-house PCR using a unique GAS primer set was used to resolve the 6 discrepant results. Overall, GASD compared to Simplexa qPCR had a sensitivity, specificity, positive predictive value, and negative predictive value of 93.1% versus 100%, 100% versus 100%, 100% versus 100%, and 98.31% versus 100%, respectively. Implementation of Simplexa qPCR in our laboratory setting would cost more but allow the high sample volume to be reported in half the time and save 0.62 medical laboratory technician (MLT) full-time equivalent (FTE). In comparison to culture, the implementation of Simplexa qPCR would save 2.79 medical laboratory assistant (MLA) FTE plus 0.94 MLT FTE. Simplexa qPCR has improved performance and diagnostic efficiency in a high-volume laboratory compared to GASD for GAS detection in throat swabs. Copyright © 2018 American Society for Microbiology.

  19. A Bioinformatics Reference Model: Towards a Framework for Developing and Organising Bioinformatic Resources

    Science.gov (United States)

    Hiew, Hong Liang; Bellgard, Matthew

    2007-11-01

    Life Science research faces the constant challenge of how to effectively handle an ever-growing body of bioinformatics software and online resources. The users and developers of bioinformatics resources have a diverse set of competing demands on how these resources need to be developed and organised. Unfortunately, there does not exist an adequate community-wide framework to integrate such competing demands. The problems that arise from this include unstructured standards development, the emergence of tools that do not meet specific needs of researchers, and often times a communications gap between those who use the tools and those who supply them. This paper presents an overview of the different functions and needs of bioinformatics stakeholders to determine what may be required in a community-wide framework. A Bioinformatics Reference Model is proposed as a basis for such a framework. The reference model outlines the functional relationship between research usage and technical aspects of bioinformatics resources. It separates important functions into multiple structured layers, clarifies how they relate to each other, and highlights the gaps that need to be addressed for progress towards a diverse, manageable, and sustainable body of resources. The relevance of this reference model to the bioscience research community, and its implications in progress for organising our bioinformatics resources, are discussed.

  20. 3D modelling of the pathogenic Leptospira protein LipL32: A bioinformatics approach.

    Science.gov (United States)

    Kumaran, Sharmilah Kumari; Bakar, Mohd Faizal Abu; Mohd-Padil, Hirzahida; Mat-Sharani, Shuhaila; Sakinah, S; Poorani, K; Alsaeedy, Hiba; Peli, Amira; Wei, Teh Seoh; Ling, Mok Pooi; Hamat, Rukman Awang; Neela, Vasantha Kumari; Higuchi, Akon; Alarfaj, Abdullah A; Rajan, Mariappan; Benelli, Giovanni; Arulselvan, Palanisamy; Kumar, S Suresh

    2017-12-01

    Leptospirosis is a widespread zoonotic disease caused by pathogenic Leptospira species (Leptospiraceae). LipL32 is an abundant lipoprotein from the outer membrane proteins (OMPs) group, highly conserved among pathogenic and intermediate Leptospira species. Several studies used LipL32 as a specific gene to identify the presence of leptospires. This research was aimed to study the characteristics of LipL32 protein gene code, to fill the knowledge gap concerning the most appropriate gene that can be used as antigen to detect the Leptospira. Here, we investigated the features of LipL32 in fourteen Leptospira pathogenic strains based on comparative analyses of their primary, secondary structures and 3D modeling using a bioinformatics approach. Furthermore, the physicochemical properties of LipL32 in different strains were studied, shedding light on the identity of signal peptides, as well as on the secondary and tertiary structure of the LipL32 protein, supported by 3D modelling assays. The results showed that the LipL32 gene was present in all the fourteen pathogenic Leptospira strains used in this study, with limited diversity in terms of sequence conservation, hydrophobic group, hydrophilic group and number of turns (random coil). Overall, these results add basic knowledge to the characteristics of LipL32 protein, contributing to the identification of potential antigen candidates in future research, in order to ensure prompt and reliable detection of pathogenic Leptospira species. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Detection of virulence genes and the phylogenetic groups of Escherichia coli isolated from dogs in Brazil

    Directory of Open Access Journals (Sweden)

    Fernanda Morcatti Coura

    2018-02-01

    Full Text Available ABSTRACT: This study identified the virulence genes, pathovars, and phylogenetic groups of Escherichia coli strains obtained from the feces of dogs with and without diarrhea. Virulence genes and phylogenetic group identification were studied using polymerase chain reaction. Thirty-seven E. coli isolates were positive for at least one virulence factor gene. Twenty-one (57.8% of the positive isolates were isolated from diarrheal feces and sixteen (43.2% were from the feces of non-diarrheic dogs. Enteropathogenic E. coli (EPEC were the most frequently (62.2% detected pathovar in dog feces and were mainly from phylogroup B1 and E. Necrotoxigenic E. coli were detected in 16.2% of the virulence-positive isolates and these contained the cytotoxic necrotizing factor 1 (cnf1 gene and were classified into phylogroups B2 and D. All E. coli strains were negative for the presence of enterotoxigenic E. coli (ETEC enterotoxin genes, but four strains were positive for ETEC-related fimbriae 987P and F18. Two isolates were Shiga toxin-producing E. coli strains and contained the toxin genesStx2 or Stx2e, both from phylogroup B1. Our data showed that EPEC was the most frequent pathovar and B1 and E were the most common phylogroups detected in E. coli isolated from the feces of diarrheic and non-diarrheic dogs.

  2. Multiplex real-time PCR SYBR Green for detection and typing of group III Clostridium botulinum.

    Science.gov (United States)

    Anniballi, Fabrizio; Auricchio, Bruna; Delibato, Elisabetta; Antonacci, Monia; De Medici, Dario; Fenicia, Lucia

    2012-01-27

    Clostridium botulinum type C and type D belonging to the group III organisms, are mainly responsible for animal botulism outbreaks. Clinical signs alone are often insufficient to make a diagnosis of botulism and a laboratory confirmation is required. Laboratory confirmation can be performed by demonstrating the presence of botulinum neurotoxins in serum, gastrointestinal contents, liver, wound of sick or dead animals, or by demonstrating the presence of C. botulinum in gastrointestinal contents, liver, and wound. Demonstration of spores in gastrointestinal contents or tissue of animals with clinical signs indicative of botulism reinforces the clinical diagnosis. With the aim of detecting and typing C. botulinum group III organisms, a multiplex real-time PCR SYBR Green was developed and in-house validated. Selectivity, limit of detection, relative accuracy, relative specificity, relative sensitivity, and repeatability of the method were investigated. The multiplex real-time PCR SYBR green used showed a 100% selectivity, 100% relative accuracy, 100% relative specificity, 100% relative sensitivity and a limit of detection of 277 and 580 DNA copies for C. botulinum type C and C. botulinum type D, respectively. The method reported here represents a suitable tool for laboratory diagnosis of type C and D botulism and for testing a large number of samples collected during the animal botulism surveillance and prevention activities. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Sequencing and bioinformatics analysis of the differentially expressed genes in herniated discs with or without calcification.

    Science.gov (United States)

    Shao, Jia; Yu, Miao; Jiang, Liang; Wu, Fengliang; Liu, Xiaoguang

    2017-01-01

    The purpose of this study was to detect the differentially expressed genes between ossified herniated discs and herniated discs without ossification. In addition, we sought to identify a few candidate genes and pathways by using bioinformatics analysis. We analyzed 6 samples each of ossified herniated discs (experimental group) and herniated discs without ossification (control group). Purified mRNA and cDNA extracted from the samples were subjected to sequencing. The NOISeq method was used to statistically identify the differentially expressed genes (DEGs) between the 2 groups. An in-depth analysis using bioinformatics tools based on the DEGs was performed using Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction network analysis. The top 6 DEGs were verified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A total of 132 DEGs was detected. A total of 129 genes in the ossified group were upregulated and 3 genes were found to be downregulated as compared to the control group. The top 3 cellular components in GO ontologies analysis were extracellular matrix components. GO functions were mainly related to the glycoprotein in the cell membrane and extracellular matrix. The GO process was related to completing response to stimulus, immune reflex and defense. The top 5 KEGG enrichment pathways were associated with infection and inflammation. Three of the top 20 DEGs [sclerostin (SOST), WNT inhibitory factor 1 (WIF1) and secreted frizzled related protein 4 (SFRP4)] were related to the inhibition of the Wnt pathway. The ossified discs exhibited a higher expression of the top 6 DEGs [SOST, joining chain of multimeric IgA and IgM (IGJ; also known as JCHAIN), defensin alpha 4 (DEFA4), SFRP4, proteinase 3 (PRTN3) and cathepsin G (CTSG)], with the associated P-values of 0.045, 0.000, 0.008, 0.010, 0.015 and 0.002, respectively, as

  4. Bioinformatics and its application in animal health: a review | Soetan ...

    African Journals Online (AJOL)

    The aim of this review is to discuss the importance of bioinformatics and emphasize the need to acquire bioinformatics training and skills so as to maximize its potentials for improved delivery of animal health. In this review, bioinformatics is introduced, challenges to effective animal disease diagnosis, prevention and control, ...

  5. Component-Based Approach for Educating Students in Bioinformatics

    Science.gov (United States)

    Poe, D.; Venkatraman, N.; Hansen, C.; Singh, G.

    2009-01-01

    There is an increasing need for an effective method of teaching bioinformatics. Increased progress and availability of computer-based tools for educating students have led to the implementation of a computer-based system for teaching bioinformatics as described in this paper. Bioinformatics is a recent, hybrid field of study combining elements of…

  6. Social Fingerprinting: detection of spambot groups through DNA-inspired behavioral modeling

    DEFF Research Database (Denmark)

    Cresci, Stefano; Di Pietro, Roberto; Petrocchi, Marinella

    2017-01-01

    it with three state-of-the-art detection algorithms. Among the peculiarities of our approach is the possibility to apply off-the-shelf DNA analysis techniques to study online users behaviors and to efficiently rely on a limited number of lightweight account characteristics....... to go undetected even by current state-of-the-art algorithms. In this paper, we show that efficient spambots detection can be achieved via an in-depth analysis of their collective behaviors exploiting the digital DNA technique for modeling the behaviors of social network users. Inspired by its...... biological counterpart, in the digital DNA representation the behavioral lifetime of a digital account is encoded in a sequence of characters. Then, we define a similarity measure for such digital DNA sequences. We build upon digital DNA and the similarity between groups of users to characterize both genuine...

  7. Cassini detection of Enceladus's cold water-group plume ionosphere

    Energy Technology Data Exchange (ETDEWEB)

    Tokar, Robert L [Los Alamos National Laboratory; Thomsen, Michelle F [Los Alamos National Laboratory; Wilson, Robert J [Los Alamos National Laboratory; Johnson, R E [UNIV OF VIRGINIA; Young, D T [SWRI; Crary, F J [SWRI; Coates, A J [MSSL; Jones, G H [MSSL; Paty, C S [GIT

    2009-01-01

    This study reports direct detection by the Cassini plasma spectrometer of freshly-produced water-group ions (O{sup +}, OH{sup +}, H{sub 2}O{sup +}, H{sub 3}O{sup +}) and heavier water dimer ions (H{sub x}O{sub 2}{sup +}) very close to Enceladus and where the plasma begins to emerge from the Enceladus plume The data wcre obtained during two close (52 and 25 km) flybys of Enceladus in 2008, and are similar to ion data in cometary comas. The ions are observed in detectors looking in the Cassini ram direction at energies consistent with the Cassini speed, indicating a nearly stagnant plasma flow in the plume. North of Enceladus the plasma slowing commences about 4 to 6 Enceladus radii away, while south of Enccladus signatures ofthe interaction are detected as far as 22 Enceladus radii away.

  8. Explain bioinformatics to your grandmother!

    Directory of Open Access Journals (Sweden)

    Virginie Bernard

    2013-10-01

    Full Text Available What are you working on? You have certainly been asked that question many times, whether it be at a Saturday night party, during a discussion with your neighbors, or at a family gathering. Communicating with a lay audience about scientific subjects and making them attractive is a difficult task. But difficult or not, you will have to do it for many years, not only with your family and friends, but also with your colleagues and collaborators. So, better learn now! Although not usually taught, the ability to explain your work to others is an essential skill in science, where communication plays a key role. Using some examples of the French Regional Student Group activities, we discuss here (i why it is important to have such communication skills, (ii how you can get involved in these activities by using existing resources or working with people who have previous experience, and (iii what you get out of this amazing experience. We aim to motivate you and provide you with tips and ideas to get involved in promoting scientific activities while getting all the benefits.

  9. Group-specific multiplex PCR detection systems for the identification of flying insect prey.

    Directory of Open Access Journals (Sweden)

    Daniela Sint

    Full Text Available The applicability of species-specific primers to study feeding interactions is restricted to those ecosystems where the targeted prey species occur. Therefore, group-specific primer pairs, targeting higher taxonomic levels, are often desired to investigate interactions in a range of habitats that do not share the same species but the same groups of prey. Such primers are also valuable to study the diet of generalist predators when next generation sequencing approaches cannot be applied beneficially. Moreover, due to the large range of prey consumed by generalists, it is impossible to investigate the breadth of their diet with species-specific primers, even if multiplexing them. However, only few group-specific primers are available to date and important groups of prey such as flying insects have rarely been targeted. Our aim was to fill this gap and develop group-specific primers suitable to detect and identify the DNA of common taxa of flying insects. The primers were combined in two multiplex PCR systems, which allow a time- and cost-effective screening of samples for DNA of the dipteran subsection Calyptratae (including Anthomyiidae, Calliphoridae, Muscidae, other common dipteran families (Phoridae, Syrphidae, Bibionidae, Chironomidae, Sciaridae, Tipulidae, three orders of flying insects (Hymenoptera, Lepidoptera, Plecoptera and coniferous aphids within the genus Cinara. The two PCR assays were highly specific and sensitive and their suitability to detect prey was confirmed by testing field-collected dietary samples from arthropods and vertebrates. The PCR assays presented here allow targeting prey at higher taxonomic levels such as family or order and therefore improve our ability to assess (trophic interactions with flying insects in terrestrial and aquatic habitats.

  10. Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

    DEFF Research Database (Denmark)

    Boomsma, Wouter Krogh; Nielsen, Sofie Vincents; Lindorff-Larsen, Kresten

    2016-01-01

    conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology...

  11. Quantum Bio-Informatics IV

    Science.gov (United States)

    Accardi, Luigi; Freudenberg, Wolfgang; Ohya, Masanori

    2011-01-01

    The QP-DYN algorithms / L. Accardi, M. Regoli and M. Ohya -- Study of transcriptional regulatory network based on Cis module database / S. Akasaka ... [et al.] -- On Lie group-Lie algebra correspondences of unitary groups in finite von Neumann algebras / H. Ando, I. Ojima and Y. Matsuzawa -- On a general form of time operators of a Hamiltonian with purely discrete spectrum / A. Arai -- Quantum uncertainty and decision-making in game theory / M. Asano ... [et al.] -- New types of quantum entropies and additive information capacities / V. P. Belavkin -- Non-Markovian dynamics of quantum systems / D. Chruscinski and A. Kossakowski -- Self-collapses of quantum systems and brain activities / K.-H. Fichtner ... [et al.] -- Statistical analysis of random number generators / L. Accardi and M. Gabler -- Entangled effects of two consecutive pairs in residues and its use in alignment / T. Ham, K. Sato and M. Ohya -- The passage from digital to analogue in white noise analysis and applications / T. Hida -- Remarks on the degree of entanglement / D. Chruscinski ... [et al.] -- A completely discrete particle model derived from a stochastic partial differential equation by point systems / K.-H. Fichtner, K. Inoue and M. Ohya -- On quantum algorithm for exptime problem / S. Iriyama and M. Ohya -- On sufficient algebraic conditions for identification of quantum states / A. Jamiolkowski -- Concurrence and its estimations by entanglement witnesses / J. Jurkowski -- Classical wave model of quantum-like processing in brain / A. Khrennikov -- Entanglement mapping vs. quantum conditional probability operator / D. Chruscinski ... [et al.] -- Constructing multipartite entanglement witnesses / M. Michalski -- On Kadison-Schwarz property of quantum quadratic operators on M[symbol](C) / F. Mukhamedov and A. Abduganiev -- On phase transitions in quantum Markov chains on Cayley Tree / L. Accardi, F. Mukhamedov and M. Saburov -- Space(-time) emergence as symmetry breaking effect / I. Ojima

  12. Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

    Science.gov (United States)

    Schönbach, Christian; Verma, Chandra; Bond, Peter J; Ranganathan, Shoba

    2016-12-22

    The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics and BMC Systems Biology, 24 articles with a bioinformatics or systems biology focus are reviewed in this editorial. InCoB2017 is scheduled to be held in Shenzen, China, September 20-22, 2017.

  13. Concepts and introduction to RNA bioinformatics

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Hofacker, Ivo L.; Ruzzo, Walter L.

    2014-01-01

    RNA bioinformatics and computational RNA biology have emerged from implementing methods for predicting the secondary structure of single sequences. The field has evolved to exploit multiple sequences to take evolutionary information into account, such as compensating (and structure preserving) base...... changes. These methods have been developed further and applied for computational screens of genomic sequence. Furthermore, a number of additional directions have emerged. These include methods to search for RNA 3D structure, RNA-RNA interactions, and design of interfering RNAs (RNAi) as well as methods...... for interactions between RNA and proteins.Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology....

  14. Bioinformatics analysis of differentially expressed proteins in prostate cancer based on proteomics data

    Directory of Open Access Journals (Sweden)

    Chen C

    2016-03-01

    Full Text Available Chen Chen,1 Li-Guo Zhang,1 Jian Liu,1 Hui Han,1 Ning Chen,1 An-Liang Yao,1 Shao-San Kang,1 Wei-Xing Gao,1 Hong Shen,2 Long-Jun Zhang,1 Ya-Peng Li,1 Feng-Hong Cao,1 Zhi-Guo Li3 1Department of Urology, North China University of Science and Technology Affiliated Hospital, 2Department of Modern Technology and Education Center, 3Department of Medical Research Center, International Science and Technology Cooperation Base of Geriatric Medicine, North China University of Science and Technology, Tangshan, People’s Republic of China Abstract: We mined the literature for proteomics data to examine the occurrence and metastasis of prostate cancer (PCa through a bioinformatics analysis. We divided the differentially expressed proteins (DEPs into two groups: the group consisting of PCa and benign tissues (P&b and the group presenting both high and low PCa metastatic tendencies (H&L. In the P&b group, we found 320 DEPs, 20 of which were reported more than three times, and DES was the most commonly reported. Among these DEPs, the expression levels of FGG, GSN, SERPINC1, TPM1, and TUBB4B have not yet been correlated with PCa. In the H&L group, we identified 353 DEPs, 13 of which were reported more than three times. Among these DEPs, MDH2 and MYH9 have not yet been correlated with PCa metastasis. We further confirmed that DES was differentially expressed between 30 cancer and 30 benign tissues. In addition, DEPs associated with protein transport, regulation of actin cytoskeleton, and the extracellular matrix (ECM–receptor interaction pathway were prevalent in the H&L group and have not yet been studied in detail in this context. Proteins related to homeostasis, the wound-healing response, focal adhesions, and the complement and coagulation pathways were overrepresented in both groups. Our findings suggest that the repeatedly reported DEPs in the two groups may function as potential biomarkers for detecting PCa and predicting its aggressiveness. Furthermore

  15. Comprehensive decision tree models in bioinformatics.

    Science.gov (United States)

    Stiglic, Gregor; Kocbek, Simon; Pernek, Igor; Kokol, Peter

    2012-01-01

    Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly

  16. Comprehensive decision tree models in bioinformatics.

    Directory of Open Access Journals (Sweden)

    Gregor Stiglic

    Full Text Available PURPOSE: Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. METHODS: This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. RESULTS: The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. CONCLUSIONS: The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets

  17. The growing need for microservices in bioinformatics

    Directory of Open Access Journals (Sweden)

    Christopher L Williams

    2016-01-01

    Full Text Available Objective: Within the information technology (IT industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise′s overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements. Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics Conclusions: Use of the microservices framework

  18. ballaxy: web services for structural bioinformatics.

    Science.gov (United States)

    Hildebrandt, Anna Katharina; Stöckel, Daniel; Fischer, Nina M; de la Garza, Luis; Krüger, Jens; Nickels, Stefan; Röttig, Marc; Schärfe, Charlotta; Schumann, Marcel; Thiel, Philipp; Lenhof, Hans-Peter; Kohlbacher, Oliver; Hildebrandt, Andreas

    2015-01-01

    Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together. In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling.  ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy. Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/. ballaxy is licensed under the terms of the GPL. © The Author 2014. Published by Oxford University Press. All rights reserved. For

  19. Network-based group variable selection for detecting expression quantitative trait loci (eQTL

    Directory of Open Access Journals (Sweden)

    Zhang Xuegong

    2011-06-01

    Full Text Available Abstract Background Analysis of expression quantitative trait loci (eQTL aims to identify the genetic loci associated with the expression level of genes. Penalized regression with a proper penalty is suitable for the high-dimensional biological data. Its performance should be enhanced when we incorporate biological knowledge of gene expression network and linkage disequilibrium (LD structure between loci in high-noise background. Results We propose a network-based group variable selection (NGVS method for QTL detection. Our method simultaneously maps highly correlated expression traits sharing the same biological function to marker sets formed by LD. By grouping markers, complex joint activity of multiple SNPs can be considered and the dimensionality of eQTL problem is reduced dramatically. In order to demonstrate the power and flexibility of our method, we used it to analyze two simulations and a mouse obesity and diabetes dataset. We considered the gene co-expression network, grouped markers into marker sets and treated the additive and dominant effect of each locus as a group: as a consequence, we were able to replicate results previously obtained on the mouse linkage dataset. Furthermore, we observed several possible sex-dependent loci and interactions of multiple SNPs. Conclusions The proposed NGVS method is appropriate for problems with high-dimensional data and high-noise background. On eQTL problem it outperforms the classical Lasso method, which does not consider biological knowledge. Introduction of proper gene expression and loci correlation information makes detecting causal markers more accurate. With reasonable model settings, NGVS can lead to novel biological findings.

  20. Adapting bioinformatics curricula for big data

    Science.gov (United States)

    Greene, Anna C.; Giffin, Kristine A.; Greene, Casey S.

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. PMID:25829469

  1. Bringing Web 2.0 to bioinformatics.

    Science.gov (United States)

    Zhang, Zhang; Cheung, Kei-Hoi; Townsend, Jeffrey P

    2009-01-01

    Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.

  2. Bioinformatics on the cloud computing platform Azure.

    Directory of Open Access Journals (Sweden)

    Hugh P Shanahan

    Full Text Available We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development.

  3. Bioinformatics on the cloud computing platform Azure.

    Science.gov (United States)

    Shanahan, Hugh P; Owen, Anne M; Harrison, Andrew P

    2014-01-01

    We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development.

  4. Chapter 16: text mining for translational bioinformatics.

    Science.gov (United States)

    Cohen, K Bretonnel; Hunter, Lawrence E

    2013-04-01

    Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

  5. Bioinformatics training: a review of challenges, actions and support requirements.

    Science.gov (United States)

    Schneider, Maria Victoria; Watson, James; Attwood, Teresa; Rother, Kristian; Budd, Aidan; McDowall, Jennifer; Via, Allegra; Fernandes, Pedro; Nyronen, Tommy; Blicher, Thomas; Jones, Phil; Blatter, Marie-Claude; De Las Rivas, Javier; Judge, David Phillip; van der Gool, Wouter; Brooksbank, Cath

    2010-11-01

    As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first Trainer Networking Session held under the auspices of the EU-funded SLING Integrating Activity, which took place in November 2009.

  6. Bioinformatics Training: A Review of Challenges, Actions and Support Requirements

    DEFF Research Database (Denmark)

    Schneider, M.V.; Watson, J.; Attwood, T.

    2010-01-01

    As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics...... services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first...

  7. Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.

    Science.gov (United States)

    Rideout, Jai Ram; Chase, John H; Bolyen, Evan; Ackermann, Gail; González, Antonio; Knight, Rob; Caporaso, J Gregory

    2016-06-13

    Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support the concurrent editing of a single spreadsheet by different users working on different platforms. Most of the researchers who enter data are not familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis. We present Keemei, a Google Sheets Add-on, for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google's Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports the validation of two widely used tabular bioinformatics formats, the Quantitative Insights into Microbial Ecology (QIIME) sample metadata mapping file format and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others. Keemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are

  8. Accuracy of an Accelerated, Culture-Based Assay for Detection of Group B Streptococcus

    Directory of Open Access Journals (Sweden)

    Jonathan P. Faro

    2013-01-01

    Full Text Available Objective. To determine the validity of a novel Group B Streptococcus (GBS diagnostic assay for the detection of GBS in antepartum patients. Study Design. Women were screened for GBS colonization at 35 to 37 weeks of gestation. Three vaginal-rectal swabs were collected per patient; two were processed by traditional culture (commercial laboratory versus in-house culture, and the third was processed by an immunoblot-based test, in which a sample is placed over an antibody-coated nitrocellulose membrane, and after a six-hour culture, bound GBS is detected with a secondary antibody. Results. 356 patients were evaluated. Commercial processing revealed a GBS prevalence rate of 85/356 (23.6%. In-house culture provided a prevalence rate of 105/356 (29.5%. When the accelerated GBS test result was compared to the in-house GBS culture, it demonstrated a sensitivity of 97.1% and a specificity of 88.4%. Interobserver reliability for the novel GBS test was 88.2%. Conclusions. The accelerated GBS test provides a high level of validity for the detection of GBS colonization in antepartum patients within 6.5 hours and demonstrates a substantial agreement between observers.

  9. PCR detection of cytK gene in Bacillus cereus group strains isolated from food samples.

    Science.gov (United States)

    Oltuszak-Walczak, Elzbieta; Walczak, Piotr

    2013-11-01

    A method for detection of the cytotoxin K cytK structural gene and its active promoter preceded by the PlcR-binding box, controlling the expression level of this enterotoxin, was developed. The method was applied for the purpose of the analysis of 47 bacterial strains belonging to the Bacillus cereus group isolated from different food products. It was found that the majority of the analyzed strains carried the fully functional cytK gene with its PlcR regulated promoter. The cytK gene was not detected in four emetic strains of Bacillus cereus carrying the cesB gene and potentially producing an emetic toxin - cereulide. The cytotoxin K gene was detected in 4 isolates classified as Bacillus mycoides and one reference strain B. mycoides PCM 2024. The promoter region and the N-terminal part of the cytK gene from two strains of B. mycoides (5D and 19E) showed similarities to the corresponding sequences of Bacillus cereus W23 and Bacillus thuringiensis HD-789, respectively. It was shown for the first time that the cytK gene promoter region from strains 5D and 19E of Bacillus mycoides had a similar arrangement to the corresponding sequence of Bacillus cereus ATCC 14579. The presence of the cytK gene in Bacillus mycoides shows that this species, widely recognized as nonpathogenic, may pose potential biohazard to human beings. © 2013.

  10. Bearing fault detection utilizing group delay and the Hilbert-Huang transform

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Shuai; Lee, Sang-Kwon [Inha University, Incheon (Korea, Republic of)

    2017-03-15

    Vibration signals measured from a mechanical system are useful to detect system faults. Signal processing has been used to extract fault information in bearing systems. However, a wide vibration signal frequency band often affects the ability to obtain the effective fault features. In addition, a few oscillation components are not useful at the entire frequency band in a vibration signal. By contrast, useful fatigue information can be embedded in the noise oscillation components. Thus, a method to estimate which frequency band contains fault information utilizing group delay was proposed in this paper. Group delay as a measure of phase distortion can indicate the phase structure relationship in the frequency domain between original (with noise) and denoising signals. We used the empirical mode decomposition of a Hilbert-Huang transform to sift the useful intrinsic mode functions based on the results of group delay after determining the valuable frequency band. Finally, envelope analysis and the energy distribution after the Hilbert transform were used to complete the fault diagnosis. The practical bearing fault data, which were divided into inner and outer race faults, were used to verify the efficiency and quality of the proposed method.

  11. Clinical value of polymerase chain reaction in detecting group B streptococcus during labor.

    Science.gov (United States)

    Koppes, Dorothea Maria; Vriends, Antonius Arnoldus Cornelis Maria; van Rijn, Michiel; van Heesewijk, Antonine Dimphne

    2017-06-01

    To reduce the intrapartum use of antibiotics in women with prolonged rupture of the membranes (PROM) by restriction of antibiotics to women who are colonized with group B streptococci (GBS), as identified with the Cepheid Gene Xpert polymerase chain reaction (PCR) for detecting GBS. We conducted a randomized controlled trial among full-term delivering women with PROM. Fifty-four women were enrolled, based on a power calculation with a significance level of 5% and a power of 95%. Twenty-seven women received the standard treatment (rectovaginal swab [RVS] for bacterial culture and antibiotics). For another 27 women PCR was performed on the RVS and antibiotics were used only when the PCR was positive. The primary outcome was reduction in antibiotic use, defined as the percentage of women who received antibiotics during labor. 54 Women were enrolled in the study between 1 May and 18 November 2014. There were no significant differences in baseline characteristics. In total, 10 of the 54 women were GBS positive (18.5%). Of those 10 women, three were identified on bacterial culture and seven on PCR. In the bacterial culture group all the women received antibiotics. In the PCR group 10 women (37%) received antibiotics (P = 0.002). Two false-positive PCR tests were identified. There were no false-negative PCR tests. Real-time identification of GBS on PCR reduces the intrapartum use of antibiotics in women with PROM. © 2017 Japan Society of Obstetrics and Gynecology.

  12. Detection of rare blood group, Bombay (Oh phenotype patients and management by acute normovolemic hemodilution

    Directory of Open Access Journals (Sweden)

    Manisha Shrivastava

    2015-01-01

    Full Text Available Background: Due to lack of correct blood grouping practices, the rare Bombay Oh phenotype may be missed, subjecting patients to the risk of severe hemolytic transfusion reaction. In the absence of blood donor registry, transfusion management of patients needing immediate surgery is a challenge. This study presents detection of rare Bombay Oh phenotype patients and their management by acute peri-operative acute normovolemic hemodilution (ANH in a hospital from central India. Materials and Methods: Blood grouping of patients and blood donors with a standard tube method was carried out and samples identified as rare Bombay phenotype were confirmed by saliva inhibition test. Surgical management of cases needing transfusion was done by ANH, as per the British Committee for Standards in Hematology guidelines. Results: The incidence of Bombay phenotype was 0.002% or 1 in 51,924 in the study. Amongst three cases (patients identified as Bombay phenotype, one was Bombay Oh, Rh negative. Two cases were missed in the first instance and one case actually did not require transfusion. In the absence of a blood donor registry for Bombay phenotype, the cases needing transfusion were successfully managed with ANH in the operation theatre. Conclusion: A simple test like blood grouping should be done with serious intention with incorporation of both forward and reverse grouping, so that no patient receives wrong blood leading to fatal hemolysis due to transfusion. ANH is a cost-effective transfusion option for suitable patients. Appropriate clinical decision making, use of strategies to decrease peri-operative blood losses and cost-effective country based planning could be more widely applied to improve clinical transfusion practice.

  13. Conducting polymer based DNA biosensor for the detection of the Bacillus cereus group species

    Science.gov (United States)

    Velusamy, Vijayalakshmi; Arshak, Khalil; Korostynska, Olga; Oliwa, Kamila; Adley, Catherine

    2009-05-01

    Biosensor designs are emerging at a significant rate and play an increasingly important role in foodborne pathogen detection. Conducting polymers are excellent tools for the fabrication of biosensors and polypyrrole has been used in the detection of biomolecules due to its unique properties. The prime intention of this paper was to pioneer the design and fabrication of a single-strand (ss) DNA biosensor for the detection of the Bacillus cereus (B.cereus) group species. Growth of B. cereus, results in production of several highly active toxins. Therefore, consumption of food containing >106 bacteria/gm may results in emetic and diarrhoeal syndromes. The most common source of this bacterium is found in liquid food products, milk powder, mixed food products and is of particular concern in the baby formula industry. The electrochemical deposition technique, such as cyclic voltammetry, was used to develop and test a model DNA-based biosensor on a gold electrode electropolymerized with polypyrrole. The electrically conducting polymer, polypyrrole is used as a platform for immobilizing DNA (1μg) on the gold electrode surface, since it can be more easily deposited from neutral pH aqueous solutions of pyrrolemonomers. The average current peak during the electrodeposition event is 288μA. There is a clear change in the current after hybridization of the complementary oligonucleotide (6.35μA) and for the noncomplementary oligonucleotide (5.77μA). The drop in current after each event was clearly noticeable and it proved to be effective.

  14. Bioinformatic analysis of whole genome sequencing data

    OpenAIRE

    Maqbool, Khurram

    2014-01-01

    Evolution has shaped the life forms for billion of years. Domestication is an accelerated process that can be used as a model for evolutionary changes. The aim of this thesis project has been to carry out extensive bioinformatic analyses of whole genome sequencing data to reveal SNPs, InDels and selective sweeps in the chicken, pig and dog genome. Pig genome sequencing revealed loci under selection for elongation of back and increased number of vertebrae, associated with the NR6A1, PLAG1,...

  15. Top considerations for creating bioinformatics software documentation.

    Science.gov (United States)

    Karimzadeh, Mehran; Hoffman, Michael M

    2017-01-14

    Investing in documenting your bioinformatics software well can increase its impact and save your time. To maximize the effectiveness of your documentation, we suggest following a few guidelines we propose here. We recommend providing multiple avenues for users to use your research software, including a navigable HTML interface with a quick start, useful help messages with detailed explanation and thorough examples for each feature of your software. By following these guidelines, you can assure that your hard work maximally benefits yourself and others. © The Author 2017. Published by Oxford University Press.

  16. Introducing bioinformatics, the biosciences' genomic revolution

    CERN Document Server

    Zanella, Paolo

    1999-01-01

    The general audience for these lectures is mainly physicists, computer scientists, engineers or the general public wanting to know more about what’s going on in the biosciences. What’s bioinformatics and why is all this fuss being made about it ? What’s this revolution triggered by the human genome project ? Are there any results yet ? What are the problems ? What new avenues of research have been opened up ? What about the technology ? These new developments will be compared with what happened at CERN earlier in its evolution, and it is hoped that the similiraties and contrasts will stimulate new curiosity and provoke new thoughts.

  17. Robust Bioinformatics Recognition with VLSI Biochip Microsystem

    Science.gov (United States)

    Lue, Jaw-Chyng L.; Fang, Wai-Chi

    2006-01-01

    A microsystem architecture for real-time, on-site, robust bioinformatic patterns recognition and analysis has been proposed. This system is compatible with on-chip DNA analysis means such as polymerase chain reaction (PCR)amplification. A corresponding novel artificial neural network (ANN) learning algorithm using new sigmoid-logarithmic transfer function based on error backpropagation (EBP) algorithm is invented. Our results show the trained new ANN can recognize low fluorescence patterns better than the conventional sigmoidal ANN does. A differential logarithmic imaging chip is designed for calculating logarithm of relative intensities of fluorescence signals. The single-rail logarithmic circuit and a prototype ANN chip are designed, fabricated and characterized.

  18. Multiobjective optimization in bioinformatics and computational biology.

    Science.gov (United States)

    Handl, Julia; Kell, Douglas B; Knowles, Joshua

    2007-01-01

    This paper reviews the application of multiobjective optimization in the fields of bioinformatics and computational biology. A survey of existing work, organized by application area, forms the main body of the review, following an introduction to the key concepts in multiobjective optimization. An original contribution of the review is the identification of five distinct "contexts," giving rise to multiple objectives: These are used to explain the reasons behind the use of multiobjective optimization in each application area and also to point the way to potential future uses of the technique.

  19. Robust group fused lasso for multisample copy number variation detection under uncertainty.

    Science.gov (United States)

    Sharifi Noghabi, Hossein; Mohammadi, Majid; Tan, Yao-Hua

    2016-12-01

    One of the most important needs in the post-genome era is providing the researchers with reliable and efficient computational tools to extract and analyse this huge amount of biological data, in which DNA copy number variation (CNV) is a vitally important one. Array-based comparative genomic hybridisation (aCGH) is a common approach in order to detect CNVs. Most of methods for this purpose were proposed for one-dimensional profiles. However, slightly this focus has moved from one- to multi-dimensional signals. In addition, since contamination of these profiles with noise is always an issue, it is highly important to have a robust method for analysing multi-sample aCGH profiles. In this study, the authors propose robust group fused lasso which utilises the robust group total variations. Instead of l 2,1 norm, the l 1 - l 2 M-estimator is used which is more robust in dealing with non-Gaussian noise and high corruption. More importantly, Correntropy (Welsch M-estimator) is also applied for fitting error. Extensive experiments indicate that the proposed method outperforms the state-of-the art algorithms and techniques under a wide range of scenarios with diverse noises.

  20. Teaching the ABCs of bioinformatics: a brief introduction to the Applied Bioinformatics Course.

    Science.gov (United States)

    Luo, Jingchu

    2014-11-01

    With the development of the Internet and the growth of online resources, bioinformatics training for wet-lab biologists became necessary as a part of their education. This article describes a one-semester course 'Applied Bioinformatics Course' (ABC, http://abc.cbi.pku.edu.cn/) that the author has been teaching to biological graduate students at the Peking University and the Chinese Academy of Agricultural Sciences for the past 13 years. ABC is a hands-on practical course to teach students to use online bioinformatics resources to solve biological problems related to their ongoing research projects in molecular biology. With a brief introduction to the background of the course, detailed information about the teaching strategies of the course are outlined in the 'How to teach' section. The contents of the course are briefly described in the 'What to teach' section with some real examples. The author wishes to share his teaching experiences and the online teaching materials with colleagues working in bioinformatics education both in local and international universities. © The Author 2013. Published by Oxford University Press.

  1. A Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research

    Science.gov (United States)

    Magana, Alejandra J.; Taleyarkhan, Manaz; Alvarado, Daniela Rivera; Kane, Michael; Springer, John; Clase, Kari

    2014-01-01

    Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the…

  2. Bioinformatics tools for predicting GPCR gene functions.

    Science.gov (United States)

    Suwa, Makiko

    2014-01-01

    The automatic classification of GPCRs by bioinformatics methodology can provide functional information for new GPCRs in the whole 'GPCR proteome' and this information is important for the development of novel drugs. Since GPCR proteome is classified hierarchically, general ways for GPCR function prediction are based on hierarchical classification. Various computational tools have been developed to predict GPCR functions; those tools use not simple sequence searches but more powerful methods, such as alignment-free methods, statistical model methods, and machine learning methods used in protein sequence analysis, based on learning datasets. The first stage of hierarchical function prediction involves the discrimination of GPCRs from non-GPCRs and the second stage involves the classification of the predicted GPCR candidates into family, subfamily, and sub-subfamily levels. Then, further classification is performed according to their protein-protein interaction type: binding G-protein type, oligomerized partner type, etc. Those methods have achieved predictive accuracies of around 90 %. Finally, I described the future subject of research of the bioinformatics technique about functional prediction of GPCR.

  3. Detecting the Subtle Shape Differences in Hemodynamic Responses at the Group Level

    Directory of Open Access Journals (Sweden)

    Gang eChen

    2015-10-01

    Full Text Available The nature of the hemodynamic response (HDR is still not fully understood due to the multifaceted processes involved. Aside from the overall amplitude, the response may vary across cognitive states, tasks, brain regions, and subjects with respect to characteristics such as rise and fall speed, peak duration, undershoot shape, and overall duration. Here we demonstrate that the fixed-shape or adjusted-shape methods may fail to detect some shape subtleties. In contrast, the estimated-shape method (ESM through multiple basis functions can provide the opportunity to identify some subtle shape differences and achieve higher statistical power at both individual and group levels. Previously, some dimension reduction approaches focused on the peak magnitude, or made inferences based on the area under the curve or interaction, which can lead to potential misidentifications. By adopting a generic framework of multivariate modeling (MVM, we showcase a hybrid approach that is validated by simulations and real data. Unlike the few analyses that were limited to main effect, two- or three-way interactions, we extend the approach to an inclusive platform that is more adaptable than the conventional GLM, achieving a practical equipoise among representation, false positive control, statistical power, and modeling flexibility.

  4. Molecular Self-Assembly of Group 11 Pyrazolate Complexes as Phosphorescent Chemosensors for Detection of Benzene

    Science.gov (United States)

    Ghazalli, N. F.; Yuliati, L.; Lintang, H. O.

    2018-01-01

    We highlight the systematic study on vapochromic sensing of aromatic vapors such as benzene using phosphorescent trinuclear pyrazolate complexes (2) with supramolecular assembly of a weak intermolecular metal-metal interaction consisting of 4-(3,5-dimethoxybenzyl)-3,5-dimethyl pyrazole ligand (1) and group 11 metal ions (Cu(I), Ag(I), Au(I)). The resulting chemosensor 2(Cu) revealed positive response to benzene vapors in 5 mins by blue-shifting its emission band in 44 nm (from 616 to 572 nm) and emitted bright orange to green, where this change cannot be recovered even with external stimuli. Comparing to 2(Ag) with longer metal-metal distance (473 nm) with same sensing time and quenching in 37%, 2(Au) gave quenching in 81% from its original intensity at 612 nm with reusability in 82% without external stimuli and emitted less emissive of red-orange from its original color. The shifting phenomenon in 2(Cu) suggests diffusion of benzene vapors to inside molecules for formation of intermolecular interaction with Cu(I)-Cu(I) interaction while quenching phenomenon in 2(Au) suggests diffusion of benzene vapors to between the Au(I)-Au(I) interaction. These results indicate that suitable molecular structure of ligand and metal ion in pyrazolate complex is important for designing chemosensor in the detection of benzene vapors.

  5. DIVERGENOME: a bioinformatics platform to assist population genetics and genetic epidemiology studies.

    Science.gov (United States)

    Magalhães, Wagner C S; Rodrigues, Maíra R; Silva, Donnys; Soares-Souza, Giordano; Iannini, Márcia L; Cerqueira, Gustavo C; Faria-Campos, Alessandra C; Tarazona-Santos, Eduardo

    2012-05-01

    Large-scale genomics initiatives such as the HapMap project and the 1000-genomes rely on powerful bioinformatics support to assist data production and analysis. Contrastingly, few bioinformatics platforms oriented to smaller research groups exist to store, handle, share, and integrate data from different sources, as well as to assist these scientists to perform their analyses efficiently. We developed such a bioinformatics platform, DIVERGENOME, to assist population genetics and genetic epidemiology studies performed by small- to medium-sized research groups. The platform is composed of two integrated components, a relational database (DIVERGENOMEdb), and a set of tools to convert data formats as required by popular software in population genetics and genetic epidemiology (DIVERGENOMEtools). In DIVERGENOMEdb, information on genotypes, polymorphism, laboratory protocols, individuals, populations, and phenotypes is organized in projects. These can be queried according to permissions. Here, we validated DIVERGENOME through a use case regarding the analysis of SLC2A4 genetic diversity in human populations. DIVERGENOME, with its intuitive Web interface and automatic data loading capability, facilitates its use by individuals without bioinformatics background, allowing complex queries to be easily interrogated and straightforward data format conversions (not available in similar platforms). DIVERGENOME is open source, freely available, and can be accessed online (pggenetica.icb.ufmg.br/divergenome) or hosted locally. © 2012 Wiley Periodicals, Inc.

  6. Protein co-evolution: how do we combine bioinformatics and experimental approaches?

    Science.gov (United States)

    Sandler, Inga; Abu-Qarn, Mehtap; Aharoni, Amir

    2013-02-02

    Molecular co-evolution is manifested by compensatory changes in proteins designed to enable adaptation to their natural environment. In recent years, bioinformatics approaches allowed for the detection of co-evolution at the level of the whole protein or of specific residues. Such efforts enabled prediction of protein-protein interactions, functional assignments of proteins and the identification of interacting residues, thereby providing information on protein structure. Still, despite such advances, relatively little is known regarding the functional implications of sequence divergence resulting from protein co-evolution. While bioinformatics approaches usually analyze thousands of proteins to obtain a broad view of protein co-evolution, experimental evaluation of protein co-evolution serves to study only individual proteins. In this review, we describe recent advances in bioinformatics and experimental efforts aimed at examining protein co-evolution. Accordingly, we discuss possible modes of crosstalk between the bioinformatics and experimental approaches to facilitate the identification of co-evolutionary signals in proteins and to understand their implications for the structure and function of proteins.

  7. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    and dhurrin, which have not previously been characterized in blueberries. There are more than 44,500 spider species with distinct habitats and unique characteristics. Spiders are masters of producing silk webs to catch prey and using venom to neutralize. The exploration of the genetics behind these properties...... japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... has just started. We have assembled and annotated the first two spider genomes to facilitate our understanding of spiders at the molecular level. The need for analyzing the large and increasing amount of sequencing data has increased the demand for efficient, user friendly, and broadly applicable...

  8. Bioinformatic and Biometric Methods in Plant Morphology

    Directory of Open Access Journals (Sweden)

    Surangi W. Punyasena

    2014-08-01

    Full Text Available Recent advances in microscopy, imaging, and data analyses have permitted both the greater application of quantitative methods and the collection of large data sets that can be used to investigate plant morphology. This special issue, the first for Applications in Plant Sciences, presents a collection of papers highlighting recent methods in the quantitative study of plant form. These emerging biometric and bioinformatic approaches to plant sciences are critical for better understanding how morphology relates to ecology, physiology, genotype, and evolutionary and phylogenetic history. From microscopic pollen grains and charcoal particles, to macroscopic leaves and whole root systems, the methods presented include automated classification and identification, geometric morphometrics, and skeleton networks, as well as tests of the limits of human assessment. All demonstrate a clear need for these computational and morphometric approaches in order to increase the consistency, objectivity, and throughput of plant morphological studies.

  9. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... biology and genetics studies. We present an improved Lotus genome assembly and annotation, a catalog of natural variation based on re-sequencing of 29 accessions, and describe the involvement of small RNAs in the plant-bacteria symbiosis. Blueberries contain anthocyanins, other pigments and various...... polyphenolic compounds, which have been linked to protection against diabetes, cardiovascular disease and age-related cognitive decline. We present the first genome- guided approach in blueberry to identify genes involved in the synthesis of health-protective compounds. Using RNA-Seq data from five stages...

  10. Combining multiple decisions: applications to bioinformatics

    International Nuclear Information System (INIS)

    Yukinawa, N; Ishii, S; Takenouchi, T; Oba, S

    2008-01-01

    Multi-class classification is one of the fundamental tasks in bioinformatics and typically arises in cancer diagnosis studies by gene expression profiling. This article reviews two recent approaches to multi-class classification by combining multiple binary classifiers, which are formulated based on a unified framework of error-correcting output coding (ECOC). The first approach is to construct a multi-class classifier in which each binary classifier to be aggregated has a weight value to be optimally tuned based on the observed data. In the second approach, misclassification of each binary classifier is formulated as a bit inversion error with a probabilistic model by making an analogy to the context of information transmission theory. Experimental studies using various real-world datasets including cancer classification problems reveal that both of the new methods are superior or comparable to other multi-class classification methods

  11. Bioinformatic Analysis of Strawberry GSTF12 Gene

    Science.gov (United States)

    Wang, Xiran; Jiang, Leiyu; Tang, Haoru

    2018-01-01

    GSTF12 has always been known as a key factor of proanthocyanins accumulate in plant testa. Through bioinformatics analysis of the nucleotide and encoded protein sequence of GSTF12, it is more advantageous to the study of genes related to anthocyanin biosynthesis accumulation pathway. Therefore, we chosen GSTF12 gene of 11 kinds species, downloaded their nucleotide and protein sequence from NCBI as the research object, found strawberry GSTF12 gene via bioinformation analyse, constructed phylogenetic tree. At the same time, we analysed the strawberry GSTF12 gene of physical and chemical properties and its protein structure and so on. The phylogenetic tree showed that Strawberry and petunia were closest relative. By the protein prediction, we found that the protein owed one proper signal peptide without obvious transmembrane regions.

  12. Use of nonstatistical techniques for pattern recognition to detect risk groups among liquidators of the Chernobyl NPP accident aftereffects

    International Nuclear Information System (INIS)

    Blinov, N.N.; Guslistyj, V.P.; Misyurev, A.V.; Novitskaya, N.N.; Snigireva, G.P.

    1993-01-01

    Attempt of using of the nonstatistical techniques for pattern recognition to detect the risk groups among liquidators of the Chernobyl NPP accident aftereffects was described. 14 hematologic, biochemical and biophysical blood serum parameters of the group of liquidators of the Chernobyl NPP accident impact as well as the group of donors free of any radiation dose (controlled group) were taken as the diagnostic parameters. Modification of the nonstatistical techniques for pattern recognition based on the assessment calculations were used. The patients were divided into risk group at the truth ∼ 80%

  13. Rust-Bio: a fast and safe bioinformatics library

    NARCIS (Netherlands)

    J. Köster (Johannes)

    2015-01-01

    textabstractWe present Rust-Bio, the first general purpose bioinformatics library for the innovative Rust programming language. Rust-Bio leverages the unique combination of speed, memory safety and high-level syntax offered by Rust to provide a fast and safe set of bioinformatics algorithms and data

  14. Current status and future perspectives of bioinformatics in Tanzania ...

    African Journals Online (AJOL)

    The main bottleneck in advancing genomics in present times is the lack of expertise in using bioinformatics tools and approaches for data mining in raw DNA sequences generated by modern high throughput technologies such as next generation sequencing. Although bioinformatics has been making major progress and ...

  15. Recent developments in life sciences research: Role of bioinformatics

    African Journals Online (AJOL)

    Life sciences research and development has opened up new challenges and opportunities for bioinformatics. The contribution of bioinformatics advances made possible the mapping of the entire human genome and genomes of many other organisms in just over a decade. These discoveries, along with current efforts to ...

  16. Perspectives on presentation and pedagogy in aid of bioinformatics education.

    Science.gov (United States)

    Buttigieg, Pier Luigi

    2010-11-01

    Using live presentation to communicate the interdisciplinary and abstract content of bioinformatics to its educationally diverse studentship is a sizeable challenge. This review collects a number of perspectives on multimedia presentation, visual communication and pedagogy. The aim is to encourage educators to reflect on the great potential of live presentation in facilitating bioinformatics education.

  17. Concepts Of Bioinformatics And Its Application In Veterinary ...

    African Journals Online (AJOL)

    Bioinformatics has advanced the course of research and future veterinary vaccines development because it has provided new tools for identification of vaccine targets from sequenced biological data of organisms. In Nigeria, there is lack of bioinformatics training in the universities, expect for short training courses in which ...

  18. Assessment of a Bioinformatics across Life Science Curricula Initiative

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.

    2007-01-01

    At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…

  19. Generative Topic Modeling in Image Data Mining and Bioinformatics Studies

    Science.gov (United States)

    Chen, Xin

    2012-01-01

    Probabilistic topic models have been developed for applications in various domains such as text mining, information retrieval and computer vision and bioinformatics domain. In this thesis, we focus on developing novel probabilistic topic models for image mining and bioinformatics studies. Specifically, a probabilistic topic-connection (PTC) model…

  20. Evaluating an Inquiry-Based Bioinformatics Course Using Q Methodology

    Science.gov (United States)

    Ramlo, Susan E.; McConnell, David; Duan, Zhong-Hui; Moore, Francisco B.

    2008-01-01

    Faculty at a Midwestern metropolitan public university recently developed a course on bioinformatics that emphasized collaboration and inquiry. Bioinformatics, essentially the application of computational tools to biological data, is inherently interdisciplinary. Thus part of the challenge of creating this course was serving the needs and…

  1. Is there room for ethics within bioinformatics education?

    Science.gov (United States)

    Taneri, Bahar

    2011-07-01

    When bioinformatics education is considered, several issues are addressed. At the undergraduate level, the main issue revolves around conveying information from two main and different fields: biology and computer science. At the graduate level, the main issue is bridging the gap between biology students and computer science students. However, there is an educational component that is rarely addressed within the context of bioinformatics education: the ethics component. Here, a different perspective is provided on bioinformatics education, and the current status of ethics is analyzed within the existing bioinformatics programs. Analysis of the existing undergraduate and graduate programs, in both Europe and the United States, reveals the minimal attention given to ethics within bioinformatics education. Given that bioinformaticians speedily and effectively shape the biomedical sciences and hence their implications for society, here redesigning of the bioinformatics curricula is suggested in order to integrate the necessary ethics education. Unique ethical problems awaiting bioinformaticians and bioinformatics ethics as a separate field of study are discussed. In addition, a template for an "Ethics in Bioinformatics" course is provided.

  2. Virulence gene pool detected in bovine group C Streptococcus dysgalactiae subsp. dysgalactiae isolates by use of a group A S. pyogenes virulence microarray.

    Science.gov (United States)

    Rato, Márcia G; Nerlich, Andreas; Bergmann, René; Bexiga, Ricardo; Nunes, Sandro F; Vilela, Cristina L; Santos-Sanches, Ilda; Chhatwal, Gursharan S

    2011-07-01

    A custom-designed microarray containing 220 virulence genes of Streptococcus pyogenes (group A Streptococcus [GAS]) was used to test group C Streptococcus dysgalactiae subsp. dysgalactiae (GCS) field strains causing bovine mastitis and group C or group G Streptococcus dysgalactiae subsp. equisimilis (GCS/GGS) isolates from human infections, with the latter being used for comparative purposes, for the presence of virulence genes. All bovine and all human isolates carried a fraction of the 220 genes (23% and 39%, respectively). The virulence genes encoding streptolysin S, glyceraldehyde-3-phosphate dehydrogenase, the plasminogen-binding M-like protein PAM, and the collagen-like protein SclB were detected in the majority of both bovine and human isolates (94 to 100%). Virulence factors, usually carried by human beta-hemolytic streptococcal pathogens, such as streptokinase, laminin-binding protein, and the C5a peptidase precursor, were detected in all human isolates but not in bovine isolates. Additionally, GAS bacteriophage-associated virulence genes encoding superantigens, DNase, and/or streptodornase were detected in bovine isolates (72%) but not in the human isolates. Determinants located in non-bacteriophage-related mobile elements, such as the gene encoding R28, were detected in all bovine and human isolates. Several virulence genes, including genes of bacteriophage origin, were shown to be expressed by reverse transcriptase PCR (RT-PCR). Phylogenetic analysis of superantigen gene sequences revealed a high level (>98%) of identity among genes of bovine GCS, of the horse pathogen Streptococcus equi subsp. equi, and of the human pathogen GAS. Our findings indicate that alpha-hemolytic bovine GCS, an important mastitis pathogen and considered to be a nonhuman pathogen, carries important virulence factors responsible for virulence and pathogenesis in humans.

  3. Virulence Gene Pool Detected in Bovine Group C Streptococcus dysgalactiae subsp. dysgalactiae Isolates by Use of a Group A S. pyogenes Virulence Microarray ▿

    Science.gov (United States)

    Rato, Márcia G.; Nerlich, Andreas; Bergmann, René; Bexiga, Ricardo; Nunes, Sandro F.; Vilela, Cristina L.; Santos-Sanches, Ilda; Chhatwal, Gursharan S.

    2011-01-01

    A custom-designed microarray containing 220 virulence genes of Streptococcus pyogenes (group A Streptococcus [GAS]) was used to test group C Streptococcus dysgalactiae subsp. dysgalactiae (GCS) field strains causing bovine mastitis and group C or group G Streptococcus dysgalactiae subsp. equisimilis (GCS/GGS) isolates from human infections, with the latter being used for comparative purposes, for the presence of virulence genes. All bovine and all human isolates carried a fraction of the 220 genes (23% and 39%, respectively). The virulence genes encoding streptolysin S, glyceraldehyde-3-phosphate dehydrogenase, the plasminogen-binding M-like protein PAM, and the collagen-like protein SclB were detected in the majority of both bovine and human isolates (94 to 100%). Virulence factors, usually carried by human beta-hemolytic streptococcal pathogens, such as streptokinase, laminin-binding protein, and the C5a peptidase precursor, were detected in all human isolates but not in bovine isolates. Additionally, GAS bacteriophage-associated virulence genes encoding superantigens, DNase, and/or streptodornase were detected in bovine isolates (72%) but not in the human isolates. Determinants located in non-bacteriophage-related mobile elements, such as the gene encoding R28, were detected in all bovine and human isolates. Several virulence genes, including genes of bacteriophage origin, were shown to be expressed by reverse transcriptase PCR (RT-PCR). Phylogenetic analysis of superantigen gene sequences revealed a high level (>98%) of identity among genes of bovine GCS, of the horse pathogen Streptococcus equi subsp. equi, and of the human pathogen GAS. Our findings indicate that alpha-hemolytic bovine GCS, an important mastitis pathogen and considered to be a nonhuman pathogen, carries important virulence factors responsible for virulence and pathogenesis in humans. PMID:21525223

  4. Group Testing Based Detection of Web Service DDoS Attackers

    Science.gov (United States)

    Nashat, Dalia; Jiang, Xiaohong; Kameyama, Michitaka

    The Distributed Denial of Service attack (DDoS) is one of the major threats to network security that exhausts network bandwidth and resources. Recently, an efficient approach Live Baiting was proposed for detecting the identities of DDoS attackers in web service using low state overhead without requiring either the models of legitimate requests nor anomalous behavior. However, Live Baiting has two limitations. First, the detection algorithm adopted in Live Baiting starts with a suspects list containing all clients, which leads to a high false positive probability especially for large web service with a huge number of clients. Second, Live Baiting adopts a fixed threshold based on the expected number of requests in each bucket during the detection interval without the consideration of daily and weekly traffic variations. In order to address the above limitations, we first distinguish the clients activities (Active and Non-Active clients during the detection interval) in the detection process and then further propose a new adaptive threshold based on the Change Point Detection method, such that we can improve the false positive probability and avoid the dependence of detection on sites and access patterns. Extensive trace-driven simulation has been conducted on real Web trace to demonstrate the detection efficiency of the proposed scheme in comparison with the Live Baiting detection scheme.

  5. The development and application of bioinformatics core competencies to improve bioinformatics training and education

    Science.gov (United States)

    Brooksbank, Cath; Morgan, Sarah L.; Rosenwald, Anne; Warnow, Tandy; Welch, Lonnie

    2018-01-01

    Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans. PMID:29390004

  6. 4273π: Bioinformatics education on low cost ARM hardware

    Science.gov (United States)

    2013-01-01

    Background Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. Results We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012–2013. Conclusions 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost. PMID:23937194

  7. 4273π: bioinformatics education on low cost ARM hardware.

    Science.gov (United States)

    Barker, Daniel; Ferrier, David Ek; Holland, Peter Wh; Mitchell, John Bo; Plaisier, Heleen; Ritchie, Michael G; Smart, Steven D

    2013-08-12

    Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013. 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

  8. E-MSD: an integrated data resource for bioinformatics.

    Science.gov (United States)

    Velankar, S; McNeil, P; Mittard-Runte, V; Suarez, A; Barrell, D; Apweiler, R; Henrick, K

    2005-01-01

    The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

  9. Assessing an effective undergraduate module teaching applied bioinformatics to biology students.

    Science.gov (United States)

    Madlung, Andreas

    2018-01-01

    Applied bioinformatics skills are becoming ever more indispensable for biologists, yet incorporation of these skills into the undergraduate biology curriculum is lagging behind, in part due to a lack of instructors willing and able to teach basic bioinformatics in classes that don't specifically focus on quantitative skill development, such as statistics or computer sciences. To help undergraduate course instructors who themselves did not learn bioinformatics as part of their own education and are hesitant to plunge into teaching big data analysis, a module was developed that is written in plain-enough language, using publicly available computing tools and data, to allow novice instructors to teach next-generation sequence analysis to upper-level undergraduate students. To determine if the module allowed students to develop a better understanding of and appreciation for applied bioinformatics, various tools were developed and employed to assess the impact of the module. This article describes both the module and its assessment. Students found the activity valuable for their education and, in focus group discussions, emphasized that they saw a need for more and earlier instruction of big data analysis as part of the undergraduate biology curriculum.

  10. Ability of Cone-beam Computed Tomography to Detect Periapical Lesions That Were Not Detected by Periapical Radiography: A Retrospective Assessment According to Tooth Group.

    Science.gov (United States)

    Uraba, Shintaro; Ebihara, Arata; Komatsu, Kei; Ohbayashi, Naoto; Okiji, Takashi

    2016-08-01

    The detection of periapical lesions by periapical radiography (PR) can be hampered by structural noise, the impact of which differs among tooth groups. The aim of this study was to investigate the ability of cone-beam computed tomographic (CBCT) imaging to detect periapical lesions that could not be detected with PR according to tooth group. This study retrospectively evaluated teeth that (1) had previously undergone root canal treatment (178 teeth from 86 patients), (2) had coincidentally been located within the field of view of CBCT scans performed for endodontic reasons, and (3) had also been examined with PR. The teeth of interest for the CBCT examinations were excluded to avoid sampling bias. Two dentists evaluated both the CBCT and PR images for periapical lesions. The McNemar test was used to compare the ability of CBCT imaging and PR to identify periapical lesions (α = 0.05). The overall periapical lesion detection rates of PR and CBCT imaging were 31.5% and 52.2%, respectively (P periapical lesions that were not detected by PR was statistically significant for the maxillary incisors/canines (P periapical lesions that cannot be detected on PR, particularly in the maxillary incisors/canines and molars. Our findings suggest that the influence of structural noise in the maxillary anterior region and maxillary posterior region should not be overlooked during the interpretation of PR images. Copyright © 2016. Published by Elsevier Inc.

  11. [Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella].

    Science.gov (United States)

    Wang, Pengfei; Wang, Yingfang; Duan, Guangcai; Xue, Zerun; Wang, Linlin; Guo, Xiangjiao; Yang, Haiyan; Xi, Yuanlin

    2015-04-01

    This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.

  12. Detecting concealed information from groups using a dynamic questioning approach: simultaneous skin conductance measurement and immediate feedback.

    Science.gov (United States)

    Meijer, Ewout H; Bente, Gary; Ben-Shakhar, Gershon; Schumacher, Andreas

    2013-01-01

    Lie detection procedures typically aim at determining the guilt or innocence of a single suspect. The Concealed Information Test (CIT), for example, has been shown to be highly successful in detecting the presence or absence of crime-related information in a suspect's memory. Many of today's security threats, however, do not come from individuals, but from organized groups such as criminal organizations or terrorist networks. In this study, we tested whether a plan of an upcoming mock terrorist attack could be extracted from a group of suspects using a dynamic questioning approach. One-hundred participants were tested in 20 groups of 5. Each group was asked to plan a mock terrorist attack based on a list of potential countries, cities, and streets. Next, three questions referring to the country, city, and street were presented, each with five options. Skin conductance in all five members of the group was measured simultaneously during this presentation. The dynamic questioning approach entailed direct analysis of the data, and if the average skin conductance of the group to a certain option exceeded a threshold, this option was followed up, e.g., if the reaction to the option "Italy" exceeded the threshold, this was followed up by presenting five cities in Italy. Results showed that in 19 of the 20 groups the country was correctly detected using this procedure. In 13 of these remaining 19 groups the city was correctly detected. In 7 of these 13, the street was also correctly detected. The question about the country resulted in no false positives (out of 20), the question about the city resulted in two false positives (out of 19), while the question about the streets resulted in two false positives (out of 13). Furthermore, the two false positives at the city level also yielded a false positive at the street level. Even though effect sizes were only moderate, these results indicate that our dynamic questioning approach can help to unveil plans about a mock terrorist

  13. A Generalized Logistic Regression Procedure to Detect Differential Item Functioning among Multiple Groups

    Science.gov (United States)

    Magis, David; Raiche, Gilles; Beland, Sebastien; Gerard, Paul

    2011-01-01

    We present an extension of the logistic regression procedure to identify dichotomous differential item functioning (DIF) in the presence of more than two groups of respondents. Starting from the usual framework of a single focal group, we propose a general approach to estimate the item response functions in each group and to test for the presence…

  14. Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2016-06-01

    Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression.

  15. Bioinformatic landscapes for plant transcription factor system research.

    Science.gov (United States)

    Wang, Yijun; Lu, Wenjie; Deng, Dexiang

    2016-02-01

    Diverse bioinformatic resources have been developed for plant transcription factor (TF) research. This review presents the bioinformatic resources and methodologies for the elucidation of plant TF-mediated biological events. Such information is helpful to dissect the transcriptional regulatory systems in the three reference plants Arabidopsis , rice, and maize and translation to other plants. Transcription factors (TFs) orchestrate diverse biological programs by the modulation of spatiotemporal patterns of gene expression via binding cis-regulatory elements. Advanced sequencing platforms accompanied by emerging bioinformatic tools revolutionize the scope and extent of TF research. The system-level integration of bioinformatic resources is beneficial to the decoding of TF-involved networks. Herein, we first briefly introduce general and specialized databases for TF research in three reference plants Arabidopsis, rice, and maize. Then, as proof of concept, we identified and characterized heat shock transcription factor (HSF) members through the TF databases. Finally, we present how the integration of bioinformatic resources at -omics layers can aid the dissection of TF-mediated pathways. We also suggest ways forward to improve the bioinformatic resources of plant TFs. Leveraging these bioinformatic resources and methodologies opens new avenues for the elucidation of transcriptional regulatory systems in the three model systems and translation to other plants.

  16. Bioinformatics approaches for identifying new therapeutic bioactive peptides in food

    Directory of Open Access Journals (Sweden)

    Nora Khaldi

    2012-10-01

    Full Text Available ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational biology, and efficient genome mining, is appearing as the long awaited solution to this problem. By quickly mining food genomes for characteristics of certain food therapeutic ingredients, researchers can potentially find new ones in a matter of a few weeks. Yet, surprisingly, very little success has been achieved so far using bioinformatics in mining for food bioactives.The absence of food specific bioinformatic mining tools, the slow integration of both experimental mining and bioinformatics, and the important difference between different experimental platforms are some of the reasons for the slow progress of bioinformatics in the field of functional food and more specifically in bioactive peptide discovery.In this paper I discuss some methods that could be easily translated, using a rational peptide bioinformatics design, to food bioactive peptide mining. I highlight the need for an integrated food peptide database. I also discuss how to better integrate experimental work with bioinformatics in order to improve the mining of food for bioactive peptides, therefore achieving a higher success rates.

  17. The eBioKit, a stand-alone educational platform for bioinformatics.

    Science.gov (United States)

    Hernández-de-Diego, Rafael; de Villiers, Etienne P; Klingström, Tomas; Gourlé, Hadrien; Conesa, Ana; Bongcam-Rudloff, Erik

    2017-09-01

    Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative.

  18. Bioinformatics Tools for Extracellular Vesicles Research.

    Science.gov (United States)

    Keerthikumar, Shivakumar; Gangoda, Lahiru; Gho, Yong Song; Mathivanan, Suresh

    2017-01-01

    Extracellular vesicles (EVs) are a class of membranous vesicles that are released by multiple cell types into the extracellular environment. This unique class of extracellular organelles which play pivotal role in intercellular communication are conserved across prokaryotes and eukaryotes. Depending upon the cell origin and the functional state, the molecular cargo including proteins, lipids, and RNA within the EVs are modulated. Owing to this, EVs are considered as a subrepertoire of the host cell and are rich reservoirs of disease biomarkers. In addition, the availability of EVs in multiple bodily fluids including blood has created significant interest in biomarker and signaling research. With the advancement in high-throughput techniques, multiple EV studies have embarked on profiling the molecular cargo. To benefit the scientific community, existing free Web-based resources including ExoCarta, EVpedia, and Vesiclepedia catalog multiple datasets. These resources aid in elucidating molecular mechanism and pathophysiology underlying different disease conditions from which EVs are isolated. Here, the existing bioinformatics tools to perform integrated analysis to identify key functional components in the EV datasets are discussed.

  19. Bioinformatics in cancer therapy and drug design

    International Nuclear Information System (INIS)

    Horbach, D.Y.; Usanov, S.A.

    2005-01-01

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  20. Evolution of web services in bioinformatics.

    Science.gov (United States)

    Neerincx, Pieter B T; Leunissen, Jack A M

    2005-06-01

    Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to be complex and in order to understand them, it is often necessary to link many data sets and use more than one tool. Therefore, bioinformaticians have experimented with several strategies to try to integrate data sets and tools. Owing to the lack of standards for data sets and the interfaces of the tools this is not a trivial task. Over the past few years building services with web-based interfaces has become a popular way of sharing the data and tools that have resulted from many bioinformatics projects. This paper discusses the interoperability problem and how web services are being used to try to solve it, resulting in the evolution of tools with web interfaces from HTML/web form-based tools not suited for automatic workflow generation to a dynamic network of XML-based web services that can easily be used to create pipelines.

  1. An Automatic Detection System of Lung Nodule Based on Multi-Group Patch-Based Deep Learning Network.

    Science.gov (United States)

    Jiang, Hongyang; Ma, He; Qian, Wei; Gao, Mengdi; Li, Yan

    2017-07-14

    High-efficiency lung nodule detection dramatically contributes to the risk assessment of lung cancer. It is a significant and challenging task to quickly locate the exact positions of lung nodules. Extensive work has been done by researchers around this domain for approximately two decades. However, previous computer aided detection (CADe) schemes are mostly intricate and time-consuming since they may require more image processing modules, such as the computed tomography (CT) image transformation, the lung nodule segmentation and the feature extraction, to construct a whole CADe system. It is difficult for those schemes to process and analyze enormous data when the medical images continue to increase. Besides, some state of the art deep learning schemes may be strict in the standard of database. This study proposes an effective lung nodule detection scheme based on multi-group patches cut out from the lung images, which are enhanced by the Frangi filter. Through combining two groups of images, a four-channel convolution neural networks (CNN) model is designed to learn the knowledge of radiologists for detecting nodules of four levels. This CADe scheme can acquire the sensitivity of 80.06% with 4.7 false positives per scan and the sensitivity of 94% with 15.1 false positives per scan. The results demonstrate that the multi-group patch-based learning system is efficient to improve the performance of lung nodule detection and greatly reduce the false positives under a huge amount of image data.

  2. An Overview of Bioinformatics Tools and Resources in Allergy.

    Science.gov (United States)

    Fu, Zhiyan; Lin, Jing

    2017-01-01

    The rapidly increasing number of characterized allergens has created huge demands for advanced information storage, retrieval, and analysis. Bioinformatics and machine learning approaches provide useful tools for the study of allergens and epitopes prediction, which greatly complement traditional laboratory techniques. The specific applications mainly include identification of B- and T-cell epitopes, and assessment of allergenicity and cross-reactivity. In order to facilitate the work of clinical and basic researchers who are not familiar with bioinformatics, we review in this chapter the most important databases, bioinformatic tools, and methods with relevance to the study of allergens.

  3. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    NARCIS (Netherlands)

    Quevedo, Beatrice; Giertsen, Elin; Zijnge, Vincent; Luethi-Schaller, Helga; Guggenheim, Bernhard; Thurnheer, Thomas; Gmuer, Rudolf

    2011-01-01

    Background: The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to

  4. Immunohistochemical detection of fibronectin in human thymus-comparison between groups of different ages

    International Nuclear Information System (INIS)

    Ali, S.; Minhas, L.A.; Arshad, M.; Hameed, W.

    2009-01-01

    To compare distribution of fibronectin content in various parts of human thymus between groups of different ages using immunohistochemistry. Comparative study. Forty specimens from tissue sections of human thymus were separated into two groups with 20 specimens in each group: Group A consisted of specimens from the patients of 1-25 years and Group B of specimens from patients beyond 40 years. These specimens were fixed in 10% formalin solution and processed for paraffin embedding. Five micron thick sections were made. Immunohistochemical staining was utilized to localize fibronectin in various regions of human thymus (capsule, connective tissue between lobules, cortex, medulla and areas around blood vessels). Statistically highly significant difference was found between two groups with a marked increase in the distribution of fibronectin content of the thymic capsule, the connective tissue between the lobules, areas around the blood vessels, and the medulla and cortex of the thymus in Group B compared to Group A. The fibronectin content in human thymus in its various regions shows a marked increase in aged people as compared to younger ones. (author)

  5. Identification of differential item functioning in multiple-group settings: a multivariate outlier detection approach

    NARCIS (Netherlands)

    Magis, D.; de Boeck, P.

    2011-01-01

    We focus on the identification of differential item functioning (DIF) when more than two groups of examinees are considered. We propose to consider items as elements of a multivariate space, where DIF items are outlying elements. Following this approach, the situation of multiple groups is a quite

  6. Role of remote sensing, geographical information system (GIS) and bioinformatics in kala-azar epidemiology.

    Science.gov (United States)

    Bhunia, Gouri Sankar; Dikhit, Manas Ranjan; Kesari, Shreekant; Sahoo, Ganesh Chandra; Das, Pradeep

    2011-11-01

    Visceral leishmaniasis or kala-azar is a potent parasitic infection causing death of thousands of people each year. Medicinal compounds currently available for the treatment of kala-azar have serious side effects and decreased efficacy owing to the emergence of resistant strains. The type of immune reaction is also to be considered in patients infected with Leishmania donovani (L. donovani). For complete eradication of this disease, a high level modern research is currently being applied both at the molecular level as well as at the field level. The computational approaches like remote sensing, geographical information system (GIS) and bioinformatics are the key resources for the detection and distribution of vectors, patterns, ecological and environmental factors and genomic and proteomic analysis. Novel approaches like GIS and bioinformatics have been more appropriately utilized in determining the cause of visearal leishmaniasis and in designing strategies for preventing the disease from spreading from one region to another.

  7. Rope-based oral fluid sampling for early detection of classical swine fever in domestic pigs at group level.

    Science.gov (United States)

    Dietze, Klaas; Tucakov, Anna; Engel, Tatjana; Wirtz, Sabine; Depner, Klaus; Globig, Anja; Kammerer, Robert; Mouchantat, Susan

    2017-01-05

    Non-invasive sampling techniques based on the analysis of oral fluid specimen have gained substantial importance in the field of swine herd management. Methodological advances have a focus on endemic viral diseases in commercial pig production. More recently, these approaches have been adapted to non-invasive sampling of wild boar for transboundary animal disease detection for which these effective population level sampling methods have not been available. In this study, a rope-in-a-bait based oral fluid sampling technique was tested to detect classical swine fever virus nucleic acid shedding from experimentally infected domestic pigs. Separated in two groups treated identically, the course of the infection was slightly differing in terms of onset of the clinical signs and levels of viral ribonucleic acid detection in the blood and oral fluid. The technique was capable of detecting classical swine fever virus nucleic acid as of day 7 post infection coinciding with the first detection in conventional oropharyngeal swab samples from some individual animals. Except for day 7 post infection in the "slower onset group", the chances of classical swine fever virus nucleic acid detection in ropes were identical or higher as compared to the individual sampling. With the provided evidence, non-invasive oral fluid sampling at group level can be considered as additional cost-effective detection tool in classical swine fever prevention and control strategies. The proposed methodology is of particular use in production systems with reduced access to veterinary services such as backyard or scavenging pig production where it can be integrated in feeding or baiting practices.

  8. Multimodal Detection of Engagement in Groups of Children Using Rank Learning

    NARCIS (Netherlands)

    Kim, Jaebok; Truong, Khiet Phuong; Charisi, Vasiliki; Zaga, Cristina; Evers, Vanessa; Chetouani, Mohamed

    2016-01-01

    In collaborative play, children exhibit different levels of engagement. Some children are engaged with other children while some play alone. In this study, we investigated multimodal detection of individual levels of engagement using a ranking method and non-verbal features: turn-taking and body

  9. Molecular characterization of a human group C rotavirus detected first in Turkey.

    Science.gov (United States)

    Mitui, Marcelo Takahiro; Bozdayi, Gulendam; Dalgic, Buket; Bostanci, Ilknur; Nishizono, Akira; Ahmed, Kamruddin

    2009-10-01

    The present study was done to find out the prevalence of group B and C rotavirus infections in children with diarrhea presented at two major hospitals in Ankara, Turkey. Group B rotavirus was not found in any samples. One of 122 samples was positive for group C rotavirus. Phylogenetic analysis of genes for nonstructural protein NSP4, and structural proteins VP4, VP6, and VP7 confirmed the human origin of this strain. Similar to other human group C rotaviruses, one N-glycosylation site was predicted at amino acid residue 67 on the VP7 of strain GUP188. The genes of strain GUP188 were closely related to those of human group C rotavirus strain from the UK (Bristol) for NSP4, China (208 and Wu82) for VP4 and VP6, and from Colombia (Javeriana) for VP7, indicating that the Turkish group C rotavirus was unique and can serve as an additional reference strain for the molecular epidemiology of group C rotaviruses.

  10. A web services choreography scenario for interoperating bioinformatics applications.

    Science.gov (United States)

    de Knikker, Remko; Guo, Youjun; Li, Jin-Long; Kwan, Albert K H; Yip, Kevin Y; Cheung, David W; Cheung, Kei-Hoi

    2004-03-10

    Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD) that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH) category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates with these web services using a web

  11. A web services choreography scenario for interoperating bioinformatics applications

    Directory of Open Access Journals (Sweden)

    Cheung David W

    2004-03-01

    Full Text Available Abstract Background Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1 the platforms on which the applications run are heterogeneous, 2 their web interface is not machine-friendly, 3 they use a non-standard format for data input and output, 4 they do not exploit standards to define application interface and message exchange, and 5 existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. Results To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates

  12. A web services choreography scenario for interoperating bioinformatics applications

    Science.gov (United States)

    de Knikker, Remko; Guo, Youjun; Li, Jin-long; Kwan, Albert KH; Yip, Kevin Y; Cheung, David W; Cheung, Kei-Hoi

    2004-01-01

    Background Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. Results To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD) that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH) category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates with these web

  13. Bioinformatic approaches reveal metagenomic characterization of soil microbial community.

    Directory of Open Access Journals (Sweden)

    Zhuofei Xu

    Full Text Available As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.

  14. Electrochemiluminescent Detection of Hydrogen Peroxide via Some Luminol Imide Derivatives with Different Substituent Groups

    Directory of Open Access Journals (Sweden)

    Tifeng Jiao

    2013-01-01

    Full Text Available Some luminol imide derivatives with different substituent groups have been designed and synthesized. Their electrochemiluminescence properties have been measured with a view to developing new biosensors. The ECL response to hydrogen peroxide in the presence of these luminescent derivatives has been investigated taking into account crucial factors such as the applied potential value, injection volume of hydrogen peroxide, and the substituent groups in molecular structures. The experimental data demonstrated that the substituent groups in these imide derivatives can have a profound effect upon the ECL abilities of these studied compounds. The present research work affords new and useful exploration for the design and development of new soft matter for ECL biosensors with luminol functional groups.

  15. The potential of translational bioinformatics approaches for pharmacology research.

    Science.gov (United States)

    Li, Lang

    2015-10-01

    The field of bioinformatics has allowed the interpretation of massive amounts of biological data, ushering in the era of 'omics' to biomedical research. Its potential impact on pharmacology research is enormous and it has shown some emerging successes. A full realization of this potential, however, requires standardized data annotation for large health record databases and molecular data resources. Improved standardization will further stimulate the development of system pharmacology models, using translational bioinformatics methods. This new translational bioinformatics paradigm is highly complementary to current pharmacological research fields, such as personalized medicine, pharmacoepidemiology and drug discovery. In this review, I illustrate the application of transformational bioinformatics to research in numerous pharmacology subdisciplines. © 2015 The British Pharmacological Society.

  16. Development of a cloud-based Bioinformatics Training Platform

    Science.gov (United States)

    Revote, Jerico; Watson-Haigh, Nathan S.; Quenette, Steve; Bethwaite, Blair; McGrath, Annette

    2017-01-01

    Abstract The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. PMID:27084333

  17. In silico cloning and bioinformatic analysis of PEPCK gene in ...

    African Journals Online (AJOL)

    Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. According to the relative conservation of homologous gene, a bioinformatics strategy was applied to clone Fusarium ...

  18. Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

    Science.gov (United States)

    Diaz Acosta, B.

    2011-01-01

    The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

  19. Bioinformatics Education in Pathology Training: Current Scope and Future Direction

    Directory of Open Access Journals (Sweden)

    Michael R Clay

    2017-04-01

    Full Text Available Training anatomic and clinical pathology residents in the principles of bioinformatics is a challenging endeavor. Most residents receive little to no formal exposure to bioinformatics during medical education, and most of the pathology training is spent interpreting histopathology slides using light microscopy or focused on laboratory regulation, management, and interpretation of discrete laboratory data. At a minimum, residents should be familiar with data structure, data pipelines, data manipulation, and data regulations within clinical laboratories. Fellowship-level training should incorporate advanced principles unique to each subspecialty. Barriers to bioinformatics education include the clinical apprenticeship training model, ill-defined educational milestones, inadequate faculty expertise, and limited exposure during medical training. Online educational resources, case-based learning, and incorporation into molecular genomics education could serve as effective educational strategies. Overall, pathology bioinformatics training can be incorporated into pathology resident curricula, provided there is motivation to incorporate, institutional support, educational resources, and adequate faculty expertise.

  20. Bioinformatics Analyst | Center for Cancer Research

    Science.gov (United States)

    BASIC QUALIFICATIONS To be considered for this position, you must minimally meet the knowledge, skills, and abilities listed below: Bachelor’s degree in life science/bioinformatics/math/physics/computer related field from an accredited college or university according to the Council for Higher Education Accreditation (CHEA). (Additional qualifying experience may be substituted for the required education). Foreign degrees must be evaluated for U.S. equivalency. In addition to the educational requirements, a minimum of five (5) years of progressively responsible relevant experience. Must be able to obtain and maintain a security clearance. PREFERRED QUALIFICATIONS Candidates with these desired skills will be given preferential consideration: A Masters’ or PhD degree in any quantitative science is preferred. Commitment to solving biological problems and communicating these solutions. Ability to multi-task across projects. Experience in submitting data sets to public repositories. Management of large genomic data sets including integration with data available from public sources. Prior customer-facing role. Record of scientific achievements including journal publications and conference presentations. Expected Competencies: Deep understanding of and experience in processing high throughput biomedical data: data cleaning, normalization, analysis, interpretation and visualization. Ability to understand and analyze data from complex experimental designs. Proficiency in at least two of the following programming languages: Perl, Python, R, Java and C/C++. Experience in at least two of the following areas: metagenomics, ChIPSeq, RNASeq, ExomeSeq, DHS-Seq, microarray analysis. Familiarity with public databases: NCBI, Ensembl, TCGA, cBioPortal, Broad FireHose. Knowledge of working in a cluster environment.

  1. Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease

    International Nuclear Information System (INIS)

    Erles, Kerstin; Toomey, Crista; Brooks, Harriet W.; Brownlie, Joe

    2003-01-01

    An investigation into the causes of canine infectious respiratory disease was carried out in a large rehoming kennel. Tissue samples taken from the respiratory tract of diseased dogs were tested for the presence of coronaviruses using RT-PCR with conserved primers for the polymerase gene. Sequence analysis of four positive samples showed the presence of a coronavirus with high similarity to both bovine and human coronavirus (strain OC43) in their polymerase and spike genes, whereas there was a low similarity to comparable genes in the enteric canine coronavirus. This canine respiratory coronavirus (CRCV) was detected by RT-PCR in 32/119 tracheal and 20/119 lung samples, with the highest prevalence being detected in dogs with mild clinical symptoms. Serological analysis showed that the presence of antibodies against CRCV on the day of entry into the kennel decreased the risk of developing respiratory disease

  2. Line grouping using perceptual saliency and structure prediction for car detection in traffic scenes

    Science.gov (United States)

    Denasi, Sandra; Quaglia, Giorgio

    1993-08-01

    Autonomous and guide assisted vehicles make a heavy use of computer vision techniques to perceive the environment where they move. In this context, the European PROMETHEUS program is carrying on activities in order to develop autonomous vehicle monitoring that assists people to achieve safer driving. Car detection is one of the topics that are faced by the program. Our contribution proposes the development of this task in two stages: the localization of areas of interest and the formulation of object hypotheses. In particular, the present paper proposes a new approach that builds structural descriptions of objects from edge segmentations by using geometrical organization. This approach has been applied to the detection of cars in traffic scenes. We have analyzed images taken from a moving vehicle in order to formulate obstacle hypotheses: preliminary results confirm the efficiency of the method.

  3. BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.

    Science.gov (United States)

    Velloso, Henrique; Vialle, Ricardo A; Ortega, J Miguel

    2015-06-02

    Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal. Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients. Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

  4. Detection and quantification of viable Bacillus cereus group species in milk by propidium monoazide quantitative real-time PCR.

    Science.gov (United States)

    Cattani, Fernanda; Barth, Valdir C; Nasário, Jéssica S R; Ferreira, Carlos A S; Oliveira, Sílvia D

    2016-04-01

    The Bacillus cereus group includes important spore-forming bacteria that present spoilage capability and may cause foodborne diseases. These microorganisms are traditionally evaluated in food using culturing methods, which can be laborious and time-consuming, and may also fail to detect bacteria in a viable but nonculturable state. The purpose of this study was to develop a quantitative real-time PCR (qPCR) combined with a propidium monoazide (PMA) treatment to analyze the contamination of UHT milk by B. cereus group species viable cells. Thirty micrograms per milliliter of PMA was shown to be the most effective concentration for reducing the PCR amplification of extracellular DNA and DNA from dead cells. The quantification limit of the PMA-qPCR assay was 7.5 × 10(2) cfu/mL of milk. One hundred thirty-five UHT milk samples were analyzed to evaluate the association of PMA to qPCR to selectively detect viable cells. The PMA-qPCR was able to detect B. cereus group species in 44 samples (32.6%), whereas qPCR without PMA detected 78 positive samples (57.8%). Therefore, the PMA probably inhibited the amplification of DNA from cells that were killed during UHT processing, which avoided an overestimation of bacterial cells when using qPCR and, thus, did not overvalue potential health risks. A culture-based method was also used to detect and quantify B. cereus sensu stricto in the same samples and showed positive results in 15 (11.1%) samples. The culture method and PMA-qPCR allowed the detection of B. cereus sensu stricto in quantities compatible with the infective dose required to cause foodborne disease in 3 samples, indicating that, depending on the storage conditions, even after UHT treatment, infective doses may be reached in ready-to-consume products. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  5. Bioconductor: open software development for computational biology and bioinformatics

    DEFF Research Database (Denmark)

    Gentleman, R.C.; Carey, V.J.; Bates, D.M.

    2004-01-01

    into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.......The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry...

  6. Use of BEXA Family Algorithms in Bioinformatics Data Classification

    OpenAIRE

    Gasparoviča-Asīte, M; Aleksejeva, L; Gersons, V

    2012-01-01

    This article studies the possibilities of BEXA family classification algorithms – BEXA, FuzzyBexa and FuzzyBexa II in data, especially bioinformatics data, classification. Three different types of data sets were used in the study – data sets often used in the literature (like Iris data set), UCI data repository real life data sets (like breast cancer data set) and real bioinformatics data sets that have the specific character – a large number of attributes (several thousands) and a small numb...

  7. Detecting concealed information from groups using a dynamic questioning approach: simultaneous skin conductance measurement and immediate feedback

    Directory of Open Access Journals (Sweden)

    Ewout H Meijer

    2013-02-01

    Full Text Available Lie detection procedures typically aim at determining the guilt or innocence of a single suspect. The Concealed Information Test (CIT, for example, has been shown to be highly successful in detecting the presence or absence of crime-related information in a suspect’s memory. Many of today’s security threats, however, do not come from individuals, but from organized groups such as criminal organizations or terrorist networks. In this study, we tested whether a plan of an upcoming mock terrorist attack could be extracted from a group of suspects using a dynamic questioning approach. One-hundred participants were tested in 20 groups of 5. Each group was asked to plan a mock terrorist attack based on a list of potential countries, cities and streets. Next, three questions referring to the country, city, and street were presented, each with 5 options. Skin conductance in all 5 members of the group was measured simultaneously during this presentation. The dynamic questioning approach entailed direct analysis of the data, and if the average skin conductance of the group to a certain option exceeded a threshold, this option was followed up. E.g., if the reaction to the option ‘Italy’ exceeded the threshold, this was followed up by presenting 5 cities in Italy. Results showed that in 19 of the 20 groups the country was correctly detected using this procedure. In 13 of these remaining 19 groups the city was correctly detected. In 7 of these 13, the street was also correctly detected. The question about the country resulted in no false positives (out of 20, the question about the city resulted in 2 false positives (out of 19, while the question about the streets resulted in 2 false positives (out of 13. Furthermore, the 2 false positives at the city level also yielded a false positive at the street level. Taken together these results indicate our dynamic questioning approach can help to unveil plans about a mock terrorist attack.

  8. Detection of explosives (in particular landmines) by low-cost methods. Final report of an advisory group meeting

    International Nuclear Information System (INIS)

    1998-01-01

    The purpose of this Advisory Group Meeting was to put together experts from several areas of explosives (landmines) detection, both nuclear and non-nuclear, to generate ideas which might lead to development of a low-cost method for detection of explosives (in particular landmines), or to a modification of existing methods. The discussions included nuclear, acoustic, radar, infrared, x-ray, and nuclear quadrupole resonance methods for localizing and characterizing landmines. Many technologies are still under laboratory development. This document includes 8 contributed papers, each of them was indexed and abstracted

  9. Assessment of Data Reliability of Wireless Sensor Network for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Ting Dong

    2017-09-01

    Full Text Available As a focal point of biotechnology, bioinformatics integrates knowledge from biology, mathematics, physics, chemistry, computer science and information science. It generally deals with genome informatics, protein structure and drug design. However, the data or information thus acquired from the main areas of bioinformatics may not be effective. Some researchers combined bioinformatics with wireless sensor network (WSN into biosensor and other tools, and applied them to such areas as fermentation, environmental monitoring, food engineering, clinical medicine and military. In the combination, the WSN is used to collect data and information. The reliability of the WSN in bioinformatics is the prerequisite to effective utilization of information. It is greatly influenced by factors like quality, benefits, service, timeliness and stability, some of them are qualitative and some are quantitative. Hence, it is necessary to develop a method that can handle both qualitative and quantitative assessment of information. A viable option is the fuzzy linguistic method, especially 2-tuple linguistic model, which has been extensively used to cope with such issues. As a result, this paper introduces 2-tuple linguistic representation to assist experts in giving their opinions on different WSNs in bioinformatics that involve multiple factors. Moreover, the author proposes a novel way to determine attribute weights and uses the method to weigh the relative importance of different influencing factors which can be considered as attributes in the assessment of the WSN in bioinformatics. Finally, an illustrative example is given to provide a reasonable solution for the assessment.

  10. Detection of Alzheimer's disease using group lasso SVM-based region selection

    Science.gov (United States)

    Sun, Zhuo; Fan, Yong; Lelieveldt, Boudewijn P. F.; van de Giessen, Martijn

    2015-03-01

    Alzheimer's disease (AD) is one of the most frequent forms of dementia and an increasing challenging public health problem. In the last two decades, structural magnetic resonance imaging (MRI) has shown potential in distinguishing patients with Alzheimer's disease and elderly controls (CN). To obtain AD-specific biomarkers, previous research used either statistical testing to find statistically significant different regions between the two clinical groups, or l1 sparse learning to select isolated features in the image domain. In this paper, we propose a new framework that uses structural MRI to simultaneously distinguish the two clinical groups and find the bio-markers of AD, using a group lasso support vector machine (SVM). The group lasso term (mixed l1- l2 norm) introduces anatomical information from the image domain into the feature domain, such that the resulting set of selected voxels are more meaningful than the l1 sparse SVM. Because of large inter-structure size variation, we introduce a group specific normalization factor to deal with the structure size bias. Experiments have been performed on a well-designed AD vs. CN dataset1 to validate our method. Comparing to the l1 sparse SVM approach, our method achieved better classification performance and a more meaningful biomarker selection. When we vary the training set, the selected regions by our method were more stable than the l1 sparse SVM. Classification experiments showed that our group normalization lead to higher classification accuracy with fewer selected regions than the non-normalized method. Comparing to the state-of-art AD vs. CN classification methods, our approach not only obtains a high accuracy with the same dataset, but more importantly, we simultaneously find the brain anatomies that are closely related to the disease.

  11. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    Science.gov (United States)

    2011-01-01

    Background The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotrophia/Granulicatella. Results As lactobacilli are known for notorious resistance to probe penetration, probe-specific assay protocols were experimentally developed to provide maximum cell wall permeability, probe accessibility, hybridization stringency, and fluorescence intensity. The new assays were then applied in a pilot study to three biofilm samples harvested from variably demineralized bovine enamel discs that had been carried in situ for 10 days by different volunteers. Best probe penetration and fluorescent labeling of reference strains were obtained after combined lysozyme and achromopeptidase treatment followed by exposure to lipase. Hybridization stringency had to be established strictly for each probe. Thereafter all probes showed the expected specificity with reference strains and labeled the anticipated morphotypes in dental plaques. Applied to in situ grown biofilms the set of probes detected only Lactobacillus fermentum and bacteria of the Lactobacillus casei group. The most cariogenic biofilm contained two orders of magnitude higher L. fermentum cell numbers than the other biofilms. Abiotrophia/Granulicatella and streptococci from the mitis group were found in all samples at high levels, whereas Streptococcus mutans was detected in only one sample in very low numbers. Conclusions Application of these new group- and species-specific FISH probes to oral biofilm-forming lactic acid bacteria will allow a clearer understanding of the supragingival biome, its spatial architecture and of structure-function relationships implicated during plaque homeostasis and caries development. The probes should prove of value far beyond the field of oral microbiology, as many of

  12. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    Directory of Open Access Journals (Sweden)

    Thurnheer Thomas

    2011-01-01

    Full Text Available Abstract Background The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotrophia/Granulicatella. Results As lactobacilli are known for notorious resistance to probe penetration, probe-specific assay protocols were experimentally developed to provide maximum cell wall permeability, probe accessibility, hybridization stringency, and fluorescence intensity. The new assays were then applied in a pilot study to three biofilm samples harvested from variably demineralized bovine enamel discs that had been carried in situ for 10 days by different volunteers. Best probe penetration and fluorescent labeling of reference strains were obtained after combined lysozyme and achromopeptidase treatment followed by exposure to lipase. Hybridization stringency had to be established strictly for each probe. Thereafter all probes showed the expected specificity with reference strains and labeled the anticipated morphotypes in dental plaques. Applied to in situ grown biofilms the set of probes detected only Lactobacillus fermentum and bacteria of the Lactobacillus casei group. The most cariogenic biofilm contained two orders of magnitude higher L. fermentum cell numbers than the other biofilms. Abiotrophia/Granulicatella and streptococci from the mitis group were found in all samples at high levels, whereas Streptococcus mutans was detected in only one sample in very low numbers. Conclusions Application of these new group- and species-specific FISH probes to oral biofilm-forming lactic acid bacteria will allow a clearer understanding of the supragingival biome, its spatial architecture and of structure-function relationships implicated during plaque homeostasis and caries development. The probes should prove of value far beyond the field of

  13. Reduction of snapshots for MIMO radar detection by block/group orthogonal matching pursuit

    KAUST Repository

    Ali, Hussain El Hosiny

    2014-10-01

    Multiple-input multiple-output (MIMO) radar works on the principle of transmission of independent waveforms at each element of its antenna array and is widely used for surveillance purposes. In this work, we investigate MIMO radar target localization problem with compressive sensing. Specifically, we try to solve the problem of estimation of target location in MIMO radar by group and block sparsity algorithms. It will lead us to a reduced number of snapshots required and also we can achieve better radar resolution. We will use group orthogonal matching pursuit (GOMP) and block orthogonal matching pursuit (BOMP) for our problem. © 2014 IEEE.

  14. Rhesus monkeys (Macaca mulatta) detect rhythmic groups in music, but not the beat

    NARCIS (Netherlands)

    Honing, H.; Merchant, H.; Háden, G.P.; Prado, L.; Bartolo, R.

    2012-01-01

    It was recently shown that rhythmic entrainment, long considered a human-specific mechanism, can be demonstrated in a selected group of bird species, and, somewhat surprisingly, not in more closely related species such as nonhuman primates. This observation supports the vocal learning hypothesis

  15. First molecular detection of group A rotaviruses in drinking water sources in Beijing, China.

    Science.gov (United States)

    He, X Q; Cheng, L; Zhang, D Y; Li, W; Xie, X M; Ma, M; Wang, Z J

    2009-07-01

    The most prevalent group A rotavirus found in the diarrheic children was also determined in drinking water sources including raw water, treated water and tap water in Beijing, and then the possible contamination contributions to tap water for human consumption were discussed in this study. A total of 26 raw water samples, 77 treated water samples and 143 tap water samples in Beijing were collected for analysis of group A rotavirus from April 2006 to August 2007. According to the results, it was shown that group A rotaviruses occurred in 9 raw water samples (34.6%), 9 treated water samples (11.7%) and 32 tap water samples (22.4%) during the sampling period, and low disinfectant residuals or a vulnerability of the distribution system to pressure transients, in addition to raw water, may account for the group A rotaviruses contamination to tap water. The rotavirus contamination observed in this study may highlight a potential public health risk and illustrate the importance of including routine virological analysis of drinking water supplies during winter time in Beijing.

  16. Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.

    Science.gov (United States)

    Graña, Osvaldo; López-Fernández, Hugo; Fdez-Riverola, Florentino; González Pisano, David; Glez-Peña, Daniel

    2018-04-15

    High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data. Bicycle analyzes whole genome bisulfite sequencing data, targeted bisulfite sequencing data and hydroxymethylation data. To show how bicycle overtakes other available pipelines, we compared them on a defined number of features that are summarized in a table. We also tested bicycle with both simulated and real datasets, to show its level of performance, and compared it to different state-of-the-art methylation analysis pipelines. Bicycle is publicly available under GNU LGPL v3.0 license at http://www.sing-group.org/bicycle. Users can also download a customized Ubuntu LiveCD including bicycle and other bisulfite sequencing data pipelines compared here. In addition, a docker image with bicycle and its dependencies, which allows a straightforward use of bicycle in any platform (e.g. Linux, OS X or Windows), is also available. ograna@cnio.es or dgpena@uvigo.es. Supplementary data are available at Bioinformatics online.

  17. Evaluation of United States-Licensed Human Immunodeficiency Virus Immunoassays for Detection of Group M Viral Variants

    OpenAIRE

    Koch, Walter H.; Sullivan, Patrick S.; Roberts, Charles; Francis, Kori; Downing, Robert; Mastro, Timothy D.; Nkengasong, John; Hu, Dale; Masciotra, Silvina; Schable, Charles; Lal, Renu B.

    2001-01-01

    Six Food and Drug Administration (FDA)-licensed human immunodeficiency virus type 1 (HIV-1) and HIV-1/2 immunoassays, including five enzyme immunoassays and one rapid test, were challenged with up to 250 serum samples collected from various global sites. The serum samples were from individuals known to be infected with variants of HIV-1 including group M subtypes A, B, B′, C, D, E, F, and G and group O. All immunoassays detected the vast majority of samples tested. Three samples produced low ...

  18. Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups

    OpenAIRE

    Cesconeto, Robson Jose; Joost, Stéphane; McManus, Concepta Margaret; Paiva, Samuel Rezende; Cobuci, Jaime Araujo; Braccini, Jose

    2017-01-01

    Abstract Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as FST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in b...

  19. Combinatorial Methods for Detecting Surface Subgroups in Right-Angled Artin Groups

    OpenAIRE

    Bell, Robert W.

    2010-01-01

    We give a short proof of the following theorem of Sang-hyun Kim: if $A(\\Gamma)$ is a right-angled Artin group with defining graph $\\Gamma$, then $A(\\Gamma)$ contains a hyperbolic surface subgroup if $\\Gamma$ contains an induced subgraph $\\bar{C}_n$ for some $n \\geq 5$, where $\\bar{C}_n$ denotes the complement graph of an $n$-cycle. Furthermore, we give a new proof of Kim's co-contraction theorem.

  20. Functionalization of Polymers with Fluorescent and Neutron Sensitive Groups for Efficient Neutron and Gamma Detection

    Science.gov (United States)

    Mahl, Adam; Yemam, Henok; Remedes, Tyler; Stuntz, Jack; Koldemir, Unsal; Sellinger, Alan; Greife, Uwe

    2015-10-01

    This presentation will review the efforts made by an interdisciplinary development project aimed at cost-effective, thermal neutron sensitive, plastic scintillators as part of the communities efforts towards replacing 3He based detectors. Colorado School of Mines researchers with backgrounds in Physics and Chemistry have worked on the incorporation of 10B in plastics through admixture of various commercial and novel dopants developed at CSM. In addition, new fluorescent dopants have been developed for plastic scintillators in an effort towards better understanding quenching effects and scintillator response to thermal neutrons via pulse shape discrimination methods. Results on transparent samples using fluorescent spectroscopy and gamma/neutron excitation will be presented. Funded via Department of Homeland Security - Domestic Nuclear Detection Office.

  1. Development of an Enzyme-Linked Immunosorbent Assay Method Specific for the Detection of G-Group Aflatoxins.

    Science.gov (United States)

    Li, Peiwu; Zhou, Qian; Wang, Ting; Zhou, Haiyan; Zhang, Wen; Ding, Xiaoxia; Zhang, Zhaowei; Chang, Perng-Kuang; Zhang, Qi

    2015-12-28

    To detect and monitor G-group aflatoxins in agricultural products, we generated class-specific monoclonal antibodies that specifically recognized aflatoxins G₁ and G₂. Of the final three positive and stable hybridomas obtained, clone 2G6 produced a monoclonal antibody that had equal sensitivity to aflatoxins G₁ and G₂, and did not cross-react with aflatoxins B₁, B₂, or M₁. Its IC50 values for aflatoxins G₁ and G₂ were 17.18 ng·mL(-1) and 19.75 ng·mL(-1), respectively. Using this new monoclonal antibody, we developed a competitive indirect enzyme-linked immunosorbent assay (CI-ELISA); the method had a limit of detection of 0.06 ng·mL(-1). To validate this CI-ELISA, we spiked uncontaminated peanut samples with various amounts of aflatoxins G₁ and G₂ and compared recovery rates with those determined by a standard HPLC method. The recovery rates of the CI-ELISA ranging from 94% to 103% were comparable to those of the HPLC (92% to 102%). We also used both methods to determine the amounts of G-group aflatoxins in five peanut samples contaminated by aflatoxin B₁-positive, and their relative standard deviations ranged from 8.4% to 17.7% (under 20%), which demonstrates a good correlation between the two methods. We further used this CI-ELISA to assess the ability of 126 fungal strains isolated from peanuts or field soils to produce G-group aflatoxins. Among these, seven stains producing different amounts of G-group aflatoxins were identified. Our results showed that the monoclonal antibody 2 G6-based CI-ELISA was suitable for the detection of G-group aflatoxins present in peanuts and also those produced by fungi.

  2. Improvement in the determination of HIV-1 tropism using the V3 gene sequence and a combination of bioinformatic tools.

    Science.gov (United States)

    Chueca, Natalia; Garrido, Carolina; Alvarez, Marta; Poveda, Eva; de Dios Luna, Juan; Zahonero, Natalia; Hernández-Quero, José; Soriano, Vicente; Maroto, Carmen; de Mendoza, Carmen; García, Federico

    2009-05-01

    Assessment of HIV tropism using bioinformatic tools based on V3 sequences correlates poorly with results provided by phenotypic tropism assays, particularly for recognizing X4 viruses. This may represent an obstacle for the use of CCR5 antagonists. An algorithm combining several bioinformatic tools might improve the correlation with phenotypic tropism results. A total of 200 V3 sequences from HIV-1 subtype B, available in several databases with known phenotypic tropism results, were used to evaluate the sensitivity and specificity of seven different bioinformatic tools (PSSM, SVM, C4.5 decision tree generator and C4.5, PART, Charge Rule, and Geno2pheno). The best predictive bioinformatic tools were identified, and a model combining several of these was built. Using the 200 reference sequences, SVM and geno2-pheno showed the highest sensitivity for detecting X4 viruses (98.8% and 93.7%, respectively); however, their specificity was relatively low (62.5% and 86.6%, respectively). For R5 viruses, PSSM and C4.5 gave the same results and outperformed other bioinformatic tools (95.7% sensitivity, 82% specificity). When results from three out of these four tools were concordant, the sensitivity and specificity, taking as reference the results from phenotypic tropism assays, were over 90% in predicting either R5 or X4 viruses (AUC: 0.9701; 95% CI: 0.9358-0.9889). An algorithm combining four distinct bioinformatic tools (SVM, geno2pheno, PSSM and C4.5), improves the genotypic prediction of HIV tropism, and merits further evaluation, as it might prove useful as a screening strategy in clinical practice. Copyright 2009 Wiley-Liss, Inc.

  3. [Errors in detection of subgroups in the ABO blood group system].

    Science.gov (United States)

    Sato, C; Maeda, H

    1997-09-01

    In the ABO blood group system, several subgroups have been described based on: 1) the difference of reactivities of the red cells with anti-A, anti-B, anti-A1, and anti-H, 2) the presence or absence of anti-A, anti-B, anti-A1, anti-H, and anti-HI in serum, and 3) the presence of A, B, H substances in the saliva of ABH secretors. Subgroups of A are more frequent in Caucasians than in Japanese, while those of B are more frequent in Japanese. Both the red cell typing (testing red cells for A and B antigens) and serum typing (testing the antibodies in the serum against red cells of known ABO groups) are important to identify and not to overlook these ABO subgroups. When transfusion is required in individuals with these subgroups, compatible blood products must be selected according to the presence or absence of antibodies active at 37 degrees C.

  4. Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups.

    Science.gov (United States)

    Cesconeto, Robson Jose; Joost, Stéphane; McManus, Concepta Margaret; Paiva, Samuel Rezende; Cobuci, Jaime Araujo; Braccini, Jose

    2017-11-01

    Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as F ST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in both methods, with a Kappa value of 0.073 (95% CI: 0.011-0.134). The frequency of these markers indicated a clear north-south country division that reflects Brazilian environmental differences in temperature, solar radiation, and precipitation. Global spatial territory correlation for environmental variables corroborates this finding (average Moran's I = 0.89, range from 0.55 to 0.97). The distribution of alleles over the territory was not strongly correlated with the breed/genetic groups. These results are congruent with previous mtDNA studies and should be used to direct germplasm collection for the National gene bank.

  5. Comparison of different sampling techniques and of different culture methods for detection of group B streptococcus carriage in pregnant women

    Directory of Open Access Journals (Sweden)

    Verhelst Rita

    2010-09-01

    Full Text Available Abstract Background Streptococcus agalactiae (group B streptococcus; GBS is a significant cause of perinatal and neonatal infections worldwide. To detect GBS colonization in pregnant women, the CDC recommends isolation of the bacterium from vaginal and anorectal swab samples by growth in a selective enrichment medium, such as Lim broth (Todd-Hewitt broth supplemented with selective antibiotics, followed by subculture on sheep blood agar. However, this procedure may require 48 h to complete. We compared different sampling and culture techniques for the detection of GBS. Methods A total of 300 swabs was taken from 100 pregnant women at 35-37 weeks of gestation. For each subject, one rectovaginal, one vaginal and one rectal ESwab were collected. Plating onto Columbia CNA agar (CNA, group B streptococcus differential agar (GBSDA (Granada Medium and chromID Strepto B agar (CA, with and without Lim broth enrichment, were compared. The isolates were confirmed as S. agalactiae using the CAMP test on blood agar and by molecular identification with tDNA-PCR or by 16S rRNA gene sequence determination. Results The overall GBS colonization rate was 22%. GBS positivity for rectovaginal sampling (100% was significantly higher than detection on the basis of vaginal sampling (50%, but not significantly higher than for rectal sampling (82%. Direct plating of the rectovaginal swab on CNA, GBSDA and CA resulted in detection of 59, 91 and 95% of the carriers, respectively, whereas subculturing of Lim broth yielded 77, 95 and 100% positivity, respectively. Lim broth enrichment enabled the detection of only one additional GBS positive subject. There was no significant difference between GBSDA and CA, whereas both were more sensitive than CNA. Direct culture onto GBSDA or CA (91 and 95% detected more carriers than Lim broth enrichment and subculture onto CNA (77%. One false negative isolate was observed on GBSDA, and three false positives on CA. Conclusions In

  6. Detection of Hidden Hostile/Terrorist Groups in Harsh Territories by Using Animals as Mobile Biological Sensors

    Directory of Open Access Journals (Sweden)

    Tuncay Ercan

    2008-07-01

    Full Text Available Terrorism is the greatest threat to national security and cannot be defeated by conventional military force alone. In critical areas such as Iraq, Afghanistan and Turkey, regular forces cannot reach these hostile/terrorist groups, the instigators of terrorism. These groups have a clear understanding of the relative ineffectiveness of counter-guerrilla operations and rely on guerrilla warfare to avoid major combat as their primary means of continuing the conflict with the governmental structures. In Internal Security Operations, detection of terrorist and hostile groups in their hiding places such as caves, lairs, etc. can only be achieved by professionally trained people such as Special Forces or intelligence units with the necessary experience and tools suitable for collecting accurate information in these often harsh, rugged and mountainous countries. To assist these forces, commercial micro-sensors with wireless interfaces could be utilized to study and monitor a variety of phenomena and environments from a certain distance for military purposes. In order to locate hidden terrorist groups and enable more effective use of conventional military resources, this paper proposes an active remote sensing model implanted into animals capable of living in these environments. By using these mobile sensor devices, improving communications for data transfer from the source, and developing better ways to monitor and detect threats, terrorist ability to carry out attacks can be severely disrupted.

  7. Detection of Hidden Hostile/Terrorist Groups in Harsh Territories by Using Animals as Mobile Biological Sensors.

    Science.gov (United States)

    Sahin, Yasar Guneri; Ercan, Tuncay

    2008-07-25

    Terrorism is the greatest threat to national security and cannot be defeated by conventional military force alone. In critical areas such as Iraq, Afghanistan and Turkey, regular forces cannot reach these hostile/terrorist groups, the instigators of terrorism. These groups have a clear understanding of the relative ineffectiveness of counter-guerrilla operations and rely on guerrilla warfare to avoid major combat as their primary means of continuing the conflict with the governmental structures. In Internal Security Operations, detection of terrorist and hostile groups in their hiding places such as caves, lairs, etc. can only be achieved by professionally trained people such as Special Forces or intelligence units with the necessary experience and tools suitable for collecting accurate information in these often harsh, rugged and mountainous countries. To assist these forces, commercial micro-sensors with wireless interfaces could be utilized to study and monitor a variety of phenomena and environments from a certain distance for military purposes. In order to locate hidden terrorist groups and enable more effective use of conventional military resources, this paper proposes an active remote sensing model implanted into animals capable of living in these environments. By using these mobile sensor devices, improving communications for data transfer from the source, and developing better ways to monitor and detect threats, terrorist ability to carry out attacks can be severely disrupted.

  8. Importance of physical examination in early detection of lump in breast in women of different age groups.

    Science.gov (United States)

    Abbas, Hafsa; Imran, Saira; Waris, Noorul-ain-Hafeez; Khanam, Andleeb; Khurshid, Rukshshan

    2010-01-01

    The spectrum of breast lesions in adolescents varies markedly from that for adults, with the former lesions being overwhelmingly benign. Fine needle biopsy can be used to distinguish benign and malignant tumour. This study examined the characteristics and outcome of women with different age groups in whom physical examination was their sole method of lump in breast detection. A total of 200 patients were included in the study. These were divided into 3 groups. Group A was consisting of 75 girls with age of pubescent. Group B included 69 suspected breast cancer women with age range 26-38 years. Fifty-six suspected breast cancer women with age range 41-60 year were included as group C. Study was carried out in patients admitted in the Department/Out-door of Surgery, Sir Ganga Ram Hospital, Lahore, Pakistan. Study period was 6 months. All women received a physical examination by a breast surgeon. Proforma including demographic and clinical characteristics were filled. The diagnosis for patients in this study was achieved by core needle biopsy using a 14-gauge cutting needle. It was observed that early age at menarche (25 may be a risk factor in peri/post menopausal women. Active life style is more important with increasing age as it decreases the risk of developing tumour state. Family history was more common in women with peri/post menopausal status as compared to other age groups. Clinical characteristics showed that lump size early detection or clinical examination with FNA cut out the patients from harassment of malignancy and complications especially in the pubescent age. It is also found that Physical examination remain the useful indicators of prognosis in diagnosing cancer. Further research is needed to fully understand the reasons for variations in breast disease outcomes i.e. malignant or benign.

  9. Detection of HPV DNA in esophageal cancer specimens from different regions and ethnic groups: a descriptive study

    International Nuclear Information System (INIS)

    Wang, Xueqian; Zhang, Qingying; Zhang, Donghong; Shen, Zhongying; Li, Feng; Harris, Curtis C; Cai, Hong; Ke, Yang; Tian, Xiuyun; Liu, Fangfang; Zhao, Yiqiang; Sun, Min; Chen, Dafang; Lu, Changdong; Wang, Zhong; Shi, Xiaotian

    2010-01-01

    HPV has been found repeatedly in esophageal carcinoma tissues. However, reported detection rates of HPV DNA in these tumors have varied markedly. Differences in detection methods, sample types, and geographic regions of sample origin have been suggested as potential causes of this discrepancy. HPV L1 DNA and HPV genotypes were evaluated in 435 esophageal carcinoma specimens collected from four geographic regions with different ethnicities including Anyang in north China, Shantou in south China, Xinjiang in west China, and the United States. The HPV L1 fragment was detected using SPF1/GP6+ primers. HPV genotyping was performed using genotype specific PCR. Two hundred and forty four of 435 samples (56.1%) tested positive for HPV L1. Significant differences in detection rate were observed neither among the three areas of China nor between China and the US. HPV6, 16, 18, 26, 45, 56, 57, and 58 were identified in L1 positive samples. HPV16 and 57 were the most common types in all regions, followed by HPV26 and HPV18. HPV infection is common in esophageal carcinoma independent of region and ethnic group of origin. Findings in this study raise the possibility that HPV is involved in esophageal carcinogenesis. Further investigation with a larger sample size over broader geographic areas may be warranted

  10. The first detection and whole genome characterization of the G6P[15] group A rotavirus strain from roe deer.

    Science.gov (United States)

    Jamnikar-Ciglenecki, Urska; Kuhar, Urska; Sturm, Sabina; Kirbis, Andrej; Racki, Nejc; Steyer, Andrej

    2016-08-15

    Although rotaviruses have been detected in a variety of host species, there are only limited records of their occurrence in deer, where their role is unknown. In this study, group A rotavirus was identified in roe deer during a study of enteric viruses in game animals. 102 samples of intestinal content were collected from roe deer (56), wild boars (29), chamois (10), red deer (6) and mouflon (1), but only one sample from roe deer was positive. Following whole genome sequence analysis, the rotavirus strain D38/14 was characterized by next generation sequencing. The genotype constellation, comprising 11 genome segments, was G6-P[15]-I2-R2-C2-M2-A3-N2-T6-E2-H3. Phylogenetic analysis of the VP7 genome segment showed that the D38/14 rotavirus strain is closely related to the various G6 zoonotic rotavirus strains of bovine-like origin frequently detected in humans. In the VP4 segment, this strain showed high variation compared to that in the P[15] strain found in sheep and in a goat. This finding suggests that rotaviruses from deer are similar to those in other DS-1 rotavirus groups and could constitute a source of zoonotically transmitted rotaviruses. The epidemiological status of group A rotaviruses in deer should be further investigated. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Swarm intelligence in bioinformatics: methods and implementations for discovering patterns of multiple sequences.

    Science.gov (United States)

    Cui, Zhihua; Zhang, Yi

    2014-02-01

    As a promising and innovative research field, bioinformatics has attracted increasing attention recently. Beneath the enormous number of open problems in this field, one fundamental issue is about the accurate and efficient computational methodology that can deal with tremendous amounts of data. In this paper, we survey some applications of swarm intelligence to discover patterns of multiple sequences. To provide a deep insight, ant colony optimization, particle swarm optimization, artificial bee colony and artificial fish swarm algorithm are selected, and their applications to multiple sequence alignment and motif detecting problem are discussed.

  12. Survey of MapReduce frame operation in bioinformatics.

    Science.gov (United States)

    Zou, Quan; Li, Xu-Bin; Jiang, Wen-Rui; Lin, Zi-Yu; Li, Gui-Lin; Chen, Ke

    2014-07-01

    Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  13. Developing expertise in bioinformatics for biomedical research in Africa.

    Science.gov (United States)

    Karikari, Thomas K; Quansah, Emmanuel; Mohamed, Wael M Y

    2015-09-01

    Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases) that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are helping to develop bioinformatics into an important discipline in Africa. These contributions are leading to the establishment of world-class research facilities, biorepositories, training programmes, scientific networks and funding schemes to improve studies into disease and health in Africa. With increased contribution from all stakeholders, these developments could be further enhanced. Here, we discuss how the recent developments are contributing to the advancement of bioinformatics in Africa.

  14. Developing expertise in bioinformatics for biomedical research in Africa

    Directory of Open Access Journals (Sweden)

    Thomas K. Karikari

    2015-09-01

    Full Text Available Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are helping to develop bioinformatics into an important discipline in Africa. These contributions are leading to the establishment of world-class research facilities, biorepositories, training programmes, scientific networks and funding schemes to improve studies into disease and health in Africa. With increased contribution from all stakeholders, these developments could be further enhanced. Here, we discuss how the recent developments are contributing to the advancement of bioinformatics in Africa.

  15. Bioinformatics in the Netherlands: the value of a nationwide community.

    Science.gov (United States)

    van Gelder, Celia W G; Hooft, Rob W W; van Rijswijk, Merlijn N; van den Berg, Linda; Kok, Ruben G; Reinders, Marcel; Mons, Barend; Heringa, Jaap

    2017-09-15

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics community will be reviewed. We will show that the most valuable resource that we have built over these years is the close-knit national expert community that is well engaged in basic and translational life science research programmes. The Dutch bioinformatics community is accustomed to facing the ever-changing landscape of data challenges and working towards solutions together. In addition, this community is the stable factor on the road towards sustainability, especially in times where existing funding models are challenged and change rapidly. © The Author 2017. Published by Oxford University Press.

  16. Temporal Patterns in Sheep Fetal Heart Rate Variability Correlate to Systemic Cytokine Inflammatory Response: A Methodological Exploration of Monitoring Potential Using Complex Signals Bioinformatics.

    Directory of Open Access Journals (Sweden)

    Christophe L Herry

    Full Text Available Fetal inflammation is associated with increased risk for postnatal organ injuries. No means of early detection exist. We hypothesized that systemic fetal inflammation leads to distinct alterations of fetal heart rate variability (fHRV. We tested this hypothesis deploying a novel series of approaches from complex signals bioinformatics. In chronically instrumented near-term fetal sheep, we induced an inflammatory response with lipopolysaccharide (LPS injected intravenously (n = 10 observing it over 54 hours; seven additional fetuses served as controls. Fifty-one fHRV measures were determined continuously every 5 minutes using Continuous Individualized Multi-organ Variability Analysis (CIMVA. CIMVA creates an fHRV measures matrix across five signal-analytical domains, thus describing complementary properties of fHRV. We implemented, validated and tested methodology to obtain a subset of CIMVA fHRV measures that matched best the temporal profile of the inflammatory cytokine IL-6. In the LPS group, IL-6 peaked at 3 hours. For the LPS, but not control group, a sharp increase in standardized difference in variability with respect to baseline levels was observed between 3 h and 6 h abating to baseline levels, thus tracking closely the IL-6 inflammatory profile. We derived fHRV inflammatory index (FII consisting of 15 fHRV measures reflecting the fetal inflammatory response with prediction accuracy of 90%. Hierarchical clustering validated the selection of 14 out of 15 fHRV measures comprising FII. We developed methodology to identify a distinctive subset of fHRV measures that tracks inflammation over time. The broader potential of this bioinformatics approach is discussed to detect physiological responses encoded in HRV measures.

  17. MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales.

    Science.gov (United States)

    Jain, Sourabh; Panda, Arup; Colson, Philippe; Raoult, Didier; Pontarotti, Pierre

    2017-04-07

    With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the major drawback in gene acquisition studies is the focus on few MV families or putative families with large variation in their genetic structure. Thus, here we have tried to develop a methodology by which we can detect horizontal gene transfers (HGTs), taking into consideration orthologous groups of distantly related Megavirale families. Here, we report an automated workflow MimiLook, prepared as a Perl command line program, that deduces orthologous groups (OGs) from ORFomes of Megavirales and constructs phylogenetic trees by performing alignment generation, alignment editing and protein-protein BLAST (BLASTP) searching across the National Center for Biotechnology Information (NCBI) non-redundant (nr) protein sequence database. Finally, this tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detection of HGTs, along with retrieval of information about those OGs that are monophyletic with organisms from cellular domains of life. By implementing MimiLook, we noticed that nine percent of Megavirale gene families (i.e., OGs) have been acquired by HGT, 80% OGs were Megaviralespecific and eight percent were found to be sharing common ancestry with members of cellular domains (Eukaryote, Bacteria, Archaea, Phages or other viruses) and three percent were ambivalent. The results are briefly discussed to emphasize methodology. Also, MimiLook is relevant for detecting evolutionary scenarios in other targeted phyla with user defined modifications. It can be accessed at

  18. Development and performance evaluation of a recombinase polymerase amplification assay for the rapid detection of group B streptococcus.

    Science.gov (United States)

    Clarke, Christina; O'Connor, Louise; Carré-Skinner, Heather; Piepenburg, Olaf; Smith, Terry J

    2016-09-22

    Despite the implementation of prevention guidelines, group B Streptococcal (GBS) infection remains a leading cause of sepsis, pneumonia, and meningitis, resulting in significant neonatal morbidity and mortality. Preventive approaches that identify women at risk of transmitting GBS have reduced the incidence of neonatal GBS disease, and dramatically decreased the associated mortality rates. However, there is an on-going requirement for a near-patient diagnostic test for GBS that can be carried out at the time of delivery, ideally in the labour ward setting, particularly for women of unknown GBS colonisation status at the time of delivery. In this study, a Recombinase Polymerase Amplification (RPA) assay was developed and performance evaluated for the detection of group B Streptococcus in vaginal swabs. The assay uses the cAMP factor (cfb) gene of GBS as the target gene. The analytical performance of the assay was evaluated by testing a panel of GBS reference strains and clinical isolates, and non-GBS organisms. The limit of detection was determined and the clinical performance was evaluated by testing 124 vaginal swabs from women with both GBS positive and negative status. Based on specificity testing carried out the assay was shown to be specific for the target of interest. The limit of detection of the assay was shown to be between six and 12 genome copies and was comparable to that of a real-time PCR assay, both achieving a limit of detection below 12.5 genome copies. The performance of both assays when applied to clinical samples was identical. A specific, sensitive RPA assay for GBS was developed. The performance of the assay for testing of clinical samples is within the acceptable range.

  19. Bioinformatic training needs at a health sciences campus.

    Science.gov (United States)

    Oliver, Jeffrey C

    2017-01-01

    Health sciences research is increasingly focusing on big data applications, such as genomic technologies and precision medicine, to address key issues in human health. These approaches rely on biological data repositories and bioinformatic analyses, both of which are growing rapidly in size and scope. Libraries play a key role in supporting researchers in navigating these and other information resources. With the goal of supporting bioinformatics research in the health sciences, the University of Arizona Health Sciences Library established a Bioinformation program. To shape the support provided by the library, I developed and administered a needs assessment survey to the University of Arizona Health Sciences campus in Tucson, Arizona. The survey was designed to identify the training topics of interest to health sciences researchers and the preferred modes of training. Survey respondents expressed an interest in a broad array of potential training topics, including "traditional" information seeking as well as interest in analytical training. Of particular interest were training in transcriptomic tools and the use of databases linking genotypes and phenotypes. Staff were most interested in bioinformatics training topics, while faculty were the least interested. Hands-on workshops were significantly preferred over any other mode of training. The University of Arizona Health Sciences Library is meeting those needs through internal programming and external partnerships. The results of the survey demonstrate a keen interest in a variety of bioinformatic resources; the challenge to the library is how to address those training needs. The mode of support depends largely on library staff expertise in the numerous subject-specific databases and tools. Librarian-led bioinformatic training sessions provide opportunities for engagement with researchers at multiple points of the research life cycle. When training needs exceed library capacity, partnering with intramural and

  20. Development and Validation of Monoclonal Antibody-Based Antigen Capture ELISA for Detection of Group A Porcine Rotavirus.

    Science.gov (United States)

    Memon, Atta Muhammad; Bhuyan, Anjuman Ara; Chen, Fangzhou; Guo, Xiaozhen; Menghwar, Harish; Zhu, Yinxing; Ku, Xugang; Chen, Shuhua; Li, Zhonghua; He, Qigai

    2017-05-01

    Porcine rotavirus-A (PoRVA) is one of the common causes of mild to severe dehydrating diarrhea, leading to losses in weaning and postweaning piglets. A rapid, highly specific, and sensitive antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) was developed for detection of PoRVA, by using VP6 (a highly conserved and antigenic protein of group-A rotavirus)-directed rabbit polyclonal antibodies (capture antibody) and murine monoclonal antibodies (detector antibody). The detection limit of AC-ELISA was found to be equal to that of conventional reverse transcription-polymerase chain reaction (RT-PCR; about 10 2.5 TCID 50 /mL). For validation of the in-house AC-ELISA, 295 porcine fecal/diarrhea samples, collected from different provinces of China, were evaluated and compared with conventional RT-PCR and TaqMan RT-quantitative PCR (qPCR). The sensitivity and specificity of this in-house AC-ELISA relative to RT-qPCR were found to be 91.67% and 100%, respectively, with the strong agreement (kappa = 0.972) between these two techniques. Total detection rate with AC-ELISA, conventional RT-PCR, and RT-qPCR were found to be 11.2%, 11.5%, and 12.2%, respectively, without any statistical significant difference. Moreover, AC-ELISA failed to detect any cross-reactivity with porcine epidemic diarrhea virus, transmissible gastroenteritis virus, pseudorabies virus, and porcine circovirus-2. These results suggested that our developed method was rapid, highly specific, and sensitive, which may help in large-scale surveillance, timely detection, and preventive control of rotavirus infection in porcine farms.

  1. Group method of data handling and neral networks applied in monitoring and fault detection in sensors in nuclear power plants

    International Nuclear Information System (INIS)

    Bueno, Elaine Inacio

    2011-01-01

    The increasing demand in the complexity, efficiency and reliability in modern industrial systems stimulated studies on control theory applied to the development of Monitoring and Fault Detection system. In this work a new Monitoring and Fault Detection methodology was developed using GMDH (Group Method of Data Handling) algorithm and Artificial Neural Networks (ANNs) which was applied to the IEA-R1 research reactor at IPEN. The Monitoring and Fault Detection system was developed in two parts: the first was dedicated to preprocess information, using GMDH algorithm; and the second part to the process information using ANNs. The GMDH algorithm was used in two different ways: firstly, the GMDH algorithm was used to generate a better database estimated, called matrix z , which was used to train the ANNs. After that, the GMDH was used to study the best set of variables to be used to train the ANNs, resulting in a best monitoring variable estimative. The methodology was developed and tested using five different models: one Theoretical Model and four Models using different sets of reactor variables. After an exhausting study dedicated to the sensors Monitoring, the Fault Detection in sensors was developed by simulating faults in the sensors database using values of 5%, 10%, 15% and 20% in these sensors database. The results obtained using GMDH algorithm in the choice of the best input variables to the ANNs were better than that using only ANNs, thus making possible the use of these methods in the implementation of a new Monitoring and Fault Detection methodology applied in sensors. (author)

  2. Information Visualization Techniques in Bioinformatics during the Postgenomic Era

    Science.gov (United States)

    Tao, Ying; Liu, Yang; Friedman, Carol

    2010-01-01

    Information visualization techniques, which take advantage of the bandwidth of human vision, are powerful tools for organizing and analyzing a large amount of data. In the postgenomic era, information visualization tools are indispensable for biomedical research. This paper aims to present an overview of current applications of information visualization techniques in bioinformatics for visualizing different types of biological data, such as from genomics, proteomics, expression profiling and structural studies. Finally, we discuss the challenges of information visualization in bioinformatics related to dealing with more complex biological information in the emerging fields of systems biology and systems medicine. PMID:20976032

  3. Bioinformatic scaling of allosteric interactions in biomedical isozymes

    Science.gov (United States)

    Phillips, J. C.

    2016-09-01

    Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit cancer cell metabolism. Many parallel features are apparent, which explain how even one amino acid mutation, remote from active sites, can alter medical results. The enzyme twins involved are cyclooxygenase (aspirin) and isocitrate dehydrogenase (IDH). The IDH results are accurate to 1% and are overdetermined by adjusting a single bioinformatic scaling parameter. It appears that the final stage in optimizing protein functionality may involve leveling of the hydrophobic limits of the arms of conformational hydrophilic hinges.

  4. Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

    DEFF Research Database (Denmark)

    Leclère, Valérie; Weber, Tilmann; Jacques, Philippe

    2016-01-01

    This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes and the decip......This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes...

  5. [Expression profiles and bioinformatic analysis of miRNA in human dental pulp cells during endothelial differentiation].

    Science.gov (United States)

    Gong, Qimei; Jiang, Hongwei; Wang, Jinming; Ling, Junqi

    2014-05-01

    To investigate the differential expression profile and bioinformatic analysis of microRNA (miRNA) in human dental pulp cells (DPC) during endothelial differentiation. DPC were cultured in endothelial induction medium (50 µg/L vascular endothelial growth factor, 10 µg/L basic fibroblast growth factor and 2% fetal calf serum) for 7 days. Meanwhile non-induced DPC were used as control.Quantitative real-time PCR (qRT-PCR) was applied to detect vascular endothelial marker genes [CD31, von Willebrand factor (vWF) and vascular endothelial-cadherin (VE-cadherin)] and in vitro tube formation on matrigel was used to analyze the angiogenic ability of differentiated cells. And then miRNA expression profiles of DPC were examined using miRNA microarray and then the differentially expressed miRNA were validated by qRT-PCR. Furthermore, bioinformatic analysis was employed to predict the target genes of miRNA and to analyze the possible biological functions and signaling pathways that were involved in DPC after induction. The relative mRNA level of CD31, vWF and VE-cadherin in the control group were (3.48 ± 0.22) ×10(-4), (3.13 ± 0.31) ×10(-4) and (39.60 ± 2.36) ×10(-4), and (19.57 ± 2.20) ×10(-4), (48.13 ± 0.54) ×10(-4) and (228.00 ± 8.89) ×10(-4) in the induced group. The expressions of CD31, vWF and VE-cadherin were increased significantly in endothelial induced DPC compared to the control group (P functions, such as the regulation of transcription, cell motion, blood vessel morphogenesis, angiogenesis and cytoskeletal protein, and signaling pathways including the mitogen-activated protein kinase (MAPK) and the Wnt signaling pathway. The differential miRNA expression identified in this study may be involved in governing DPC endothelial differentiation, thus contributing to the future research on regulatory mechanisms in dental pulp angiogenesis.

  6. Importance of physical examination in early detection of lump in breast in women of different age groups

    International Nuclear Information System (INIS)

    Abbas, H.; Imran, S.; Waris, Noorul-ain-Hafeez; Khanam, A.; Khurshid, R.

    2010-01-01

    Background: The spectrum of breast lesions in adolescents varies markedly from that for adults, with the former lesions being overwhelmingly benign. Fine needle biopsy can be used to distinguish benign and malignant tumour. Study Design: This study examined the characteristics and outcome of women with different age groups in whom physical examination was their sole method of lump in breast detection. Patients and Methods: A total of 200 patients were included in the study. These were divided into 3 groups. Group A was consisting of 75 girls with age of pubescent. Group B included 69 suspected breast cancer women with age range 26-38 years. Fifty-six suspected breast cancer women with age range 41-60 year were included as group C. Study was carried out in patients admitted in the Department/Out-door of Surgery, Sir Ganga Ram Hospital, Lahore, Pakistan. Study period was 6 months. All women received a physical examination by a breast surgeon. Proforma including demographic and clinical characteristics were filled. The diagnosis for patients in this study was achieved by core needle biopsy using a 14-gauge cutting needle. Results: It was observed that early age at menarche ( 25 may be a risk factor in peri/post menopausal women. Active life style is more important with increasing age as it decreases the risk of developing tumour state. Family history was more common in women with peri/post menopausal status as compared to other age groups. Clinical characteristics showed that lump size <2.5 cm was more common in both pubescent and reproductive age. While lump size with a range of 2.5-5.0 cm, was observed in all groups of patients. Fibroadenoma is observed in almost all women with pubescent age while both benign and malignant tumour observed in women with reproductive age. Malignant tumour was observed mostly in women with peri/post menopausal status. Conclusion: Study concluded that early detection or clinical examination with FNA cut out the patients from harassment

  7. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    Energy Technology Data Exchange (ETDEWEB)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics

  8. Detecting and locating volcanic tremors on the Klyuchevskoy group of volcanoes (Kamchatka) based on correlations of continuous seismic records

    Science.gov (United States)

    Droznin, D. V.; Shapiro, N. M.; Droznina, S. Ya.; Senyukov, S. L.; Chebrov, V. N.; Gordeev, E. I.

    2015-11-01

    We analyse daily cross-correlation computed from continuous records by permanent stations operating in vicinity of the Klyuchevskoy group of volcanoes (Kamchatka). Seismic waves generated by volcanic tremors are clearly seen on the cross-correlations between some pairs of stations as strong signals at frequencies between 0.2 and 2 Hz and with traveltimes typically shorter than those corresponding to interstation propagation. First, we develop a 2-D source-scanning algorithm based on summation of the envelops of cross-correlations to detect seismic tremors and to determine locations from which the strong seismic energy is continuously emitted. In an alternative approach, we explore the distinctive character of the cross-correlation waveforms corresponding to tremors emitted by different volcanoes and develop a phase-matching method for detecting volcanic tremors. Application of these methods allows us to detect and to distinguish tremors generated by the Klyuchevskoy and the Tolbachik, volcanoes and to monitor evolution of their intensity in time.

  9. Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group.

    Science.gov (United States)

    Tuck, Melissa K; Chan, Daniel W; Chia, David; Godwin, Andrew K; Grizzle, William E; Krueger, Karl E; Rom, William; Sanda, Martin; Sorbara, Lynn; Stass, Sanford; Wang, Wendy; Brenner, Dean E

    2009-01-01

    Specimen collection is an integral component of clinical research. Specimens from subjects with various stages of cancers or other conditions, as well as those without disease, are critical tools in the hunt for biomarkers, predictors, or tests that will detect serious diseases earlier or more readily than currently possible. Analytic methodologies evolve quickly. Access to high-quality specimens, collected and handled in standardized ways that minimize potential bias or confounding factors, is key to the "bench to bedside" aim of translational research. It is essential that standard operating procedures, "the how" of creating the repositories, be defined prospectively when designing clinical trials. Small differences in the processing or handling of a specimen can have dramatic effects in analytical reliability and reproducibility, especially when multiplex methods are used. A representative working group, Standard Operating Procedures Internal Working Group (SOPIWG), comprised of members from across Early Detection Research Network (EDRN) was formed to develop standard operating procedures (SOPs) for various types of specimens collected and managed for our biomarker discovery and validation work. This report presents our consensus on SOPs for the collection, processing, handling, and storage of serum and plasma for biomarker discovery and validation.

  10. Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology.

    Science.gov (United States)

    Schlaberg, Robert; Queen, Krista; Simmon, Keith; Tardif, Keith; Stockmann, Chris; Flygare, Steven; Kennedy, Brett; Voelkerding, Karl; Bramley, Anna; Zhang, Jing; Eilbeck, Karen; Yandell, Mark; Jain, Seema; Pavia, Andrew T; Tong, Suxiang; Ampofo, Krow

    2017-05-01

    Community-acquired pneumonia (CAP) is a leading cause of pediatric hospitalization. Pathogen identification fails in approximately 20% of children but is critical for optimal treatment and prevention of hospital-acquired infections. We used two broad-spectrum detection strategies to identify pathogens in test-negative children with CAP and asymptomatic controls. Nasopharyngeal/oropharyngeal (NP/OP) swabs from 70 children <5 years with CAP of unknown etiology and 90 asymptomatic controls were tested by next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR for 19 viral families. Association of viruses with CAP was assessed by adjusted odds ratios (aOR) and 95% confidence intervals controlling for season and age group. RNA-seq/PVG PCR detected previously missed, putative pathogens in 34% of patients. Putative viral pathogens included human parainfluenza virus 4 (aOR 9.3, P = .12), human bocavirus (aOR 9.1, P < .01), Coxsackieviruses (aOR 5.1, P = .09), rhinovirus A (aOR 3.5, P = .34), and rhinovirus C (aOR 2.9, P = .57). RNA-seq was more sensitive for RNA viruses whereas PVG PCR detected more DNA viruses. RNA-seq and PVG PCR identified additional viruses, some known to be pathogenic, in NP/OP specimens from one-third of children hospitalized with CAP without a previously identified etiology. Both broad-range methods could be useful tools in future epidemiologic and diagnostic studies. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

  11. Genome bioinformatics of tomato and potato

    NARCIS (Netherlands)

    Datema, E.

    2011-01-01

    In the past two decades genome sequencing has developed from a laborious and costly technology employed by large international consortia to a widely used, automated and affordable tool used worldwide by many individual research groups. Genome sequences of many food animals and crop plants have been

  12. Genome bioinformatics of tomato and potato

    NARCIS (Netherlands)

    Datema, E.

    2011-01-01

    In the past two decades genome sequencing has developed from a laborious and costly technology employed by large international consortia to a widely used, automated and affordable tool used worldwide by many individual research groups. Genome sequences of many food animals and crop plants have

  13. Probabilistic models and machine learning in structural bioinformatics.

    Science.gov (United States)

    Hamelryck, Thomas

    2009-10-01

    Structural bioinformatics is concerned with the molecular structure of biomacromolecules on a genomic scale, using computational methods. Classic problems in structural bioinformatics include the prediction of protein and RNA structure from sequence, the design of artificial proteins or enzymes, and the automated analysis and comparison of biomacromolecules in atomic detail. The determination of macromolecular structure from experimental data (for example coming from nuclear magnetic resonance, X-ray crystallography or small angle X-ray scattering) has close ties with the field of structural bioinformatics. Recently, probabilistic models and machine learning methods based on Bayesian principles are providing efficient and rigorous solutions to challenging problems that were long regarded as intractable. In this review, I will highlight some important recent developments in the prediction, analysis and experimental determination of macromolecular structure that are based on such methods. These developments include generative models of protein structure, the estimation of the parameters of energy functions that are used in structure prediction, the superposition of macromolecules and structure determination methods that are based on inference. Although this review is not exhaustive, I believe the selected topics give a good impression of the exciting new, probabilistic road the field of structural bioinformatics is taking.

  14. Science Academies' Refresher Course on Bioinformatics in Modern ...

    Indian Academy of Sciences (India)

    IAS Admin

    A Refresher Course on 'Bioinformatics in Modern Biology' for graduate and postgraduate college/university teachers will be held at School of Life Sciences, Manipal University, Manipal for two weeks from 5 to 17 May 2014. The objective of this Course is to improvise on teaching methodologies incorporating online teaching ...

  15. The structural bioinformatics library: modeling in biomolecular science and beyond.

    Science.gov (United States)

    Cazals, Frédéric; Dreyfus, Tom

    2017-04-01

    Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  16. Bioinformatics in the Netherlands : The value of a nationwide community

    NARCIS (Netherlands)

    van Gelder, Celia W.G.; Hooft, Rob; van Rijswijk, Merlijn; van den Berg, Linda; Kok, Ruben; Reinders, M.J.T.; Mons, Barend; Heringa, Jaap

    2017-01-01

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures

  17. Bioinformatic tools and guideline for PCR primer design | Abd ...

    African Journals Online (AJOL)

    Bioinformatics has become an essential tool not only for basic research but also for applied research in biotechnology and biomedical sciences. Optimal primer sequence and appropriate primer concentration are essential for maximal specificity and efficiency of PCR. A poorly designed primer can result in little or no ...

  18. A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

    Science.gov (United States)

    A Bioinformatic Strategy to Rapidly Characterize cDNA LibrariesG. Charles Ostermeier1, David J. Dix2 and Stephen A. Krawetz1.1Departments of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, & Institute for Scientific Computing, Wayne State Univer...

  19. Robust enzyme design: bioinformatic tools for improved protein stability.

    Science.gov (United States)

    Suplatov, Dmitry; Voevodin, Vladimir; Švedas, Vytas

    2015-03-01

    The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Science Academies' Refresher Course on Bioinformatics in Modern ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 2. Science Academies' Refresher Course on Bioinformatics in Modern Biology. Information and Announcements Volume 19 Issue 2 February 2014 pp 192-192. Fulltext. Click here to view fulltext PDF. Permanent link:

  1. Bioinformatics Analysis of Envelope Glycoprotein E epitopes of ...

    African Journals Online (AJOL)

    User

    2011-05-02

    May 2, 2011 ... A virus-neutralizing antibody by a virus-specific synthetic peptide. J. Virol. 55(3): 836-839. Geourjon C, Deléage G (1995). SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics, 11(6): 681-684. Guex N, Peitsch MC ...

  2. CROSSWORK for Glycans: Glycan Identificatin Through Mass Spectrometry and Bioinformatics

    DEFF Research Database (Denmark)

    Rasmussen, Morten; Thaysen-Andersen, Morten; Højrup, Peter

      We have developed "GLYCANthrope " - CROSSWORKS for glycans:  a bioinformatics tool, which assists in identifying N-linked glycosylated peptides as well as their glycan moieties from MS2 data of enzymatically digested glycoproteins. The program runs either as a stand-alone application or as a plug...

  3. Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

    Science.gov (United States)

    Lima, Andre O. S.; Garces, Sergio P. S.

    2006-01-01

    Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

  4. Learning Genetics through an Authentic Research Simulation in Bioinformatics

    Science.gov (United States)

    Gelbart, Hadas; Yarden, Anat

    2006-01-01

    Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process…

  5. Bioinformatic analyses of kappa casein gene in mammalian ...

    African Journals Online (AJOL)

    Kappa casein (CSN3) gene is a variant of the milk protein highly conserved in mammalian species. Genetic variations in CSN3 gene of six mammalian livestock species were investigated using bioinformatics approach. A total of twenty-seven CSN3 gene sequences with corresponding amino acids belonging to the six ...

  6. Hidden in the Middle: Culture, Value and Reward in Bioinformatics

    Science.gov (United States)

    Lewis, Jamie; Bartlett, Andrew; Atkinson, Paul

    2016-01-01

    Bioinformatics--the so-called shotgun marriage between biology and computer science--is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised…

  7. BIOINFORMATICS SOFTWARE FROM INDIA: CURRENT STATUS AND CHALLENGES

    Directory of Open Access Journals (Sweden)

    Deepti D. Deobagkar

    2017-09-01

    Full Text Available Bioinformatics software and visualisation tools have been a key factor in the rapid and phenomenal advances in genomics, proteomics, medicine, drug discovery, systems approaches and in fact in every area of new development. Indian scientists have also made a mark in a few specific areas. India has an advantage of an early start and extensive and organised network in the Bioinformatics education and research with substantial inputs from the Indian government. India has a strong hold in computation and IT and has a pool of bright and young talent with demographic dividend along with experienced and excellent mentors and researchers. Although small in number and scale, Bioinformatics Industry also has a presence and is making its mark in India. There are a number of high throughput and extremely useful resources available which are critical in biological data analysis and interpretation. This has made a paradigm shift in the way research can be carried out and discoveries can be made in any area of biological, biochemical and chemical research. This article summarises the current status and contributions from India in the development of software and web servers for Bioinformatics applications.

  8. Bioinformatics and phylogenetic analysis of human Tp73 gene

    African Journals Online (AJOL)

    Imtiaz

    2013-06-26

    Jun 26, 2013 ... 2Bioinformatics and Biotechnology, DES, FBAS International Islamic University, Islamabad, Pakistan. Accepted 26 April, 2013. The Tp73 ... New discoveries about the control and function of p73 are still in progress and it is ..... modern research for diagnostics and evolutionary history of p73. REFERENCES.

  9. Using Bioinformatics Tools for Identification and Characterization of Transcriptome Derived EST-SSRs in Silver Fir (Abies alba Mill.

    Directory of Open Access Journals (Sweden)

    Dragos POSTOLACHE

    2017-05-01

    Full Text Available Bioinformatics tools have been used to evaluate silver fir de novo assembled 454 transcriptome. A total of 3500 EST-SSRs were detected in the 454 transcriptome of silver fir. Most abundant are tri-nucleotide SSRs being followed by tetra- SSRs and di- SSRs. In addition, we determined the density, frequency, average length and average repeat number of EST-SSRs in the 454 transcriptome of silver fir.

  10. Bioinformatic survey of ABC transporters in dermatophytes.

    Science.gov (United States)

    Gadzalski, Marek; Ciesielska, Anita; Stączek, Paweł

    2016-01-15

    ATP binding cassette (ABC) transporters constitute a very large and ubiquitous superfamily of membrane proteins. They are responsible for ATP hydrolysis driven translocation of countless substrates. Being a very old and diverse group of proteins present in all organisms they share a common feature, which is the presence of an evolutionary conservative nucleotide binding domain (NBD)--the engine that drives the transport. Another common domain is a transmembrane domain (TMD) which consists of several membrane-spanning helices. This part of protein is substrate-specific, thus it is much more variable. ABC transporters are known for driving drug efflux in many pathogens and cancer cells, therefore they are the subject of extensive studies. There are many examples of conferring a drug resistance phenotype in fungal pathogens by ABC transporters, however, little is known about these proteins in dermatophytes--a group of fungi causing superficial mycoses. So far only a single ABC transporter has been extensively studied in this group of pathogens. We analyzed available genomic sequences of seven dermatophyte species in order to provide an insight into dermatophyte ABC protein inventory. Phylogenetic studies of ABC transporter genes and their products were conducted and included ABC transporters of other fungi. Our results show that each dermatophyte genome studied possesses a great variety of ABC transporter genes. Detailed analysis of selected genes and their products indicates that relatively recent duplication of ABC transporter genes could lead to novel substrate specificity. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. BioWarehouse: a bioinformatics database warehouse toolkit

    Directory of Open Access Journals (Sweden)

    Stringer-Calvert David WJ

    2006-03-01

    Full Text Available Abstract Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the

  12. Bioclipse: an open source workbench for chemo- and bioinformatics

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

    Full Text Available Abstract Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL, an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

  13. Molecular gene profiling of Clostridium botulinum group III and its detection in naturally contaminated samples originating from various European countries.

    Science.gov (United States)

    Woudstra, Cedric; Le Maréchal, Caroline; Souillard, Rozenn; Bayon-Auboyer, Marie-Hélène; Anniballi, Fabrizio; Auricchio, Bruna; De Medici, Dario; Bano, Luca; Koene, Miriam; Sansonetti, Marie-Hélène; Desoutter, Denise; Hansbauer, Eva-Maria; Dorner, Martin B; Dorner, Brigitte G; Fach, Patrick

    2015-04-01

    We report the development of real-time PCR assays for genotyping Clostridium botulinum group III targeting the newly defined C. novyi sensu lato group; the nontoxic nonhemagglutinin (NTNH)-encoding gene ntnh; the botulinum neurotoxin (BoNT)-encoding genes bont/C, bont/C/D, bont/D, and bont/D/C; and the flagellin (fliC) gene. The genetic diversity of fliC among C. botulinum group III strains resulted in the definition of five major subgroups named fliC-I to fliC-V. Investigation of fliC subtypes in 560 samples, with various European origins, showed that fliC-I was predominant and found exclusively in samples contaminated by C. botulinum type C/D, fliC-II was rarely detected, no sample was recorded as fliC-III or fliC-V, and only C. botulinum type D/C samples tested positive for fliC-IV. The lack of genetic diversity of the flagellin gene of C. botulinum type C/D would support a clonal spread of type C/D strains in different geographical areas. fliC-I to fliC-III are genetically related (87% to 92% sequence identity), whereas fliC-IV from C. botulinum type D/C is more genetically distant from the other fliC types (with only 50% sequence identity). These findings suggest fliC-I to fliC-III have evolved in a common environment and support a different genetic evolution for fliC-IV. A combination of the C. novyi sensu lato, ntnh, bont, and fliC PCR assays developed in this study allowed better characterization of C. botulinum group III and showed the group to be less genetically diverse than C. botulinum groups I and II, supporting a slow genetic evolution of the strains belonging to C. botulinum group III. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  14. Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.

    Science.gov (United States)

    Wright, Victoria Ann; Vaughan, Brendan W; Laurent, Thomas; Lopez, Rodrigo; Brooksbank, Cath; Schneider, Maria Victoria

    2010-11-01

    Today's molecular life scientists are well educated in the emerging experimental tools of their trade, but when it comes to training on the myriad of resources and tools for dealing with biological data, a less ideal situation emerges. Often bioinformatics users receive no formal training on how to make the most of the bioinformatics resources and tools available in the public domain. The European Bioinformatics Institute, which is part of the European Molecular Biology Laboratory (EMBL-EBI), holds the world's most comprehensive collection of molecular data, and training the research community to exploit this information is embedded in the EBI's mission. We have evaluated eLearning, in parallel with face-to-face courses, as a means of training users of our data resources and tools. We anticipate that eLearning will become an increasingly important vehicle for delivering training to our growing user base, so we have undertaken an extensive review of Learning Content Management Systems (LCMSs). Here, we describe the process that we used, which considered the requirements of trainees, trainers and systems administrators, as well as taking into account our organizational values and needs. This review describes the literature survey, user discussions and scripted platform testing that we performed to narrow down our choice of platform from 36 to a single platform. We hope that it will serve as guidance for others who are seeking to incorporate eLearning into their bioinformatics training programmes.

  15. Missing "Links" in Bioinformatics Education: Expanding Students' Conceptions of Bioinformatics Using a Biodiversity Database of Living and Fossil Reef Corals

    Science.gov (United States)

    Nehm, Ross H.; Budd, Ann F.

    2006-01-01

    NMITA is a reef coral biodiversity database that we use to introduce students to the expansive realm of bioinformatics beyond genetics. We introduce a series of lessons that have students use this database, thereby accessing real data that can be used to test hypotheses about biodiversity and evolution while targeting the "National Science …

  16. Bioinformatic identification of novel putative photoreceptor specific cis-elements

    Directory of Open Access Journals (Sweden)

    Knox Barry E

    2007-10-01

    Full Text Available Abstract Background Cell specific gene expression is largely regulated by different combinations of transcription factors that bind cis-elements in the upstream promoter sequence. However, experimental detection of cis-elements is difficult, expensive, and time-consuming. This provides a motivation for developing bioinformatic methods to identify cis-elements that could prioritize future experimental studies. Here, we use motif discovery algorithms to predict transcription factor binding sites involved in regulating the differences between murine rod and cone photoreceptor populations. Results To identify highly conserved motifs enriched in promoters that drive expression in either rod or cone photoreceptors, we assembled a set of murine rod-specific, cone-specific, and non-photoreceptor background promoter sequences. These sets were used as input to a newly devised motif discovery algorithm called Iterative Alignment/Modular Motif Selection (IAMMS. Using IAMMS, we predicted 34 motifs that may contribute to rod-specific (19 motifs or cone-specific (15 motifs expression patterns. Of these, 16 rod- and 12 cone-specific motifs were found in clusters near the transcription start site. New findings include the observation that cone promoters tend to contain TATA boxes, while rod promoters tend to be TATA-less (exempting Rho and Cnga1. Additionally, we identify putative sites for IL-6 effectors (in rods and RXR family members (in cones that can explain experimental data showing changes to cell-fate by activating these signaling pathways during rod/cone development. Two of the predicted motifs (NRE and ROP2 have been confirmed experimentally to be involved in cell-specific expression patterns. We provide a full database of predictions as additional data that may contain further valuable information. IAMMS predictions are compared with existing motif discovery algorithms, DME and BioProspector. We find that over 60% of IAMMS predictions are confirmed by

  17. Message Collision Avoidance Protocols for Detecting Stray Nodes in a Scuba Diving Group Using Ultrasonic Multi-Hop Message Communication

    Directory of Open Access Journals (Sweden)

    Shinya Kaido

    2017-12-01

    Full Text Available Recent years have seen a growing interest in underwater communication and some progress has been made in this area. However, underwater communication is still immature compared with terrestrial communication. A prime reason for this is that the underwater environment is intrinsically not suitable for propagation of electric waves. Instead, ultrasonic waves are mainly used for underwater communication. Since ultrasonic waves cannot provide sufficient communication speed or capacity, they cannot use existing network technologies, which assume use of radio waves. In particular, communication in shallow water is still an uncharted territory. Few communication technologies are employed in environments where people enjoy scuba diving. This paper addresses problems faced by recreational scuba divers. It proposes constructing an ad hoc mesh-shaped network between divers within a group and use ultrasonic waves as transmission media in order to enable the detection of a stray diver. It also proposes a communication protocol in which messages are relayed in multiple hops, and a message collision avoidance method, which is intended to reduce the rate of packet loss caused by message propagation delay. We have implemented the proposed methods in a network simulator, and compared them with an existing communication method that has no message collision avoidance function, in terms of the packet loss rate, the stray driver detection rate, and the rate of the ability to communicate in multiple hops.

  18. Introductory Bioinformatics Exercises Utilizing Hemoglobin and Chymotrypsin to Reinforce the Protein Sequence-Structure-Function Relationship

    Science.gov (United States)

    Inlow, Jennifer K.; Miller, Paige; Pittman, Bethany

    2007-01-01

    We describe two bioinformatics exercises intended for use in a computer laboratory setting in an upper-level undergraduate biochemistry course. To introduce students to bioinformatics, the exercises incorporate several commonly used bioinformatics tools, including BLAST, that are freely available online. The exercises build upon the students'…

  19. Vertical and Horizontal Integration of Bioinformatics Education: A Modular, Interdisciplinary Approach

    Science.gov (United States)

    Furge, Laura Lowe; Stevens-Truss, Regina; Moore, D. Blaine; Langeland, James A.

    2009-01-01

    Bioinformatics education for undergraduates has been approached primarily in two ways: introduction of new courses with largely bioinformatics focus or introduction of bioinformatics experiences into existing courses. For small colleges such as Kalamazoo, creation of new courses within an already resource-stretched setting has not been an option.…

  20. Report on the EMBER Project--A European Multimedia Bioinformatics Educational Resource

    Science.gov (United States)

    Attwood, Terri K.; Selimas, Ioannis; Buis, Rob; Altenburg, Ruud; Herzog, Robert; Ledent, Valerie; Ghita, Viorica; Fernandes, Pedro; Marques, Isabel; Brugman, Marc

    2005-01-01

    EMBER was a European project aiming to develop bioinformatics teaching materials on the Web and CD-ROM to help address the recognised skills shortage in bioinformatics. The project grew out of pilot work on the development of an interactive web-based bioinformatics tutorial and the desire to repackage that resource with the help of a professional…

  1. Applying Instructional Design Theories to Bioinformatics Education in Microarray Analysis and Primer Design Workshops

    Science.gov (United States)

    Shachak, Aviv; Ophir, Ron; Rubin, Eitan

    2005-01-01

    The need to support bioinformatics training has been widely recognized by scientists, industry, and government institutions. However, the discussion of instructional methods for teaching bioinformatics is only beginning. Here we report on a systematic attempt to design two bioinformatics workshops for graduate biology students on the basis of…

  2. Bioinformatic Analysis of Potential Biomarkers for Spinal Cord Injured Patients With Intractable Neuropathic Pain.

    Science.gov (United States)

    Wang, Yimin; Ye, Fang; Huang, Chanyan; Xue, Faling; Li, Yingyuan; Gao, Shaowei; Qiu, Zeting; Li, Si; Chen, Qinchang; Zhou, Huaqiang; Song, Yiyan; Huang, Wenqi; Tan, Wulin; Wang, Zhongxing

    2018-03-15

    Neuropathic pain is one of the common complications after spinal cord injury (SCI), affecting patients' life quality. The molecular mechanism for neuropathic pain after SCI is still unclear. We aimed to discover potential genes and MicroRNAs(miRNAs) related to neuropathic pain by bioinformatics method. Microarray data of GSE69901 were obtained from Gene Expression Omnibus (GEO) database. Peripheral blood samples from patients with or without neuropathic pain after spinal cord injury (SCI) were collected. 12 samples with neuropathic pain and 13 samples without pain as control were included in the downloaded microarray. Differentially expressed genes (DEGs) between neuropathic pain group and control group were detected using GEO2R online tool. Functional enrichment analysis of DEGs was performed using DAVID database. Protein-protein interaction (PPI) network was constructed from STRING database. MiRNAs targeting these DEGs were obtained from miRNet database. A merged miRNA-DEG network was constructed and analyzed with Cytoscape software. Total 1134 DEGs were identified between patients with or without neuropathic pain(case and control) and 454 biological processes were enriched. We identified 4 targeted miRNAs, including mir-204-5p, mir-519d-3p, mir-20b-5p, mir-6838-5p, which may be the potential biomarker for SCI patients. Protein modification and regulation biological process of central nervous system may be a risk factor of in SCI patients. Certain genes and miRNAs may be potential biomarkers for the prediction of and potential targets for prevention and treatment of neuropathic pain after SCI.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http

  3. Quantum Bio-Informatics II From Quantum Information to Bio-Informatics

    Science.gov (United States)

    Accardi, L.; Freudenberg, Wolfgang; Ohya, Masanori

    2009-02-01

    / H. Kamimura -- Massive collection of full-length complementary DNA clones and microarray analyses: keys to rice transcriptome analysis / S. Kikuchi -- Changes of influenza A(H5) viruses by means of entropic chaos degree / K. Sato and M. Ohya -- Basics of genome sequence analysis in bioinformatics - its fundamental ideas and problems / T. Suzuki and S. Miyazaki -- A basic introduction to gene expression studies using microarray expression data analysis / D. Wanke and J. Kilian -- Integrating biological perspectives: a quantum leap for microarray expression analysis / D. Wanke ... [et al.].

  4. Development and In silico Evaluation of Large-Scale Metabolite Identification Methods using Functional Group Detection for Metabolomics

    Directory of Open Access Journals (Sweden)

    Joshua M Mitchell

    2014-07-01

    Full Text Available Large-scale identification of metabolites is key to elucidating and modeling metabolism at the systems level. Advances in metabolomics technologies, particularly ultra-high resolution mass spectrometry enable comprehensive and rapid analysis of metabolites. However, a significant barrier to meaningful data interpretation is the identification of a wide range of metabolites including unknowns and the determination of their role(s in various metabolic networks. Chemoselective (CS probes to tag metabolite functional groups combined with high mass accuracy provide additional structural constraints for metabolite identification and quantification. We have developed a novel algorithm, Chemically Aware Substructure Search (CASS that efficiently detects functional groups within existing metabolite databases, allowing for combined molecular formula and functional group (from CS tagging queries to aid in metabolite identification without a priori knowledge. Analysis of the isomeric compounds in both Human Metabolome Database (HMDB and KEGG Ligand demonstrated a high percentage of isomeric molecular formulae (43% and 28% respectively, indicating the necessity for techniques such as CS-tagging. Furthermore, these two databases have only moderate overlap in molecular formulae. Thus, it is prudent to use multiple databases in metabolite assignment, since each major metabolite database represents different portions of metabolism within the biosphere. In silico analysis of various CS-tagging strategies under different conditions for adduct formation demonstrate that combined FT-MS derived molecular formulae and CS-tagging can uniquely identify up to 71% of KEGG and 37% of the combined KEGG/HMDB database versus 41% and 17% respectively without adduct formation. This difference between database isomer disambiguation highlights the strength of CS-tagging for non-lipid metabolite identification. However, unique identification of complex lipids still needs

  5. Hidden Markov Models in Bioinformatics: SNV Inference from Next Generation Sequence.

    Science.gov (United States)

    Bian, Jiawen; Zhou, Xiaobo

    2017-01-01

    The rapid development of next generation sequencing (NGS) technology provides a novel avenue for genomic exploration and research. Hidden Markov models (HMMs) have wide applications in pattern recognition as well as Bioinformatics such as transcription factor binding sites and cis-regulatory modules detection. An application of HMM is introduced in this chapter with the in-deep developing of NGS. Single nucleotide variants (SNVs) inferred from NGS are expected to reveal gene mutations in cancer. However, NGS has lower sequence coverage and poor SNV detection capability in the regulatory regions of the genome. A specific HMM is developed for this purpose to infer the genotype for each position on the genome by incorporating the mapping quality of each read and the corresponding base quality on the reads into the emission probability of HMM. The procedure and the implementation of the algorithm is presented in detail for understanding and programming.

  6. Open discovery: An integrated live Linux platform of Bioinformatics tools.

    Science.gov (United States)

    Vetrivel, Umashankar; Pilla, Kalabharath

    2008-01-01

    Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

  7. Statistical modelling in biostatistics and bioinformatics selected papers

    CERN Document Server

    Peng, Defen

    2014-01-01

    This book presents selected papers on statistical model development related mainly to the fields of Biostatistics and Bioinformatics. The coverage of the material falls squarely into the following categories: (a) Survival analysis and multivariate survival analysis, (b) Time series and longitudinal data analysis, (c) Statistical model development and (d) Applied statistical modelling. Innovations in statistical modelling are presented throughout each of the four areas, with some intriguing new ideas on hierarchical generalized non-linear models and on frailty models with structural dispersion, just to mention two examples. The contributors include distinguished international statisticians such as Philip Hougaard, John Hinde, Il Do Ha, Roger Payne and Alessandra Durio, among others, as well as promising newcomers. Some of the contributions have come from researchers working in the BIO-SI research programme on Biostatistics and Bioinformatics, centred on the Universities of Limerick and Galway in Ireland and fu...

  8. Data Mining for Grammatical Inference with Bioinformatics Criteria

    Science.gov (United States)

    López, Vivian F.; Aguilar, Ramiro; Alonso, Luis; Moreno, María N.; Corchado, Juan M.

    In this paper we describe both theoretical and practical results of a novel data mining process that combines hybrid techniques of association analysis and classical sequentiation algorithms of genomics to generate grammatical structures of a specific language. We used an application of a compilers generator system that allows the development of a practical application within the area of grammarware, where the concepts of the language analysis are applied to other disciplines, such as Bioinformatic. The tool allows the complexity of the obtained grammar to be measured automatically from textual data. A technique of incremental discovery of sequential patterns is presented to obtain simplified production rules, and compacted with bioinformatics criteria to make up a grammar.

  9. 2nd Colombian Congress on Computational Biology and Bioinformatics

    CERN Document Server

    Cristancho, Marco; Isaza, Gustavo; Pinzón, Andrés; Rodríguez, Juan

    2014-01-01

    This volume compiles accepted contributions for the 2nd Edition of the Colombian Computational Biology and Bioinformatics Congress CCBCOL, after a rigorous review process in which 54 papers were accepted for publication from 119 submitted contributions. Bioinformatics and Computational Biology are areas of knowledge that have emerged due to advances that have taken place in the Biological Sciences and its integration with Information Sciences. The expansion of projects involving the study of genomes has led the way in the production of vast amounts of sequence data which needs to be organized, analyzed and stored to understand phenomena associated with living organisms related to their evolution, behavior in different ecosystems, and the development of applications that can be derived from this analysis.  .

  10. Bioinformatics data distribution and integration via Web Services and XML.

    Science.gov (United States)

    Li, Xiao; Zhang, Yizheng

    2003-11-01

    It is widely recognized that exchange, distribution, and integration of biological data are the keys to improve bioinformatics and genome biology in post-genomic era. However, the problem of exchanging and integrating biology data is not solved satisfactorily. The eXtensible Markup Language (XML) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the World Wide Web (WWW). Web service is the next generation of WWW and is founded upon the open standards of W3C (World Wide Web Consortium) and IETF (Internet Engineering Task Force). This paper presents XML and Web Services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration.

  11. Architecture exploration of FPGA based accelerators for bioinformatics applications

    CERN Document Server

    Varma, B Sharat Chandra; Balakrishnan, M

    2016-01-01

    This book presents an evaluation methodology to design future FPGA fabrics incorporating hard embedded blocks (HEBs) to accelerate applications. This methodology will be useful for selection of blocks to be embedded into the fabric and for evaluating the performance gain that can be achieved by such an embedding. The authors illustrate the use of their methodology by studying the impact of HEBs on two important bioinformatics applications: protein docking and genome assembly. The book also explains how the respective HEBs are designed and how hardware implementation of the application is done using these HEBs. It shows that significant speedups can be achieved over pure software implementations by using such FPGA-based accelerators. The methodology presented in this book may also be used for designing HEBs for accelerating software implementations in other domains besides bioinformatics. This book will prove useful to students, researchers, and practicing engineers alike.

  12. Personalized medicine: challenges and opportunities for translational bioinformatics.

    Science.gov (United States)

    Overby, Casey Lynnette; Tarczy-Hornoch, Peter

    2013-07-01

    Personalized medicine can be defined broadly as a model of healthcare that is predictive, personalized, preventive and participatory. Two US President's Council of Advisors on Science and Technology reports illustrate challenges in personalized medicine (in a 2008 report) and in use of health information technology (in a 2010 report). Translational bioinformatics is a field that can help address these challenges and is defined by the American Medical Informatics Association as "the development of storage, analytic and interpretive methods to optimize the transformation of increasing voluminous biomedical data into proactive, predictive, preventative and participatory health." This article discusses barriers to implementing genomics applications and current progress toward overcoming barriers, describes lessons learned from early experiences of institutions engaged in personalized medicine and provides example areas for translational bioinformatics research inquiry.

  13. Bioinformatics meets user-centred design: a perspective.

    Directory of Open Access Journals (Sweden)

    Katrina Pavelin

    Full Text Available Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI, and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.

  14. Molecular Detection and Identification of Spotted Fever Group Rickettsiae in Ticks Collected from the West Bank, Palestinian Territories.

    Directory of Open Access Journals (Sweden)

    Suheir Ereqat

    2016-01-01

    Full Text Available Tick-borne rickettsioses are caused by obligate intracellular bacteria belonging to the spotted fever group (SFG rickettsiae. Although Spotted Fever is prevalent in the Middle East, no reports for the presence of tick-borne pathogens are available or any studies on the epidemiology of this disease in the West Bank. We aimed to identify the circulating hard tick vectors and genetically characterize SFG Rickettsia species in ixodid ticks from the West Bank-Palestinian territories.A total of 1,123 ixodid ticks belonging to eight species (Haemaphysalis parva, Haemaphysalis adleri, Rhipicephalus turanicus, Rhipicephalus sanguineus, Rhipicephalus bursa, Hyalomma dromedarii, Hyalomma aegyptium and Hyalomma impeltatum were collected from goats, sheep, camels, dogs, a wolf, a horse and a tortoise in different localities throughout the West Bank during the period of January-April, 2014. A total of 867 ticks were screened for the presence of rickettsiae by PCR targeting a partial sequence of the ompA gene followed by sequence analysis. Two additional genes, 17 kDa and 16SrRNA were also targeted for further characterization of the detected Rickettsia species. Rickettsial DNA was detected in 148 out of the 867 (17% tested ticks. The infection rates in Rh. turanicus, Rh. sanguineus, H. adleri, H. parva, H. dromedarii, and H. impeltatum ticks were 41.7, 11.6, 16.7, 16.2, 11.8 and 20%, respectively. None of the ticks, belonging to the species Rh. bursa and H. aegyptium, were infected. Four SFG rickettsiae were identified: Rickettsia massiliae, Rickettsia africae, Candidatus Rickettsia barbariae and Candidatus Rickettsia goldwasserii.The results of this study demonstrate the geographic distribution of SFG rickettsiae and clearly indicate the presence of at least four of them in collected ticks. Palestinian clinicians should be aware of emerging tick-borne diseases in the West Bank, particularly infections due to R. massiliae and R. africae.

  15. [Consensus on the detection and management of prediabetes. Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society].

    Science.gov (United States)

    Mata-Cases, M; Artola, S; Escalada, J; Ezkurra-Loyola, P; Ferrer-García, J C; Fornos, J A; Girbés, J; Rica, I

    2015-01-01

    In Spain, according to the Di@bet.es study, 13.8% of the adult population suffers from diabetes and 14.8% from some form of prediabetes (impaired glucose tolerance, impaired fasting glucose or both). Since early detection of prediabetes can facilitate the implementation of therapeutic measures to prevent its progression to diabetes, we believe that preventive strategies in primary care and specialized clinical settings should be agreed. Screening for diabetes and prediabetes using a specific questionnaire (FINDRISC) and/or the measurement of fasting plasma glucose in high risk patients leads to detecting patients at risk of developing diabetes and it is necessary to consider how they should be managed. The intervention in lifestyle can reduce the progression to diabetes and reverse a prediabetic state to normal and is a cost-effective intervention. Some drugs, such as metformin, have also been shown effective in reducing the progression to diabetes but are not superior to non-pharmacological interventions. Finally, an improvement in some cardiovascular risk factors has been observed although there is no strong evidence supporting the effectiveness of screening in terms of morbility and mortality. The Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society has issued some recommendations that have been agreed by the Sociedad Española de Endocrinología y Nutrición, Sociedad Española de Endocrinología Pediátrica, Sociedad Española de Farmacia Comunitaria, Sociedad Española de Medicina Familiar y Comunitaria, Sociedad Española de Médicos Generales, Sociedad Española de Médicos de Atención Primaria, Sociedad Española de Medicina Interna, Asociación de Enfermería Comunitaria and Red de Grupos de Estudio de la Diabetes en Atención Primaria. Copyright © 2015. Publicado por Elsevier España, S.L.U.

  16. Consensus on the detection and management of prediabetes. Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society.

    Science.gov (United States)

    Mata-Cases, M; Artola, S; Escalada, J; Ezkurra-Loyola, P; Ferrer-García, J C; Fornos, J A; Girbés, J; Rica, I

    2015-03-01

    In Spain, according to the Di@bet.es study, 13.8% of the adult population suffers from diabetes and 14.8% from some form of prediabetes (impaired glucose tolerance, impaired fasting glucose or both). Since early detection of prediabetes can facilitate the implementation of therapeutic measures to prevent its progression to diabetes, we believe that preventive strategies in primary care and specialized clinical settings should be agreed. Screening for diabetes and prediabetes using a specific questionnaire (FINDRISC) and/or the measurement of fasting plasma glucose in high risk patients leads to detecting patients at risk of developing diabetes and it is necessary to consider how they should be managed. The intervention in lifestyle can reduce the progression to diabetes and reverse a prediabetic state to normal and is a cost-effective intervention. Some drugs, such as metformin, have also been shown effective in reducing the progression to diabetes but are not superior to non-pharmacological interventions. Finally, an improvement in some cardiovascular risk factors has been observed although there is no strong evidence supporting the effectiveness of screening in terms of morbility and mortality. The Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society has issued some recommendations that have been agreed by the Sociedad Española de Endocrinología y Nutrición, Sociedad Española de Endocrinología Pediátrica, Sociedad Española de Farmacia Comunitaria, Sociedad Española de Medicina Familiar y Comunitaria, Sociedad Española de Médicos Generales, Sociedad Española de Médicos de Atención Primaria, Sociedad Española de Medicina Interna, Asociación de Enfermería Comunitaria and Red de Grupos de Estudio de la Diabetes en Atención Primaria. Copyright © 2014 Elsevier España, S.L.U. All rights reserved.

  17. Peptide-Recombinant VP6 Protein Based Enzyme Immunoassay for the Detection of Group A Rotaviruses in Multiple Host Species.

    Directory of Open Access Journals (Sweden)

    Naveen Kumar

    Full Text Available We developed a novel enzyme immunoassay for the detection of group A rotavirus (RVA antigen in fecal samples of multiple host species. The assay is based on the detection of conserved VP6 protein using anti-recombinant VP6 antibodies as capture antibodies and anti-multiple antigenic peptide (identified and constructed from highly immunodominant epitopes within VP6 protein antibodies as detector antibodies. The clinical utility of the assay was evaluated using a panel of 914 diarrhoeic fecal samples from four different host species (bovine, porcine, poultry and human collected from diverse geographical locations in India. Using VP6- based reverse transcription-polymerase chain reaction (RT-PCR as the gold standard, we found that the diagnostic sensitivity (DSn and specificity (DSp of the new assay was high [bovine (DSn = 94.2% & DSp = 100%; porcine (DSn = 94.6% & DSp = 93.3%; poultry (DSn = 74.2% & DSp = 97.7% and human (DSn = 82.1% & DSp = 98.7%]. The concordance with RT-PCR was also high [weighted kappa (k = 0.831-0.956 at 95% CI = 0.711-1.0] as compared to RNA-polyacrylamide gel electrophoresis (RNA-PAGE. The performance characteristics of the new immunoassay were comparable to those of the two commercially available ELISA kits. Our results suggest that this peptide-recombinant protein based assay may serve as a preliminary assay for epidemiological surveillance of RVA antigen and for evaluation of vaccine effectiveness especially in low and middle income settings.

  18. G-DOC Plus - an integrative bioinformatics platform for precision medicine.

    Science.gov (United States)

    Bhuvaneshwar, Krithika; Belouali, Anas; Singh, Varun; Johnson, Robert M; Song, Lei; Alaoui, Adil; Harris, Michael A; Clarke, Robert; Weiner, Louis M; Gusev, Yuriy; Madhavan, Subha

    2016-04-30

    G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information. G-DOC Plus currently holds data from over 10,000 patients selected from private and public resources including Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and the recently added datasets from REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT), caArray studies of lung and colon cancer, ImmPort and the 1000 genomes data sets. The system allows researchers to explore clinical-omic data one sample at a time, as a cohort of samples; or at the level of population, providing the user with a comprehensive view of the data. G-DOC Plus tools have been leveraged in cancer and non-cancer studies for hypothesis generation and validation; biomarker discovery and multi-omics analysis, to explore somatic mutations and cancer MRI images; as well as for training and graduate education in bioinformatics, data and computational sciences. Several of these use cases are described in this paper to demonstrate its multifaceted usability. G-DOC Plus can be used to support a variety of user groups in multiple domains to enable hypothesis generation for precision medicine research. The long-term vision of G-DOC Plus is to extend this translational bioinformatics platform to stay current with emerging omics technologies and analysis methods to continue supporting novel hypothesis generation, analysis and validation for integrative biomedical research. By integrating several aspects of the disease and exposing various data elements, such as outpatient lab workup, pathology, radiology, current treatments, molecular signatures and expected outcomes over a web interface, G-DOC Plus will continue to strengthen precision medicine research. G-DOC Plus is available

  19. mORCA: sailing bioinformatics world with mobile devices.

    Science.gov (United States)

    Díaz-Del-Pino, Sergio; Falgueras, Juan; Perez-Wohlfeil, Esteban; Trelles, Oswaldo

    2018-03-01

    Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web-based world and that mobile devices are endowed with web-browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Throughout an in-depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy-to-use web-based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the service's metadata stored in catalogs or repositories. mORCA is available at http://bitlab-es.com/morca/app as a web-app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. ortrelles@uma.es. Source code, final web-app, training material and documentation is available at http://bitlab-es.com/morca. © The Author(s) 2017. Published by Oxford University Press.

  20. KBWS: an EMBOSS associated package for accessing bioinformatics web services

    Directory of Open Access Journals (Sweden)

    Tomita Masaru

    2011-04-01

    Full Text Available Abstract The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS, adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded and http://soap.g-language.org/kbws_dl.wsdl (Document/literal.

  1. A comparison of common programming languages used in bioinformatics.

    Science.gov (United States)

    Fourment, Mathieu; Gillings, Michael R

    2008-02-05

    The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from http://www.bioinformatics.org/benchmark/. This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

  2. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    Via, Allegra

    2013-06-25

    The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

  3. [Bioinformatic analysis of adenoma-normal mucosa SSH library of colon].

    Science.gov (United States)

    Lü, Bing-Jian; Cui, Jing; Xu, Jing; Zhang, Hao; Luo, Min-Jie; Zhu, Yi-Min; Lai, Mao-De

    2006-04-01

    We established a colonic adenoma-normal mucosa suppressive subtraction hybridization (SSH) library in 1999. In this study, we wanted to explore the expression profile of all candidate genes in this library. We developed an EST pipeline which contained two in-house software packages, nucleic acid analytical software and GetUni. The nucleic acid analytical software, an integrator of the universal bioinformatics tools including phred, phd2fasta, cross_match, repeatmasker and blast2.0, can blast sequences of differential clones with the downloaded non-redundant nucleotide (NR) database. GetUni can cluster these NR sequences into Unigene via matching with the downloaded Homo Sapiens UniGene database. Sixty-two candidate genes in A-N library were obtained via the high throughput automatic gene expression bioinformatics pipeline. Gene Ontology online analysis revealed that ribosome genes and immunity-regulating genes were the two most common categories in the KEGG or Biocarta Pathway. We also detected the expression of 2 genes with highest hits, Reg4 and FAM46A, by semi-quantitative RT-PCR. Both genes were up-regulated in 10 or 9 out of 10 adenomas in comparison with the paired normal mucosa, respectively. The candidate genes in A-N library would be of great significance in disclosing the molecular mechanism underlying in colonic adenoma initiation and progression.

  4. Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.

    Science.gov (United States)

    Jongeneel, C Victor; Achinike-Oduaran, Ovokeraye; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Akanle, Bola; Aron, Shaun; Ashano, Efejiro; Bendou, Hocine; Botha, Gerrit; Chimusa, Emile; Choudhury, Ananyo; Donthu, Ravikiran; Drnevich, Jenny; Falola, Oluwadamila; Fields, Christopher J; Hazelhurst, Scott; Hendry, Liesl; Isewon, Itunuoluwa; Khetani, Radhika S; Kumuthini, Judit; Kimuda, Magambo Phillip; Magosi, Lerato; Mainzer, Liudmila Sergeevna; Maslamoney, Suresh; Mbiyavanga, Mamana; Meintjes, Ayton; Mugutso, Danny; Mpangase, Phelelani; Munthali, Richard; Nembaware, Victoria; Ndhlovu, Andrew; Odia, Trust; Okafor, Adaobi; Oladipo, Olaleye; Panji, Sumir; Pillay, Venesa; Rendon, Gloria; Sengupta, Dhriti; Mulder, Nicola

    2017-06-01

    The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so.

  5. Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.

    Directory of Open Access Journals (Sweden)

    C Victor Jongeneel

    2017-06-01

    Full Text Available The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so.

  6. Can high-performance liquid chromatography coupled with fluorescence detection under all conditions be regarded as a sufficiently conclusive confirmatory method for B-group substances?

    NARCIS (Netherlands)

    Zuidema, T.; Mulder, P.P.J.; Lasaroms, J.J.P.; Stappers, S.J.W.; Rhijn, van J.A.

    2006-01-01

    Commission Decision 2002/657/EC requires confirmatory analysis of B-group compounds when detected at levels above the permitted limit. In contrast to banned substances, for B-group substances, the use of mass spectrometric techniques is not obligatory and several techniques including liquid

  7. XCluSim: a visual analytics tool for interactively comparing multiple clustering results of bioinformatics data

    Science.gov (United States)

    2015-01-01

    Background Though cluster analysis has become a routine analytic task for bioinformatics research, it is still arduous for researchers to assess the quality of a clustering result. To select the best clustering method and its parameters for a dataset, researchers have to run multiple clustering algorithms and compare them. However, such a comparison task with multiple clustering results is cognitively demanding and laborious. Results In this paper, we present XCluSim, a visual analytics tool that enables users to interactively compare multiple clustering results based on the Visual Information Seeking Mantra. We build a taxonomy for categorizing existing techniques of clustering results visualization in terms of the Gestalt principles of grouping. Using the taxonomy, we choose the most appropriate interactive visualizations for presenting individual clustering results from different types of clustering algorithms. The efficacy of XCluSim is shown through case studies with a bioinformatician. Conclusions Compared to other relevant tools, XCluSim enables users to compare multiple clustering results in a more scalable manner. Moreover, XCluSim supports diverse clustering algorithms and dedicated visualizations and interactions for different types of clustering results, allowing more effective exploration of details on demand. Through case studies with a bioinformatics researcher, we received positive feedback on the functionalities of XCluSim, including its ability to help identify stably clustered items across multiple clustering results. PMID:26328893

  8. The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

    Directory of Open Access Journals (Sweden)

    Tilmann Weber

    2016-06-01

    Full Text Available Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work. In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http://www.secondarymetabolites.org is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.

  9. Bioinformatics in microbial biotechnology – a mini review

    Directory of Open Access Journals (Sweden)

    Bansal Arvind K

    2005-06-01

    Full Text Available Abstract The revolutionary growth in the computation speed and memory storage capability has fueled a new era in the analysis of biological data. Hundreds of microbial genomes and many eukaryotic genomes including a cleaner draft of human genome have been sequenced raising the expectation of better control of microorganisms. The goals are as lofty as the development of rational drugs and antimicrobial agents, development of new enhanced bacterial strains for bioremediation and pollution control, development of better and easy to administer vaccines, the development of protein biomarkers for various bacterial diseases, and better understanding of host-bacteria interaction to prevent bacterial infections. In the last decade the development of many new bioinformatics techniques and integrated databases has facilitated the realization of these goals. Current research in bioinformatics can be classified into: (i genomics – sequencing and comparative study of genomes to identify gene and genome functionality, (ii proteomics – identification and characterization of protein related properties and reconstruction of metabolic and regulatory pathways, (iii cell visualization and simulation to study and model cell behavior, and (iv application to the development of drugs and anti-microbial agents. In this article, we will focus on the techniques and their limitations in genomics and proteomics. Bioinformatics research can be classified under three major approaches: (1 analysis based upon the available experimental wet-lab data, (2 the use of mathematical modeling to derive new information, and (3 an integrated approach that integrates search techniques with mathematical modeling. The major impact of bioinformatics research has been to automate the genome sequencing, automated development of integrated genomics and proteomics databases, automated genome comparisons to identify the genome function, automated derivation of metabolic pathways, gene

  10. SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines.

    Science.gov (United States)

    Audoux, Jérôme; Salson, Mikaël; Grosset, Christophe F; Beaumeunier, Sacha; Holder, Jean-Marc; Commes, Thérèse; Philippe, Nicolas

    2017-09-29

    for comparing the performance of RNA-Seq bioinformatics pipelines in addressing a specific biological question. We would like to see the creation of a reference corpus of data-sets that would allow accurate comparison between benchmarks performed by different groups and the publication of more benchmarks based on this public corpus. SimBA software and data-set are available at http://cractools.gforge.inria.fr/softwares/simba/ .

  11. Video Bioinformatics Analysis of Human Embryonic Stem Cell Colony Growth

    Science.gov (United States)

    Lin, Sabrina; Fonteno, Shawn; Satish, Shruthi; Bhanu, Bir; Talbot, Prue

    2010-01-01

    Because video data are complex and are comprised of many images, mining information from video material is difficult to do without the aid of computer software. Video bioinformatics is a powerful quantitative approach for extracting spatio-temporal data from video images using computer software to perform dating mining and analysis. In this article, we introduce a video bioinformatics method for quantifying the growth of human embryonic stem cells (hESC) by analyzing time-lapse videos collected in a Nikon BioStation CT incubator equipped with a camera for video imaging. In our experiments, hESC colonies that were attached to Matrigel were filmed for 48 hours in the BioStation CT. To determine the rate of growth of these colonies, recipes were developed using CL-Quant software which enables users to extract various types of data from video images. To accurately evaluate colony growth, three recipes were created. The first segmented the image into the colony and background, the second enhanced the image to define colonies throughout the video sequence accurately, and the third measured the number of pixels in the colony over time. The three recipes were run in sequence on video data collected in a BioStation CT to analyze the rate of growth of individual hESC colonies over 48 hours. To verify the truthfulness of the CL-Quant recipes, the same data were analyzed manually using Adobe Photoshop software. When the data obtained using the CL-Quant recipes and Photoshop were compared, results were virtually identical, indicating the CL-Quant recipes were truthful. The method described here could be applied to any video data to measure growth rates of hESC or other cells that grow in colonies. In addition, other video bioinformatics recipes can be developed in the future for other cell processes such as migration, apoptosis, and cell adhesion. PMID:20495527

  12. Detecting concealed information from groups using a dynamic questioning approach: simultaneous skin conductance measurement and immediate feedback

    NARCIS (Netherlands)

    Meijer, E.H.; Bente, G.; Ben-Shakhar, G.; Schumacher, A.

    2013-01-01

    Lie detection procedures typically aim at determining the guilt or innocence of a single suspect. The Concealed Information Test (CIT), for example, has been shown to be highly successful in detecting the presence or absence of crime-related information in a suspect's memory. Many of today's

  13. WU-Blast2 server at the European Bioinformatics Institute

    Science.gov (United States)

    Lopez, Rodrigo; Silventoinen, Ville; Robinson, Stephen; Kibria, Asif; Gish, Warren

    2003-01-01

    Since 1995, the WU-BLAST programs (http://blast.wustl.edu) have provided a fast, flexible and reliable method for similarity searching of biological sequence databases. The software is in use at many locales and web sites. The European Bioinformatics Institute's WU-Blast2 (http://www.ebi.ac.uk/blast2/) server has been providing free access to these search services since 1997 and today supports many features that both enhance the usability and expand on the scope of the software. PMID:12824421

  14. Multilevel Cellular Automata as a Tool for Studying Bioinformatic Processes

    Science.gov (United States)

    Hogeweg, Paulien

    The signature feature of Cellular Automata is the realization that "simple rules can give rise to complex behavior". In particular how fixed "rock-bottom" simple rules can give rise to multiple levels of organization. Here we describe Multilevel Cellular Automata, in which the microscopic entities (states) and their transition rules themselves are adjusted by the mesoscale patterns that they themselves generate. Thus we study the feedback of higher levels of organization on the lower levels. Such an approach is preeminently important for studying bioinformatic systems. We will here focus on an evolutionary approach to formalize such Multilevel Cellular Automata, and review examples of studies that use them.

  15. Bioinformatics Methods and Tools to Advance Clinical Care. Findings from the Yearbook 2015 Section on Bioinformatics and Translational Informatics.

    Science.gov (United States)

    Soualmia, L F; Lecroq, T

    2015-08-13

    To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and

  16. Protecting innovation in bioinformatics and in-silico biology.

    Science.gov (United States)

    Harrison, Robert

    2003-01-01

    Commercial success or failure of innovation in bioinformatics and in-silico biology requires the appropriate use of legal tools for protecting and exploiting intellectual property. These tools include patents, copyrights, trademarks, design rights, and limiting information in the form of 'trade secrets'. Potentially patentable components of bioinformatics programmes include lines of code, algorithms, data content, data structure and user interfaces. In both the US and the European Union, copyright protection is granted for software as a literary work, and most other major industrial countries have adopted similar rules. Nonetheless, the grant of software patents remains controversial and is being challenged in some countries. Current debate extends to aspects such as whether patents can claim not only the apparatus and methods but also the data signals and/or products, such as a CD-ROM, on which the programme is stored. The patentability of substances discovered using in-silico methods is a separate debate that is unlikely to be resolved in the near future.

  17. A review of bioinformatic methods for forensic DNA analyses.

    Science.gov (United States)

    Liu, Yao-Yuan; Harbison, SallyAnn

    2018-03-01

    Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. MOWServ: a web client for integration of bioinformatic resources

    Science.gov (United States)

    Ramírez, Sergio; Muñoz-Mérida, Antonio; Karlsson, Johan; García, Maximiliano; Pérez-Pulido, Antonio J.; Claros, M. Gonzalo; Trelles, Oswaldo

    2010-01-01

    The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user’s tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/. PMID:20525794

  19. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Fabrizio Fierro

    2017-09-01

    Full Text Available Human G-protein coupled receptors (hGPCRs constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation.

  20. Bioinformatic prediction and functional characterization of human KIAA0100 gene

    Directory of Open Access Journals (Sweden)

    He Cui

    2017-02-01

    Full Text Available Our previous study demonstrated that human KIAA0100 gene was a novel acute monocytic leukemia-associated antigen (MLAA gene. But the functional characterization of human KIAA0100 gene has remained unknown to date. Here, firstly, bioinformatic prediction of human KIAA0100 gene was carried out using online softwares; Secondly, Human KIAA0100 gene expression was downregulated by the clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated (Cas 9 system in U937 cells. Cell proliferation and apoptosis were next evaluated in KIAA0100-knockdown U937 cells. The bioinformatic prediction showed that human KIAA0100 gene was located on 17q11.2, and human KIAA0100 protein was located in the secretory pathway. Besides, human KIAA0100 protein contained a signalpeptide, a transmembrane region, three types of secondary structures (alpha helix, extended strand, and random coil , and four domains from mitochondrial protein 27 (FMP27. The observation on functional characterization of human KIAA0100 gene revealed that its downregulation inhibited cell proliferation, and promoted cell apoptosis in U937 cells. To summarize, these results suggest human KIAA0100 gene possibly comes within mitochondrial genome; moreover, it is a novel anti-apoptotic factor related to carcinogenesis or progression in acute monocytic leukemia, and may be a potential target for immunotherapy against acute monocytic leukemia.

  1. Targeting folate metabolism for therapeutic option: A bioinformatics approach.

    Science.gov (United States)

    Hande, Sneha; Goswami, Kalyan; Sharma, Richa; Bhoj, Priyanka; Jena, Lingaraj; Reddy, Maryada Venkata Rami

    2015-11-01

    Lymphatic filariasis, commonly called elephantiasis, poses a burden of estimated level of 5.09 million disability adjusted life year. Limitations of its sole drug, diethylcarbamazine (DEC) drive exploration of effective filarial target. A few plant extracts having polyphenolic ingredients and some synthetic compounds possess potential dihydrofolate reductase (DHFR) inhibitory effect. Here, we postulated a plausible link between folates and polyphenolics based on their common precursor in shikimate metabolism. Considering its implication in structural resemblance based antagonism, we have attempted to validate parasitic DHFR protein as a target. The bioinformatics approach, in the absence of crystal structure of the proposed target, used to authenticate and for virtual docking with suitable tested compounds, showed remarkably lower thermodynamic parameters as opposed to the positive control. A comparative docking analysis between human and Brugia malayi DHFR also showed effective binding parameters with lower inhibition constants of these ligands with parasitic target, but not with human counterpart highlighting safety and efficacy. This study suggests that DHFR could be a valid drug target for lymphatic filariasis, and further reveal that bioinformatics may be an effective tool in reverse pharmacological approach for drug design.

  2. MAPI: towards the integrated exploitation of bioinformatics Web Services

    Directory of Open Access Journals (Sweden)

    Karlsson Johan

    2011-10-01

    Full Text Available Abstract Background Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. Results To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. Conclusions The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others.

  3. Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.

    Science.gov (United States)

    Pauling, Josch; Klipp, Edda

    2016-12-22

    Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries. The computational biology and bioinformatics community has so far established methodology in genomics, transcriptomics and proteomics but there are many (combinatorial) challenges when it comes to structural diversity of lipids and their identification, quantification and interpretation. This review gives an overview and outlook on lipidomics research and illustrates ongoing computational and bioinformatics efforts. These efforts are important and necessary steps to advance the lipidomics field alongside analytic, biochemistry, biomedical and biology communities and to close the gap in available computational methodology between lipidomics and other omics sub-branches.

  4. Bioinformatics analysis of the predicted polyprenol reductase genes in higher plants

    Science.gov (United States)

    Basyuni, M.; Wati, R.

    2018-03-01

    The present study evaluates the bioinformatics methods to analyze twenty-four predicted polyprenol reductase genes from higher plants on GenBank as well as predicted the structure, composition, similarity, subcellular localization, and phylogenetic. The physicochemical properties of plant polyprenol showed diversity among the observed genes. The percentage of the secondary structure of plant polyprenol genes followed the ratio order of α helix > random coil > extended chain structure. The values of chloroplast but not signal peptide were too low, indicated that few chloroplast transit peptide in plant polyprenol reductase genes. The possibility of the potential transit peptide showed variation among the plant polyprenol reductase, suggested the importance of understanding the variety of peptide components of plant polyprenol genes. To clarify this finding, a phylogenetic tree was drawn. The phylogenetic tree shows several branches in the tree, suggested that plant polyprenol reductase genes grouped into divergent clusters in the tree.

  5. Performance Analysis of Hierarchical Group Key Management Integrated with Adaptive Intrusion Detection in Mobile ad hoc Networks

    Science.gov (United States)

    2016-04-05

    leader and all leaders in the system share a leader secret key ( KRL ) for efficiency purposes. In summary, there are three keys for hierarchical group...keymanagement: leader key ( KRL ), regional key (KR), and group key (KG). These keys are rekeyedproperly, in part or in whole, as events happen in the...each partitioned group will execute GDH to agree on a new leader key KRL . Groupmerge: Two groupsmaymerge into onewhen connectivity resumes. A

  6. The Bioinformatics of Integrative Medical Insights: Proposals for an International Psycho-Social and Cultural Bioinformatics Project

    Directory of Open Access Journals (Sweden)

    Ernest Rossi

    2006-01-01

    Full Text Available We propose the formation of an International Psycho-Social and Cultural Bioinformatics Project (IPCBP to explore the research foundations of Integrative Medical Insights (IMI on all levels from the molecular-genomic to the psychological, cultural, social, and spiritual. Just as The Human Genome Project identified the molecular foundations of modern medicine with the new technology of sequencing DNA during the past decade, the IPCBP would extend and integrate this neuroscience knowledge base with the technology of gene expression via DNA/proteomic microarray research and brain imaging in development, stress, healing, rehabilitation, and the psychotherapeutic facilitation of existentional wellness. We anticipate that the IPCBP will require a unique international collaboration of, academic institutions, researchers, and clinical practioners for the creation of a new neuroscience of mind-body communication, brain plasticity, memory, learning, and creative processing during optimal experiential states of art, beauty, and truth. We illustrate this emerging integration of bioinformatics with medicine with a videotape of the classical 4-stage creative process in a neuroscience approach to psychotherapy.

  7. The Bioinformatics of Integrative Medical Insights: Proposals for an International PsychoSocial and Cultural Bioinformatics Project

    Directory of Open Access Journals (Sweden)

    Ernest Rossi

    2006-01-01

    Full Text Available We propose the formation of an International PsychoSocial and Cultural Bioinformatics Project (IPCBP to explore the research foundations of Integrative Medical Insights (IMI on all levels from the molecular-genomic to the psychological, cultural, social, and spiritual. Just as The Human Genome Project identified the molecular foundations of modern medicine with the new technology of sequencing DNA during the past decade, the IPCBP would extend and integrate this neuroscience knowledge base with the technology of gene expression via DNA/proteomic microarray research and brain imaging in development, stress, healing, rehabilitation, and the psychotherapeutic facilitation of existentional wellness. We anticipate that the IPCBP will require a unique international collaboration of, academic institutions, researchers, and clinical practioners for the creation of a new neuroscience of mind-body communication, brain plasticity, memory, learning, and creative processing during optimal experiential states of art, beauty, and truth. We illustrate this emerging integration of bioinformatics with medicine with a videotape of the classical 4-stage creative process in a neuroscience approach to psychotherapy.

  8. Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Jin Hailing

    2009-04-01

    Full Text Available Abstract Background Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana. Results In the current work, we carried out a bioinformatics analysis of RNA base modifications in tRNAs and miRNAs using large numbers of cDNA sequences of small RNAs (sRNAs generated with the 454 technology and the massively parallel signature sequencing (MPSS method. We looked for sRNAs that map to the genome sequence with one-base mismatch (OMM, which indicate candidate modified nucleotides. We obtained 1,187 sites with possible RNA base modifications supported by both 454 and MPSS sequences. Seven hundred and three of these sites were within tRNA loci. Nucleotide substitutions were frequently located in the T arm (substitutions from A to U or G, upstream of the D arm (from G to C, U, or A, and downstream of the D arm (from G to U. The positions of major substitution sites corresponded with the following known RNA base modifications in tRNAs: N1-methyladenosine (m1A, N2-methylguanosine (m2G, and N2-N2-methylguanosine (m22G. Conclusion These results indicate that our bioinformatics method successfully detected modified nucleotides in tRNAs. Using this method, we also found 147 substitution sites in miRNA loci. As with tRNAs, substitutions from A to U or G and from G to C, U, or A were common, suggesting that base modifications might be similar in tRNAs and miRNAs. We suggest that miRNAs contain modified bases and such modifications might be important for miRNA maturation and/or function.

  9. Molucular gene profiling of Clostridium botulinum group III and their detection in naturally contaminated samples originating from various European countries

    NARCIS (Netherlands)

    Woudstra, C.; LeMarechal, C.; Souillard, R.; Bäyon-Auboyer, M.H.; Anniballi, F.; Auricchio, B.; Medici, De D.; Bano, L.; Koene, M.G.J.; Sansonetti, M.H.; Hansbauer, E.M.; Desoutter, D.; Dorner, M.B.; Fach, P.; Dorner, B.G.

    2015-01-01

    We report the development of real-time PCR assays for genotyping Clostridium botulinum group III targeting the newly defined C. novyi sensu lato group; the nontoxic nonhemagglutinin (NTNH)-encoding gene ntnh; the botulinum neurotoxin (BoNT)-encoding genes bont/C, bont/C/D, bont/D, and bont/D/C; and

  10. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.

    Science.gov (United States)

    He, Yongqun; Xiang, Zuoshuang

    2010-09-27

    Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis, one of the commonest zoonotic diseases found worldwide in humans and a variety of animal species. While several animal vaccines are available, there is no effective and safe vaccine for prevention of brucellosis in humans. VIOLIN (http://www.violinet.org) is a web-based vaccine database and analysis system that curates, stores, and analyzes published data of commercialized vaccines, and vaccines in clinical trials or in research. VIOLIN contains information for 454 vaccines or vaccine candidates for 73 pathogens. VIOLIN also contains many bioinformatics tools for vaccine data analysis, data integration, and vaccine target prediction. To demonstrate the applicability of VIOLIN for vaccine research, VIOLIN was used for bioinformatics analysis of existing Brucella vaccines and prediction of new Brucella vaccine targets. VIOLIN contains many literature mining programs (e.g., Vaxmesh) that provide in-depth analysis of Brucella vaccine literature. As a result of manual literature curation, VIOLIN contains information for 38 Brucella vaccines or vaccine candidates, 14 protective Brucella antigens, and 68 host response studies to Brucella vaccines from 97 peer-reviewed articles. These Brucella vaccines are classified in the Vaccine Ontology (VO) system and used for different ontological applications. The web-based VIOLIN vaccine target prediction program Vaxign was used to predict new Brucella vaccine targets. Vaxign identified 14 outer membrane proteins that are conserved in six virulent strains from B. abortus, B. melitensis, and B. suis that are pathogenic in humans. Of the 14 membrane proteins, two proteins (Omp2b and Omp31-1) are not present in B. ovis, a Brucella species that is not pathogenic in humans. Brucella vaccine data stored in VIOLIN were compared and analyzed using the VIOLIN query system. Bioinformatics curation and ontological representation of Brucella vaccines

  11. Atlas – a data warehouse for integrative bioinformatics

    Directory of Open Access Journals (Sweden)

    Yuen Macaire MS

    2005-02-01

    Full Text Available Abstract Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL calls that are implemented in a set of Application Programming Interfaces (APIs. The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD, Biomolecular Interaction Network Database (BIND, Database of Interacting Proteins (DIP, Molecular Interactions Database (MINT, IntAct, NCBI Taxonomy, Gene Ontology (GO, Online Mendelian Inheritance in Man (OMIM, LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First

  12. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN

    Science.gov (United States)

    2010-01-01

    Background Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis, one of the commonest zoonotic diseases found worldwide in humans and a variety of animal species. While several animal vaccines are available, there is no effective and safe vaccine for prevention of brucellosis in humans. VIOLIN (http://www.violinet.org) is a web-based vaccine database and analysis system that curates, stores, and analyzes published data of commercialized vaccines, and vaccines in clinical trials or in research. VIOLIN contains information for 454 vaccines or vaccine candidates for 73 pathogens. VIOLIN also contains many bioinformatics tools for vaccine data analysis, data integration, and vaccine target prediction. To demonstrate the applicability of VIOLIN for vaccine research, VIOLIN was used for bioinformatics analysis of existing Brucella vaccines and prediction of new Brucella vaccine targets. Results VIOLIN contains many literature mining programs (e.g., Vaxmesh) that provide in-depth analysis of Brucella vaccine literature. As a result of manual literature curation, VIOLIN contains information for 38 Brucella vaccines or vaccine candidates, 14 protective Brucella antigens, and 68 host response studies to Brucella vaccines from 97 peer-reviewed articles. These Brucella vaccines are classified in the Vaccine Ontology (VO) system and used for different ontological applications. The web-based VIOLIN vaccine target prediction program Vaxign was used to predict new Brucella vaccine targets. Vaxign identified 14 outer membrane proteins that are conserved in six virulent strains from B. abortus, B. melitensis, and B. suis that are pathogenic in humans. Of the 14 membrane proteins, two proteins (Omp2b and Omp31-1) are not present in B. ovis, a Brucella species that is not pathogenic in humans. Brucella vaccine data stored in VIOLIN were compared and analyzed using the VIOLIN query system. Conclusions Bioinformatics curation and ontological

  13. A group-specific, quantitative real-time PCR assay for detection of crab, a crustacean shellfish allergen, in complex food matrices.

    Science.gov (United States)

    Eischeid, Anne C; Stadig, Sarah R

    2018-04-01

    A real-time PCR assay was developed for detection of crab, a crustacean allergen, in food products. Group-specific primers and probes were developed to detect numerous species of crab. Method validation included tests of detection in complex food matrices, evaluation of commercial food products, and cross-reactivity testing on a wide variety of crustaceans. The method was able to detect several species of crab spiked into complex food matrices at levels ranging from 0.1 to 10 5 parts per million (weight/weight), worked equally well on different platforms, exhibited high specificity for crab over other types of crustaceans, and yielded much higher signals from commercial food products listing crab as an ingredient than from those containing other crustaceans. Published by Elsevier Ltd.

  14. Integration of bioinformatics into an undergraduate biology curriculum and the impact on development of mathematical skills.

    Science.gov (United States)

    Wightman, Bruce; Hark, Amy T

    2012-01-01

    The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this study, we deliberately integrated bioinformatics instruction at multiple course levels into an existing biology curriculum. Students in an introductory biology course, intermediate lab courses, and advanced project-oriented courses all participated in new course components designed to sequentially introduce bioinformatics skills and knowledge, as well as computational approaches that are common to many bioinformatics applications. In each course, bioinformatics learning was embedded in an existing disciplinary instructional sequence, as opposed to having a single course where all bioinformatics learning occurs. We designed direct and indirect assessment tools to follow student progress through the course sequence. Our data show significant gains in both student confidence and ability in bioinformatics during individual courses and as course level increases. Despite evidence of substantial student learning in both bioinformatics and mathematics, students were skeptical about the link between learning bioinformatics and learning mathematics. While our approach resulted in substantial learning gains, student "buy-in" and engagement might be better in longer project-based activities that demand application of skills to research problems. Nevertheless, in situations where a concentrated focus on project-oriented bioinformatics is not possible or desirable, our approach of integrating multiple smaller components into an existing curriculum provides an alternative. Copyright © 2012 Wiley Periodicals, Inc.

  15. Bioinformatics in the secondary science classroom: A study of state content standards and students' perceptions of, and performance in, bioinformatics lessons

    Science.gov (United States)

    Wefer, Stephen H.

    The proliferation of bioinformatics in modern Biology marks a new revolution in science, which promises to influence science education at all levels. This thesis examined state standards for content that articulated bioinformatics, and explored secondary students' affective and cognitive perceptions of, and performance in, a bioinformatics mini-unit. The results are presented as three studies. The first study analyzed secondary science standards of 49 U.S States (Iowa has no science framework) and the District of Columbia for content related to bioinformatics at the introductory high school biology level. The bionformatics content of each state's Biology standards were categorized into nine areas and the prevalence of each area documented. The nine areas were: The Human Genome Project, Forensics, Evolution, Classification, Nucleotide Variations, Medicine, Computer Use, Agriculture/Food Technology, and Science Technology and Society/Socioscientific Issues (STS/SSI). Findings indicated a generally low representation of bioinformatics related content, which varied substantially across the different areas. Recommendations are made for reworking existing standards to incorporate bioinformatics and to facilitate the goal of promoting science literacy in this emerging new field among secondary school students. The second study examined thirty-two students' affective responses to, and content mastery of, a two-week bioinformatics mini-unit. The findings indicate that the students generally were positive relative to their interest level, the usefulness of the lessons, the difficulty level of the lessons, likeliness to engage in additional bioinformatics, and were overall successful on the assessments. A discussion of the results and significance is followed by suggestions for future research and implementation for transferability. The third study presents a case study of individual differences among ten secondary school students, whose cognitive and affective percepts were

  16. Getting started with microbiome analysis: sample acquisition to bioinformatics.

    Science.gov (United States)

    Kumar, Ranjit; Eipers, Peter; Little, Rebecca B; Crowley, Michael; Crossman, David K; Lefkowitz, Elliot J; Morrow, Casey D

    2014-07-14

    Historically, in order to study microbes, it was necessary to grow them in the laboratory. It was clear though that many microbe communities were refractory to study because none of the members could be grown outside of their native habitat. The development of culture-independent methods to study microbiota using high-throughput sequencing of the 16S ribosomal RNA gene variable regions present in all prokaryotic organisms has provided new opportunities to investigate complex microbial communities. In this unit, the process for a microbiome analysis is described. Many of the components required for this process may already exist. A pipeline is described for acquisition of samples from different sites on the human body, isolation of microbial DNA, and DNA sequencing using the Illumina MiSeq sequencing platform. Finally, a new analytical workflow for basic bioinformatics data analysis, QWRAP, is described, which can be used by clinical and basic science investigators. Copyright © 2014 John Wiley & Sons, Inc.

  17. BioRuby: bioinformatics software for the Ruby programming language.

    Science.gov (United States)

    Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

    2010-10-15

    The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

  18. Bioinformatics and the Politics of Innovation in the Life Sciences

    Science.gov (United States)

    Zhou, Yinhua; Datta, Saheli; Salter, Charlotte

    2016-01-01

    The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation. PMID:27546935

  19. A bioinformatics roadmap for the human vaccines project.

    Science.gov (United States)

    Scheuermann, Richard H; Sinkovits, Robert S; Schenkelberg, Theodore; Koff, Wayne C

    2017-06-01

    Biomedical research has become a data intensive science in which high throughput experimentation is producing comprehensive data about biological systems at an ever-increasing pace. The Human Vaccines Project is a new public-private partnership, with the goal of accelerating development of improved vaccines and immunotherapies for global infectious diseases and cancers by decoding the human immune system. To achieve its mission, the Project is developing a Bioinformatics Hub as an open-source, multidisciplinary effort with the overarching goal of providing an enabling infrastructure to support the data processing, analysis and knowledge extraction procedures required to translate high throughput, high complexity human immunology research data into biomedical knowledge, to determine the core principles driving specific and durable protective immune responses.

  20. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal

    2012-07-28

    Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we introduce our Adaptive Hybrid Multiprocessor technique to accelerate the implementation of the Smith-Waterman algorithm. Our technique utilizes both the graphics processing unit (GPU) and the central processing unit (CPU). It adapts to the implementation according to the number of CPUs given as input by efficiently distributing the workload between the processing units. Using existing resources (GPU and CPU) in an efficient way is a novel approach. The peak performance achieved for the platforms GPU + CPU, GPU + 2CPUs, and GPU + 3CPUs is 10.4 GCUPS, 13.7 GCUPS, and 18.6 GCUPS, respectively (with the query length of 511 amino acid). © 2010 IEEE.

  1. Logical comparison over RDF resources in bio-informatics.

    Science.gov (United States)

    Colucci, S; Donini, F M; Di Sciascio, E

    2017-12-01

    Comparison of resources is a frequent task in different bio-informatics applications, including drug-target interaction, drug repositioning and mechanism of action understanding, among others. This paper proposes a general method for the logical comparison of resources modeled in Resource Description Framework and shows its distinguishing features with reference to the comparison of drugs. In particular, the method returns a description of the commonalities between resources, rather than a numerical value estimating their similarity and/or relatedness. The approach is domain-independent and may be flexibly adapted to heterogeneous use cases, according to a process for setting parameters which is completely explicit. The paper also presents an experiment using the dataset Bioportal as knowledge source; the experiment is fully reproducible, thanks to the elicitation of criteria and values for parameter customization. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. ISEV position paper: extracellular vesicle RNA analysis and bioinformatics

    Directory of Open Access Journals (Sweden)

    Andrew F. Hill

    2013-12-01

    Full Text Available Extracellular vesicles (EVs are the collective term for the various vesicles that are released by cells into the extracellular space. Such vesicles include exosomes and microvesicles, which vary by their size and/or protein and genetic cargo. With the discovery that EVs contain genetic material in the form of RNA (evRNA has come the increased interest in these vesicles for their potential use as sources of disease biomarkers and potential therapeutic agents. Rapid developments in the availability of deep sequencing technologies have enabled the study of EV-related RNA in detail. In October 2012, the International Society for Extracellular Vesicles (ISEV held a workshop on “evRNA analysis and bioinformatics.” Here, we report the conclusions of one of the roundtable discussions where we discussed evRNA analysis technologies and provide some guidelines to researchers in the field to consider when performing such analysis.

  3. Achievements and challenges in structural bioinformatics and computational biophysics.

    Science.gov (United States)

    Samish, Ilan; Bourne, Philip E; Najmanovich, Rafael J

    2015-01-01

    The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field. © The Author 2014. Published by Oxford University Press.

  4. Bioinformatics tools in predictive ecology: applications to fisheries

    Science.gov (United States)

    Tucker, Allan; Duplisea, Daniel

    2012-01-01

    There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their ‘crossover potential’ with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse. PMID:22144390

  5. Bioinformatics approaches to single-cell analysis in developmental biology.

    Science.gov (United States)

    Yalcin, Dicle; Hakguder, Zeynep M; Otu, Hasan H

    2016-03-01

    Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology. © The Author 2015. Published by Oxford University Press on behalf of the European

  6. Target-specific NMR detection of protein-ligand interactions with antibody-relayed 15N-group selective STD.

    Science.gov (United States)

    Hetényi, Anasztázia; Hegedűs, Zsófia; Fajka-Boja, Roberta; Monostori, Éva; Kövér, Katalin E; Martinek, Tamás A

    2016-12-01

    Fragment-based drug design has been successfully applied to challenging targets where the detection of the weak protein-ligand interactions is a key element. 1 H saturation transfer difference (STD) NMR spectroscopy is a powerful technique for this work but it requires pure homogeneous proteins as targets. Monoclonal antibody (mAb)-relayed 15 N-GS STD spectroscopy has been developed to resolve the problem of protein mixtures and impure proteins. A 15 N-labelled target-specific mAb is selectively irradiated and the saturation is relayed through the target to the ligand. Tests on the anti-Gal-1 mAb/Gal-1/lactose system showed that the approach is experimentally feasible in a reasonable time frame. This method allows detection and identification of binding molecules directly from a protein mixture in a multicomponent system.

  7. The Atacama Cosmology Telescope: Detection or Sunyaev-Zel'Dovich Decrement in Groups and Clusters Associated with Luminous Red Galaxies

    Science.gov (United States)

    Hand, Nick; Appel, John William; Battaglia, Nick; Bond, J. Richard; Das, Sudeep; Devlin, Mark J.; Dunkley, Joanna; Dunner, Rolando; Essinger-Hileman, Thomas; Fowler, Joseph W.; hide

    2010-01-01

    We present a detection of the Sunyaev-Zel'dovich (SZ) decrement associated with the Luminous Red Galaxy (LRG) sample of the Sloan Digital Sky Survey. The SZ data come from 148 GHz maps of the equatorial region made by the Atacama Cosmology Telescope (ACT). The LRG sample is divided by luminosity into four bins, and estimates for the central Sunyaev-Zel'dovich temperature decrement are calculated through a stacking process. We detect and account for a bias of the SZ signal due to weak radio sources. We use numerical simulations to relate the observed decrement to Y(sub 200) and clustering properties to relate the galaxy luminosity bins to mass. We also use a relation between BCG luminosity and cluster mass based on stacked gravitational lensing measurements to estimate the characteristic halo masses. The masses are found to be in the range approx.10(exp 13) - 10(exp 14)/h Stellar Mass, a lower range than has been previously probed.

  8. Detecting and accounting for multiple sources of positional variance in peak list registration analysis and spin system grouping.

    Science.gov (United States)

    Smelter, Andrey; Rouchka, Eric C; Moseley, Hunter N B

    2017-08-01

    Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include automated protein resonance assignment and protein structure calculation software tools. Prior to these analyses, peak lists must be aligned to each other and sets of related peaks must be grouped based on common chemical shift dimensions. Even when programs can perform peak grouping, they require the user to provide uniform match tolerances or use default values. However, peak grouping is further complicated by multiple sources of variance in peak position limiting the effectiveness of grouping methods that utilize uniform match tolerances. In addition, no method currently exists for deriving peak positional variances from single peak lists for grouping peaks into spin systems, i.e. spin system grouping within a single peak list. Therefore, we developed a complementary pair of peak list registration analysis and spin system grouping algorithms designed to overcome these limitations. We have implemented these algorithms into an approach that can identify multiple dimension-specific positional variances that exist in a single peak list and group peaks from a single peak list into spin systems. The resulting software tools generate a variety of useful statistics on both a single peak list and pairwise peak list alignment, especially for quality assessment of peak list datasets. We used a range of low and high quality experimental solution NMR and solid-state NMR peak lists to assess performance of our registration analysis and grouping algorithms. Analyses show that an algorithm using a single iteration and uniform match tolerances approach is only able to recover from 50 to 80% of the spin systems due to the presence of multiple sources of variance. Our algorithm recovers additional spin systems by reevaluating match tolerances in multiple iterations. To facilitate evaluation of the

  9. Detection of Mycobacterium chelonae, Mycobacterium abscessus Group, and Mycobacterium fortuitum Complex by a Multiplex Real-Time PCR Directly from Clinical Samples Using the BD MAX System.

    Science.gov (United States)

    Rocchetti, Talita T; Silbert, Suzane; Gostnell, Alicia; Kubasek, Carly; Campos Pignatari, Antonio C; Widen, Raymond

    2017-03-01

    A new multiplex PCR test was designed to detect Mycobacterium chelonae, Mycobacterium abscessus group, and Mycobacterium fortuitum complex on the BD MAX System. A total of 197 clinical samples previously submitted for mycobacterial culture were tested using the new protocol. Samples were first treated with proteinase K, and then each sample was inoculated into the BD MAX Sample Buffer Tube. Extraction and multiplex PCR were performed by the BD MAX System, using the BD MAX ExK TNA-3 extraction kit and BD TNA Master Mix, along with specific in-house designed primers and probes for each target. The limit of detection of each target, as well as specificity, was evaluated. Of 197 clinical samples included in this study, 133 were positive and 60 were negative for mycobacteria by culture, and another 4 negative samples were spiked with M. chelonae ATCC 35752. The new multiplex PCR on the BD MAX had 97% concordant results with culture for M. abscessus group detection, 99% for M. chelonae, and 100% for M. fortuitum complex. The new multiplex PCR test performed on the BD MAX System proved to be a sensitive and specific test to detect M. chelonae, M. abscessus group, and M. fortuitum complex by real-time PCR on an automated sample-in results-out platform. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  10. Exploring Cystic Fibrosis Using Bioinformatics Tools: A Module Designed for the Freshman Biology Course

    Science.gov (United States)

    Zhang, Xiaorong

    2011-01-01

    We incorporated a bioinformatics component into the freshman biology course that allows students to explore cystic fibrosis (CF), a common genetic disorder, using bioinformatics tools and skills. Students learn about CF through searching genetic databases, analyzing genetic sequences, and observing the three-dimensional structures of proteins…

  11. Comparative Proteome Bioinformatics: Identification of Phosphotyrosine Signaling Proteins in the Unicellular Protozoan Ciliate Tetrahymena

    DEFF Research Database (Denmark)

    Gammeltoft, Steen; Christensen, Søren Tvorup; Joachimiak, Marcin

    2005-01-01

    Tetrahymena, bioinformatics, cilia, evolution, signaling, TtPTK1, PTK, Grb2, SH-PTP 2, Plcy, Src, PTP, PI3K, SH2, SH3, PH......Tetrahymena, bioinformatics, cilia, evolution, signaling, TtPTK1, PTK, Grb2, SH-PTP 2, Plcy, Src, PTP, PI3K, SH2, SH3, PH...

  12. Bioinformatics Methods for Interpreting Toxicogenomics Data: The Role of Text-Mining

    NARCIS (Netherlands)

    Hettne, K.M.; Kleinjans, J.; Stierum, R.H.; Boorsma, A.; Kors, J.A.

    2014-01-01

    This chapter concerns the application of bioinformatics methods to the analysis of toxicogenomics data. The chapter starts with an introduction covering how bioinformatics has been applied in toxicogenomics data analysis, and continues with a description of the foundations of a specific

  13. Integration of Bioinformatics into an Undergraduate Biology Curriculum and the Impact on Development of Mathematical Skills

    Science.gov (United States)

    Wightman, Bruce; Hark, Amy T.

    2012-01-01

    The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this…

  14. A Summer Program Designed to Educate College Students for Careers in Bioinformatics

    Science.gov (United States)

    Krilowicz, Beverly; Johnston, Wendie; Sharp, Sandra B.; Warter-Perez, Nancy; Momand, Jamil

    2007-01-01

    A summer program was created for undergraduates and graduate students that teaches bioinformatics concepts, offers skills in professional development, and provides research opportunities in academic and industrial institutions. We estimate that 34 of 38 graduates (89%) are in a career trajectory that will use bioinformatics. Evidence from…

  15. Making Bioinformatics Projects a Meaningful Experience in an Undergraduate Biotechnology or Biomedical Science Programme

    Science.gov (United States)

    Sutcliffe, Iain C.; Cummings, Stephen P.

    2007-01-01

    Bioinformatics has emerged as an important discipline within the biological sciences that allows scientists to decipher and manage the vast quantities of data (such as genome sequences) that are now available. Consequently, there is an obvious need to provide graduates in biosciences with generic, transferable skills in bioinformatics. We present…

  16. A Portable Bioinformatics Course for Upper-Division Undergraduate Curriculum in Sciences

    Science.gov (United States)

    Floraino, Wely B.

    2008-01-01

    This article discusses the challenges that bioinformatics education is facing and describes a bioinformatics course that is successfully taught at the California State Polytechnic University, Pomona, to the fourth year undergraduate students in biological sciences, chemistry, and computer science. Information on lecture and computer practice…

  17. Influenza research database: an integrated bioinformatics resource for influenza virus research

    Science.gov (United States)

    The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics, an...

  18. Implementing a Web-Based Introductory Bioinformatics Course for Non-Bioinformaticians That Incorporates Practical Exercises

    Science.gov (United States)

    Vincent, Antony T.; Bourbonnais, Yves; Brouard, Jean-Simon; Deveau, Hélène; Droit, Arnaud; Gagné, Stéphane M.; Guertin, Michel; Lemieux, Claude; Rathier, Louis; Charette, Steve J.; Lagüe, Patrick

    2018-01-01

    A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become…

  19. Bioinformatics in Middle East Program Curricula--A Focus on the Arabian Gulf

    Science.gov (United States)

    Loucif, Samia

    2014-01-01

    The purpose of this paper is to investigate the inclusion of bioinformatics in program curricula in the Middle East, focusing on educational institutions in the Arabian Gulf. Bioinformatics is a multidisciplinary field which has emerged in response to the need for efficient data storage and retrieval, and accurate and fast computational and…

  20. Teaching Bioinformatics and Neuroinformatics by Using Free Web-Based Tools

    Science.gov (United States)

    Grisham, William; Schottler, Natalie A.; Valli-Marill, Joanne; Beck, Lisa; Beatty, Jackson

    2010-01-01

    This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with…

  1. Incorporating a Collaborative Web-Based Virtual Laboratory in an Undergraduate Bioinformatics Course

    Science.gov (United States)

    Weisman, David

    2010-01-01

    Face-to-face bioinformatics courses commonly include a weekly, in-person computer lab to facilitate active learning, reinforce conceptual material, and teach practical skills. Similarly, fully-online bioinformatics courses employ hands-on exercises to achieve these outcomes, although students typically perform this work offsite. Combining a…

  2. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

    Science.gov (United States)

    Likic, Vladimir A.

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  3. Bioinformatics in High School Biology Curricula: A Study of State Science Standards

    Science.gov (United States)

    Wefer, Stephen H.; Sheppard, Keith

    2008-01-01

    The proliferation of bioinformatics in modern biology marks a modern revolution in science that promises to influence science education at all levels. This study analyzed secondary school science standards of 49 U.S. states (Iowa has no science framework) and the District of Columbia for content related to bioinformatics. The bioinformatics…

  4. Green Fluorescent Protein-Focused Bioinformatics Laboratory Experiment Suitable for Undergraduates in Biochemistry Courses

    Science.gov (United States)

    Rowe, Laura

    2017-01-01

    An introductory bioinformatics laboratory experiment focused on protein analysis has been developed that is suitable for undergraduate students in introductory biochemistry courses. The laboratory experiment is designed to be potentially used as a "stand-alone" activity in which students are introduced to basic bioinformatics tools and…

  5. Visualizing and Sharing Results in Bioinformatics Projects: GBrowse and GenBank Exports

    Science.gov (United States)

    Effective tools for presenting and sharing data are necessary for collaborative projects, typical for bioinformatics. In order to facilitate sharing our data with other genomics, molecular biology, and bioinformatics researchers, we have developed software to export our data to GenBank and combined ...

  6. Bioinformatics goes to school--new avenues for teaching contemporary biology.

    Science.gov (United States)

    Wood, Louisa; Gebhardt, Philipp

    2013-01-01

    Since 2010, the European Molecular Biology Laboratory's (EMBL) Heidelberg laboratory and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training courses developed specifically for secondary school science teachers within Europe and EMBL member states. These courses focus on introducing bioinformatics, databases, and data-intensive biology, allowing participants to explore resources and providing classroom-ready materials to support them in sharing this new knowledge with their students. In this article, we chart our progress made in creating and running three bioinformatics training courses, including how the course resources are received by participants and how these, and bioinformatics in general, are subsequently used in the classroom. We assess the strengths and challenges of our approach, and share what we have learned through our interactions with European science teachers.

  7. 9th International Conference on Practical Applications of Computational Biology and Bioinformatics

    CERN Document Server

    Rocha, Miguel; Fdez-Riverola, Florentino; Paz, Juan

    2015-01-01

    This proceedings presents recent practical applications of Computational Biology and  Bioinformatics. It contains the proceedings of the 9th International Conference on Practical Applications of Computational Biology & Bioinformatics held at University of Salamanca, Spain, at June 3rd-5th, 2015. The International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB) is an annual international meeting dedicated to emerging and challenging applied research in Bioinformatics and Computational Biology. Biological and biomedical research are increasingly driven by experimental techniques that challenge our ability to analyse, process and extract meaningful knowledge from the underlying data. The impressive capabilities of next generation sequencing technologies, together with novel and ever evolving distinct types of omics data technologies, have put an increasingly complex set of challenges for the growing fields of Bioinformatics and Computational Biology. The analysis o...

  8. 'Candidatus Rickettsia mendelii', a novel basal group rickettsia detected in Ixodes ricinus ticks in the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Hajdušková, Eva; Literák, I.; Papoušek, I.; Costa, F.B.; Nováková, M.; Labruna, M. B.; Zdražilová-Dubská, L.

    2016-01-01

    Roč. 7, č. 3 (2016), s. 482-486 ISSN 1877-959X Institutional support: RVO:60077344 Keywords : Rickettsiae * Candidatus Rickettsia mendelii * Ixodes ricinus * basal group rickettsiae * ticks * Czech Republic Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.230, year: 2016

  9. Building Point Detection from Vehicle-Borne LiDAR Data Based on Voxel Group and Horizontal Hollow Analysis

    Directory of Open Access Journals (Sweden)

    Yu Wang

    2016-05-01

    Full Text Available Information extraction and three-dimensional (3D reconstruction of buildings using the vehicle-borne laser scanning (VLS system is significant for many applications. Extracting LiDAR points, from VLS, belonging to various types of building in large-scale complex urban environments still retains some problems. In this paper, a new technical framework for automatic and efficient building point extraction is proposed, including three main steps: (1 voxel group-based shape recognition; (2 category-oriented merging; and (3 building point identification by horizontal hollow ratio analysis. This article proposes a concept of “voxel group” based on the voxelization of VLS points: each voxel group is composed of several voxels that belong to one single real-world object. Then the shapes of point clouds in each voxel group are recognized and this shape information is utilized to merge voxel group. This article puts forward a characteristic nature of vehicle-borne LiDAR building points, called “horizontal hollow ratio”, for efficient extraction. Experiments are analyzed from two aspects: (1 building-based evaluation for overall experimental area; and (2 point-based evaluation for individual building using the completeness and correctness. The experimental results indicate that the proposed framework is effective for the extraction of LiDAR points belonging to various types of buildings in large-scale complex urban environments.

  10. Spotted fever group rickettsiae detected in immature stages of ticks parasitizing on Iberian endemic lizard Lacerta schreiberi Bedriaga, 1878

    Czech Academy of Sciences Publication Activity Database

    Kubelová, M.; Papoušek, I.; Bělohlávek, T.; Goüy de Bellocq, Joëlle; Baird, Stuart J. E.; Široký, P.

    2015-01-01

    Roč. 6, č. 6 (2015), s. 711-714 ISSN 1877-959X Institutional support: RVO:68081766 Keywords : Spotted fever group rickettsiae * Rickettsia monacensis * Rickettsia helvetica * Ixodes ricinus * Lacerta schreiberi Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 2.690, year: 2015

  11. Digital PCR technology for detection of palm infecting phytoplasmas belonging to group 16SrIV that occur in Florida

    Science.gov (United States)

    Phytoplasmas are an economically important group of plant pathogens that negatively impact a wide variety of plants in agricultural and natural ecosystems. In Florida, palms are essential elements in the nursery and landscaping industries that suffer from diseases caused by phytoplasmas that are rel...

  12. Localization-Free Detection of Replica Node Attacks in Wireless Sensor Networks Using Similarity Estimation with Group Deployment Knowledge

    Directory of Open Access Journals (Sweden)

    Chao Ding

    2017-01-01

    Full Text Available Due to the unattended nature and poor security guarantee of the wireless sensor networks (WSNs, adversaries can easily make replicas of compromised nodes, and place them throughout the network to launch various types of attacks. Such an attack is dangerous because it enables the adversaries to control large numbers of nodes and extend the damage of attacks to most of the network with quite limited cost. To stop the node replica attack, we propose a location similarity-based detection scheme using deployment knowledge. Compared with prior solutions, our scheme provides extra functionalities that prevent replicas from generating false location claims without deploying resource-consuming localization techniques on the resource-constraint sensor nodes. We evaluate the security performance of our proposal under different attack strategies through heuristic analysis, and show that our scheme achieves secure and robust replica detection by increasing the cost of node replication. Additionally, we evaluate the impact of network environment on the proposed scheme through theoretic analysis and simulation experiments, and indicate that our scheme achieves effectiveness and efficiency with substantially lower communication, computational, and storage overhead than prior works under different situations and attack strategies.

  13. Hydrazide and hydrazine reagents as reactive matrices for matrix-assisted laser desorption/ionization mass spectrometry to detect steroids with carbonyl groups.

    Science.gov (United States)

    Shigeri, Yasushi; Yasuda, Akikazu; Sakai, Masamichi; Ikeda, Shinya; Arakawa, Ryuichi; Sato, Hiroaki; Kinumi, Tomoya

    2015-01-01

    Fifty-one reagents (37 hydrazides and 14 hydrazines) were examined to determine if they could function as reactive matrices for the detection of steroids with carbonyl groups in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Among these reagents, 3-hydroxy-2-naphthoic acid hydrazide reacted most efficiently with steroids with carbonyl groups, allowing detection of them at the 1pmol level. Results from accurate mass measurement with a JMS-S3000 Spiral-TOF suggested that the ion peaks corresponding to the protonated fragment of a hydrazone were observed, in addition to the protonated molecular peaks of the resulting hydrazones ([M(D)+H](+)) and their sodium adduct ([M(D)+Na](+)). 3-Hydroxy-2-naphthoic acid hydrazide also could detect cortisol (1.93ng) spiked in a human serum certified reference material, as well as cortisone and cortisol in a human saliva sample collected in the morning. Using a combination of 3-hydroxy-2-naphthoic acid hydrazide and α- cyano-4-hydroxycinammic acid (CHCA) (3-hydroxy-2-naphthoic acid hydrazide:CHCA=4:1, v/v), even cortisone and cortisol in a human saliva sample collected in the afternoon, when levels are typically low, could be detected effectively.

  14. An Ionic 1,4-Bis(styrylbenzene-Based Fluorescent Probe for Mercury(II Detection in Water via Deprotection of the Thioacetal Group

    Directory of Open Access Journals (Sweden)

    Van Sang Le

    2016-12-01

    Full Text Available Highly sensitive and selective mercury detection in aqueous media is urgently needed because mercury poisoning usually results from exposure to water-soluble forms of mercury by inhalation and/or ingesting. An ionic conjugated oligoelectrolye (M1Q based on 1,4-bis(styrylbenzene was synthesized as a fluorescent mercury(II probe. The thioacetal moiety and quaternized ammonium group were incorporated for Hg2+ recognition and water solubility. A neutral Hg2+ probe (M1 was also prepared based on the same molecular backbone, and their sensor characteristics were investigated in a mixture of acetonitrile/water and in water. In the presence of Hg2+, the thioacetal group was converted to aldehyde functionality, and the resulting photoluminescence intensity decreased. In water, M1Q successfully demonstrated highly sensitive detection, showing a binding toward Hg2+ that was ~15 times stronger and a signal on/off ratio twice as high, compared to M1 in acetonitrile/water. The thioacetal deprotection by Hg2+ ions was substantially facilitated in water without an organic cosolvent. The limit of detection was measured to be 7 nM with a detection range of 10–180 nM in 100% aqueous medium.

  15. Comparative evaluation of Strepto B ID chromogenic medium and Granada media for the detection of Group B streptococcus from vaginal samples of pregnant women.

    Science.gov (United States)

    Tazi, Asmaa; Réglier-Poupet, Hélène; Dautezac, François; Raymond, Josette; Poyart, Claire

    2008-06-01

    Two types of selective media, the chromogenic medium Strepto B ID and two non-chromogenic media Strepto B agar and the Granada medium, were tested and compared to blood agar plates (BAP) for screening of Group B streptococcus vaginal colonization in pregnant women. All tested media were comparable in terms of sensitivity however, their use in routine laboratories may markedly facilitate the rapid detection of GBS in vaginal samples.

  16. Selective versus non-selective culture medium for group B streptococcus detection in pregnancies complicated by preterm labor or preterm-premature rupture of membranes

    Directory of Open Access Journals (Sweden)

    Marcelo Luís Nomura

    Full Text Available The objective of this study was to identify group B streptococcus (GBS colonization rates and compare detection efficiency of selective versus non-selective culture media and anorectal versus vaginal cultures in women with preterm labor and preterm-premature rupture of membranes (PROM. A prospective cohort study of 203 women was performed. Two vaginal and two anorectal samples from each woman were collected using sterile swabs. Two swabs (one anorectal and one vaginal were placed separately in Stuart transport media and cultured in blood-agar plates for 48 hours; the other two swabs were inoculated separately in Todd-Hewitt selective media for 24 hours and then subcultured in blood-agar plates. Final GBS identification was made by the CAMP test. A hundred thrity-two cultures out of 812 were positive. The maternal colonization rate was 27.6%. Colonization rates were 30% for preterm PROM and 25.2% for preterm labor. Todd-Hewitt selective medium detected 87.5% and non-selective medium 60.7% GBS-positive women. Vaginal samples and anorectal samples had the same detection rate of 80.3%. Anorectal selective cultures detected 75% of carriers; 39% of GBS-positive women were detected only in selective medium. A combined vaginal-anorectal selective culture is appropriate for GBS screening in this population, minimizing laboratory costs.

  17. Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.

    Science.gov (United States)

    Martin, Guillaume; Baurens, Franc-Christophe; Droc, Gaëtan; Rouard, Mathieu; Cenci, Alberto; Kilian, Andrzej; Hastie, Alex; Doležel, Jaroslav; Aury, Jean-Marc; Alberti, Adriana; Carreel, Françoise; D'Hont, Angélique

    2016-03-16

    Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa acuminata). We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of Musa acuminata. Genotyping by sequencing (GBS) of a segregating population and paired-end sequencing were used to detect and correct scaffold misassemblies. Long insert size paired-end reads identified scaffold junctions and fusions missed by automated assembly methods. GBS markers were used to anchor scaffolds to pseudo-molecules with a new bioinformatics approach that avoids the tedious step of marker ordering during genetic map construction. Furthermore, a genome map was constructed and used to assemble scaffolds into super scaffolds. Finally, a consensus gene annotation was projected on the new assembly from two pre-existing annotations. This approach reduced the total Musa scaffold number from 7513 to 1532 (i.e. by 80%), with an N50 that increased from 1.3 Mb (65 scaffolds) to 3.0 Mb (26 scaffolds). 89.5% of the assembly was anchored to the 11 Musa chromosomes compared to the previous 70%. Unknown sites (N) were reduced from 17.3 to 10.0%. The release of the Musa acuminata reference genome version 2 provides a platform for detailed analysis of banana genome variation, function and evolution. Bioinformatics tools developed in this work can be used to improve genome sequence assemblies in

  18. Prevalence and global initiative for chronic obstructive lung disease group distribution of chronic obstructive pulmonary disease detected by preoperative pulmonary function test.

    Directory of Open Access Journals (Sweden)

    Sun Mi Choi

    Full Text Available Despite being a major public health problem, chronic obstructive pulmonary disease (COPD remains underdiagnosed, and only 2.4% COPD patients are aware of their disease in Korea. The objective of this study was to estimate the prevalence of COPD detected by spirometry performed as a preoperative screening test and to determine the Global Initiative for Chronic Obstructive Lung Disease (GOLD group distribution and self-awareness of COPD.We reviewed the medical records of adults (age, ≥ 40 years who had undergone spirometry during preoperative screening between April and August 2013 at a tertiary hospital in Korea. COPD was defined as a postbronchodilator forced expiratory volume in 1 s/forced vital capacity ratio of 40 years who had undergone spirometry as a preoperative screening test, 474 (15.6%; 404 men; median age, 70 years; range, 44-93 years were diagnosed with COPD. Only 26 (5.5% patients reported previous diagnosis of COPD (2.1%, emphysema (0.8%, or chronic bronchitis (2.5%. The GOLD group distribution was as follows: 63.3% in group A, 31.2% in group B, 1.7% in group C, and 3.8% in group D.The prevalence of COPD diagnosed by preoperative spirometry was 15.6%, and only 5.5% patients were aware of their disease. Approximately one-third of the COPD patients belonged to GOLD groups B, C, and D, which require regular treatment.

  19. Highly sensitive detection of the group A Rotavirus using Apolipoprotein H-coated ELISA plates compared to quantitative real-time PCR

    Directory of Open Access Journals (Sweden)

    Veas Francisco

    2011-02-01

    Full Text Available Abstract Background The principle of a capture ELISA is binding of specific capture antibodies (polyclonal or monoclonal to the surface of a suitable 96 well plate. These immobilized antibodies are capable of specifically binding a virus present in a clinical sample. Subsequently, the captured virus is detected using a specific detection antibody. The drawback of this method is that a capture ELISA can only function for a single virus captured by the primary antibody. Human Apolipoprotein H (ApoH or β2-glycoprotein 1 is able to poly-specifically bind viral pathogens. Replacing specific capture antibodies by ApoH should allow poly-specific capture of different viruses that subsequently could be revealed using specific detection antibodies. Thus, using a single capture ELISA format different viruses could be analysed depending on the detection antibody that is applied. In order to demonstrate that this is a valid approach we show detection of group A rotaviruses from stool samples as a proof of principle for a new method of capture ELISA that should also be applicable to other viruses. Results Stool samples of different circulating common human and potentially zoonotic group A rotavirus strains, which were pretested in commercial EIAs and genotyped by PCR, were tested in parallel in an ApoH-ELISA set-up and by quantitative real-time PCR (qPCR. Several control samples were included in the analysis. The ApoH-ELISA was suitable for the capture of rotavirus-particles and the detection down to 1,000 infectious units (TCID50/ml. Subsets of diagnostic samples of different G- and P-types were tested positive in the ApoH-ELISA in different dilutions. Compared to the qPCR results, the analysis showed high sensitivity, specificity and low cross-reactivity for the ApoH-ELISA, which was confirmed in receiver operating characteristics (ROC analysis. Conclusions In this study the development of a highly sensitive and specific capture ELISA was demonstrated by

  20. A review of bioinformatics training applied to research in molecular medicine, agriculture and biodiversity in Costa Rica and Central America.

    Science.gov (United States)

    Orozco, Allan; Morera, Jessica; Jiménez, Sergio; Boza, Ricardo

    2013-09-01

    Today, Bioinformatics has become a scientific discipline with great relevance for the Molecular Biosciences and for the Omics sciences in general. Although developed countries have progressed with large strides in Bioinformatics education and research, in other regions, such as Central America, the advances have occurred in a gradual way and with little support from the Academia, either at the undergraduate or graduate level. To address this problem, the University of Costa Rica's Medical School, a regional leader in Bioinformatics in Central America, has been conducting a series of Bioinformatics workshops, seminars and courses, leading to the creation of the region's first Bioinformatics Master's Degree. The recent creation of the Central American Bioinformatics Network (BioCANET), associated to the deployment of a supporting computational infrastructure (HPC Cluster) devoted to provide computing support for Molecular Biology in the region, is providing a foundational stone for the development of Bioinformatics in the area. Central American bioinformaticians have participated in the creation of as well as co-founded the Iberoamerican Bioinformatics Society (SOIBIO). In this article, we review the most recent activities in education and research in Bioinformatics from several regional institutions. These activities have resulted in further advances for Molecular Medicine, Agriculture and Biodiversity research in Costa Rica and the rest of the Central American countries. Finally, we provide summary information on the first Central America Bioinformatics International Congress, as well as the creation of the first Bioinformatics company (Indromics Bioinformatics), spin-off the Academy in Central America and the Caribbean.

  1. Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades.

    Science.gov (United States)

    Wren, Jonathan D

    2016-09-01

    To analyze the relative proportion of bioinformatics papers and their non-bioinformatics counterparts in the top 20 most cited papers annually for the past two decades. When defining bioinformatics papers as encompassing both those that provide software for data analysis or methods underlying data analysis software, we find that over the past two decades, more than a third (34%) of the most cited papers in science were bioinformatics papers, which is approximately a 31-fold enrichment relative to the total number of bioinformatics papers published. More than half of the most cited papers during this span were bioinformatics papers. Yet, the average 5-year JIF of top 20 bioinformatics papers was 7.7, whereas the average JIF for top 20 non-bioinformatics papers was 25.8, significantly higher (P bioinformatics journals tended to have higher Gini coefficients, suggesting that development of novel bioinformatics resources may be somewhat 'hit or miss'. That is, relative to other fields, bioinformatics produces some programs that are extremely widely adopted and cited, yet there are fewer of intermediate success. jdwren@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Science.gov (United States)

    Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

    2016-01-01

    Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  3. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Directory of Open Access Journals (Sweden)

    Michael Römer

    Full Text Available Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  4. 'Candidatus Rickettsia mendelii', a novel basal group rickettsia detected in Ixodes ricinus ticks in the Czech Republic.

    Science.gov (United States)

    Hajduskova, Eva; Literak, Ivan; Papousek, Ivo; Costa, Francisco B; Novakova, Marketa; Labruna, Marcelo B; Zdrazilova-Dubska, Lenka

    2016-04-01

    A novel rickettsial sequence in the citrate synthase gltA gene indicating a novel Rickettsia species has been detected in 7 out of 4524 Ixodes ricinus ticks examined within several surveys performed in the Czech Republic from 2005 to 2009. This new Candidatus Rickettsia sp. sequence has been found in 2 nymphs feeding on wild birds (Luscinia megarhynchos and Erithacus rubecula), in a male tick from vegetation, and 4 ticks feeding on a dog (3 males, 1 female tick). Portions of the ompA, ompB, sca4, and htrA genes were not amplifiable in these samples. A maximum likelihood tree of rickettsiae based on comparisons of partial amino acid sequences of citrate synthase and nucleotide sequences of 16S rDNA genes and phylogenetic analysis revealed a basal position of the novel species in the proximity of R. bellii and R. canadensis. The novel species has been named 'Candidatus Rickettsia mendelii' after the founder of genetics, Gregor Mendel. Copyright © 2016 Elsevier GmbH. All rights reserved.

  5. Molecular characterization of group A rotaviruses detected in children with gastroenteritis in Ireland in 2006-2009.

    LENUS (Irish Health Repository)

    Cashman, O

    2012-02-01

    SUMMARYCommunity and hospital-acquired cases of human rotavirus are responsible for millions of gastroenteritis cases in children worldwide, chiefly in developing countries, and vaccines are now available. During surveillance activity for human rotavirus infections in Ireland, between 2006 and 2009, a total of 420 rotavirus strains were collected and analysed. Upon either PCR genotyping and sequence analysis, a variety of VP7 (G1-G4 and G9) and VP4 (P[4], P[6], P[8] and P[9]) genotypes were detected. Strains G1P[8] were found to be predominant throughout the period 2006-2008, with slight fluctuations seen in the very limited samples available in 2008-2009. Upon either PCR genotyping and sequence analysis of selected strains, the G1, G3 and G9 viruses were found to contain E1 (Wa-like) NSP4 and I1 VP6 genotypes, while the analysed G2 strains possessed E2 NSP4 and I2 VP6 genotypes, a genetic make-up which is highly conserved in the major human rotavirus genogroups Wa- and Kun-like, respectively. Upon sequence analysis of the most common VP4 genotype, P[8], at least two distinct lineages were identified, both unrelated to P[8] Irish rotaviruses circulating in previous years, and more closely related to recent European humans rotaviruses. Moreover, sequence analysis of the VP7 of G1 rotaviruses revealed the onset of a G1 variant, previously unseen in the Irish population.

  6. Detection of MYCN Gene Amplification in Neuroblastoma by Fluorescence In Situ Hybridization: A Pediatric Oncology Group Study

    Directory of Open Access Journals (Sweden)

    Prasad Mathew

    2001-01-01

    Full Text Available To assess the utility of fluorescence in situ hybridization (FISH for analysis of MYCN gene amplification in neuroblastoma, we compared this assay with Southern blot analysis using tumor specimens collected from 232 patients with presenting characteristics typical of this disease. The FISH technique identified MYCN amplification in 47 cases, compared with 39 by Southern blotting, thus increasing the total number of positive cases by 21%. The major cause of discordancy was a low fraction of tumor cells (≤30% replacement in clinical specimens, which prevented an accurate estimate of MYCN copy number by Southern blotting. With FISH, by contrast, it was possible to analyze multiple interphase nuclei of tumor cells, regardless of the proportion of normal peripheral blood, bone marrow, or stromal cells in clinical samples. Thus, FISH could be performed accurately with very small numbers of tumor cells from touch preparations of needle biopsies. Moreover, this procedure allowed us to discern the heterogeneous pattern of MYCN amplification that is characteristic of neuroblastoma. We conclude that FISH improves the detection of MYCN gene amplification in childhood neuroblastomas in a clinical setting, thus facilitating therapeutic decisions based on the presence or absence of this prognostically important biologic marker.

  7. Quantitative detection of Streptococcus mutans and bacteria of dental caries and no caries groups in permanent teeth from a north China population.

    Science.gov (United States)

    Wang, Zhan-Yong; Wang, Jian-Qiu; Zhou, Yan; Zhao, Dong; Xiao, Bai

    2012-11-01

    Streptococcus mutans (S. mutans) is the prime pathogen of dental caries. There are few reports that studied the relationship between S. mutans, bacteria and dental caries in permanent teeth when compared to those in primary teeth. This study aimed to detect S. mutans and bacteria of dental caries and non-caries groups in permanent teeth from a north China population by real-time polymerase chain reaction (PCR) and compare the relationship between the number of these bacteria and the prevalence of dental caries in permanent teeth. Human saliva samples were collected from 142 subjects with permanent teeth. According to their dental tooth (DT), 142 subjects were divided into a dental caries group (DT ≥ 1) and a non-caries group (DT = 0). With specific primers for S. mutans and 16S rRNA, the total number of S. mutans and total bacteria of 142 saliva samples were detected by real-time PCR and statistically analyzed. There was no significant difference between the detection rates of S. mutans (P = 0.118) and medians of S. mutans (P = 0.115). The ratio of S. mutans to total bacteria in people with dental caries was significantly higher than in those without caries (P dental caries was significantly lower than in those without caries (P caries in the permanent teeth of several individuals from a north China population. The ratios of S. mutans to total bacteria in saliva detected by real-time PCR with Sm479F/R and 16S RNA primers were closely associated with the prevalence of dental caries in the same population. These assays may be useful for the assessment of an individual's risk of dental caries.

  8. Learning structural bioinformatics and evolution with a snake puzzle

    Directory of Open Access Journals (Sweden)

    Gonzalo S. Nido

    2016-12-01

    Full Text Available We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master’s course at the Universidad Autónoma de Madrid (Spain, the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Order. It also allows a simple representation of misfolded conformations and their free energy. These concepts will motivate evolutionary questions, which we will address by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material (see ‘Data Availability’ to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.

  9. Progress and challenges in bioinformatics approaches for enhancer identification

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2017-02-03

    Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene expression. Identifying enhancers is an important step for understanding distinct gene expression programs that may reflect normal and pathogenic cellular conditions. Experimental identification of enhancers is constrained by the set of conditions used in the experiment. This requires multiple experiments to identify enhancers, as they can be active under specific cellular conditions but not in different cell types/tissues or cellular states. This has opened prospects for computational prediction methods that can be used for high-throughput identification of putative enhancers to complement experimental approaches. Potential functions and properties of predicted enhancers have been catalogued and summarized in several enhancer-oriented databases. Because the current methods for the computational prediction of enhancers produce significantly different enhancer predictions, it will be beneficial for the research community to have an overview of the strategies and solutions developed in this field. In this review, we focus on the identification and analysis of enhancers by bioinformatics approaches. First, we describe a general framework for computational identification of enhancers, present relevant data types and discuss possible computational solutions. Next, we cover over 30 existing computational enhancer identification methods that were developed since 2000. Our review highlights advantages, limitations and potentials, while suggesting pragmatic guidelines for development of more efficient computational enhancer prediction methods. Finally, we discuss challenges and open problems of this topic, which require further consideration.

  10. WeBIAS: a web server for publishing bioinformatics applications.

    Science.gov (United States)

    Daniluk, Paweł; Wilczyński, Bartek; Lesyng, Bogdan

    2015-11-02

    One of the requirements for a successful scientific tool is its availability. Developing a functional web service, however, is usually considered a mundane and ungratifying task, and quite often neglected. When publishing bioinformatic applications, such attitude puts additional burden on the reviewers who have to cope with poorly designed interfaces in order to assess quality of presented methods, as well as impairs actual usefulness to the scientific community at large. In this note we present WeBIAS-a simple, self-contained solution to make command-line programs accessible through web forms. It comprises a web portal capable of serving several applications and backend schedulers which carry out computations. The server handles user registration and authentication, stores queries and results, and provides a convenient administrator interface. WeBIAS is implemented in Python and available under GNU Affero General Public License. It has been developed and tested on GNU/Linux compatible platforms covering a vast majority of operational WWW servers. Since it is written in pure Python, it should be easy to deploy also on all other platforms supporting Python (e.g. Windows, Mac OS X). Documentation and source code, as well as a demonstration site are available at http://bioinfo.imdik.pan.pl/webias . WeBIAS has been designed specifically with ease of installation and deployment of services in mind. Setting up a simple application requires minimal effort, yet it is possible to create visually appealing, feature-rich interfaces for query submission and presentation of results.

  11. Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Wei Li

    2016-04-01

    Full Text Available Mitogen‐activated protein kinase kinase kinase (MAPKKK is a component of the MAPK cascade pathway that plays an important role in plant growth, development, and response to abiotic stress, the functions of which have been well characterized in several plant species, such as Arabidopsis, rice, and maize. In this study, we performed genome‐wide and systemic bioinformatics analysis of MAPKKK family genes in Medicago truncatula. In total, there were 73 MAPKKK family members identified by search of homologs, and they were classified into three subfamilies, MEKK, ZIK, and RAF. Based on the genomic duplication function, 72 MtMAPKKK genes were located throughout all chromosomes, but they cluster in different chromosomes. Using microarray data and high‐throughput sequencing‐data, we assessed their expression profiles in growth and development processes; these results provided evidence for exploring their important functions in developmental regulation, especially in the nodulation process. Furthermore, we investigated their expression in abiotic stresses by RNA‐seq, which confirmed their critical roles in signal transduction and regulation processes under stress. In summary, our genome‐wide, systemic characterization and expressional analysis of MtMAPKKK genes will provide insights that will be useful for characterizing the molecular functions of these genes in M. truncatula.

  12. Accurate Prediction of Coronary Artery Disease Using Bioinformatics Algorithms

    Directory of Open Access Journals (Sweden)

    Hajar Shafiee

    2016-06-01

    Full Text Available Background and Objectives: Cardiovascular disease is one of the main causes of death in developed and Third World countries. According to the statement of the World Health Organization, it is predicted that death due to heart disease will rise to 23 million by 2030. According to the latest statistics reported by Iran’s Minister of health, 3.39% of all deaths are attributed to cardiovascular diseases and 19.5% are related to myocardial infarction. The aim of this study was to predict coronary artery disease using data mining algorithms. Methods: In this study, various bioinformatics algorithms, such as decision trees, neural networks, support vector machines, clustering, etc., were used to predict coronary heart disease. The data used in this study was taken from several valid databases (including 14 data. Results: In this research, data mining techniques can be effectively used to diagnose different diseases, including coronary artery disease. Also, for the first time, a prediction system based on support vector machine with the best possible accuracy was introduced. Conclusion: The results showed that among the features, thallium scan variable is the most important feature in the diagnosis of heart disease. Designation of machine prediction models, such as support vector machine learning algorithm can differentiate between sick and healthy individuals with 100% accuracy.

  13. The European Bioinformatics Institute in 2017: data coordination and integration

    Science.gov (United States)

    Cochrane, Guy; Apweiler, Rolf; Birney, Ewan

    2018-01-01

    Abstract The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists in all disciplines can explore life in ever-increasing detail. We maintain over 40 data resources, many of which are run collaboratively with partners in 16 countries (https://www.ebi.ac.uk/services). Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes. Recent advances in cellular imaging and single-cell sequencing techniques are generating a vast amount of high-dimensional data, bringing to light new cell types and new perspectives on anatomy. Accordingly, one of our main focus areas is integrating high-quality information from bioimaging, biobanking and other types of molecular data. This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch of the Omics Discovery Index. This update gives a birds-eye view of EMBL-EBI’s approach to data integration and service development as genomics begins to enter the clinic. PMID:29186510

  14. Phylogenetic diversity (PD and biodiversity conservation: some bioinformatics challenges

    Directory of Open Access Journals (Sweden)

    Daniel P. Faith

    2006-01-01

    Full Text Available Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, “PD”, has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a. While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, “cryptic”, taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based “species” designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data.

  15. Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

    Directory of Open Access Journals (Sweden)

    Zheng Sun

    2014-01-01

    Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

  16. Immunogenicity of novel Dengue virus epitopes identified by bioinformatic analysis.

    Science.gov (United States)

    Sánchez-Burgos, Gilma; Ramos-Castañeda, José; Cedillo-Rivera, Roberto; Dumonteil, Eric

    2010-10-01

    We used T cell epitope prediction tools to identify epitopes from Dengue virus polyprotein sequences, and evaluated in vivo and in vitro the immunogenicity and antigenicity of the corresponding synthetic vaccine candidates. Twenty-two epitopes were predicted to have a high affinity for MHC class I (H-2Kd, H-2Dd, H-2Ld alleles) or class II (IAd alleles). These epitopes were conserved between the four virus serotypes, but with no similarity to human and mouse sequences. Thirteen synthetic peptides induced specific antibodies production with or without T cells activation in mice. Three synthetic peptides induced mostly IgG antibodies, and one of these from the E gene induced a neutralizing response. Ten peptides induced a combination of humoral and cellular responses by CD4+ and CD8+ T cells. Twelve peptides were novel B and T cell epitopes. These results indicate that our bioinformatics strategy is a powerful tool for the identification of novel antigens and its application to human HLA may lead to a potent epitope-based vaccine against Dengue virus and many other pathogens. (c) 2010 Elsevier B.V. All rights reserved.

  17. MEMOSys: Bioinformatics platform for genome-scale metabolic models.

    Science.gov (United States)

    Pabinger, Stephan; Rader, Robert; Agren, Rasmus; Nielsen, Jens; Trajanoski, Zlatko

    2011-01-31

    Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in order to gain novel biological insights. One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models. MEMOSys (MEtabolic MOdel research and development System) is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains six annotated microbial metabolic models. We have developed a web-based system designed to provide researchers a novel application facilitating the management and development of metabolic models. The system is freely available at http://www.icbi.at/MEMOSys.

  18. MEMOSys: Bioinformatics platform for genome-scale metabolic models

    Directory of Open Access Journals (Sweden)

    Agren Rasmus

    2011-01-01

    Full Text Available Abstract Background Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in order to gain novel biological insights. One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models. Results MEMOSys (MEtabolic MOdel research and development System is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains six annotated microbial metabolic models. Conclusions We have developed a web-based system designed to provide researchers a novel application facilitating the management and development of metabolic models. The system is freely available at http://www.icbi.at/MEMOSys.

  19. Exploiting graphics processing units for computational biology and bioinformatics.

    Science.gov (United States)

    Payne, Joshua L; Sinnott-Armstrong, Nicholas A; Moore, Jason H

    2010-09-01

    Advances in the video gaming industry have led to the production of low-cost, high-performance graphics processing units (GPUs) that possess more memory bandwidth and computational capability than central processing units (CPUs), the standard workhorses of scientific computing. With the recent release of generalpurpose GPUs and NVIDIA's GPU programming language, CUDA, graphics engines are being adopted widely in scientific computing applications, particularly in the fields of computational biology and bioinformatics. The goal of this article is to concisely present an introduction to GPU hardware and programming, aimed at the computational biologist or bioinformaticist. To this end, we discuss the primary differences between GPU and CPU architecture, introduce the basics of the CUDA programming language, and discuss important CUDA programming practices, such as the proper use of coalesced reads, data types, and memory hierarchies. We highlight each of these topics in the context of computing the all-pairs distance between instances in a dataset, a common procedure in numerous disciplines of scientific computing. We conclude with a runtime analysis of the GPU and CPU implementations of the all-pairs distance calculation. We show our final GPU implementation to outperform the CPU implementation by a factor of 1700.

  20. Graphics processing units in bioinformatics, computational biology and systems biology.

    Science.gov (United States)

    Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

    2017-09-01

    Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

  1. Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

    Science.gov (United States)

    Stockinger, Heinz; Altenhoff, Adrian M; Arnold, Konstantin; Bairoch, Amos; Bastian, Frederic; Bergmann, Sven; Bougueleret, Lydie; Bucher, Philipp; Delorenzi, Mauro; Lane, Lydie; Le Mercier, Philippe; Lisacek, Frédérique; Michielin, Olivier; Palagi, Patricia M; Rougemont, Jacques; Schwede, Torsten; von Mering, Christian; van Nimwegen, Erik; Walther, Daniel; Xenarios, Ioannis; Zavolan, Mihaela; Zdobnov, Evgeny M; Zoete, Vincent; Appel, Ron D

    2014-07-01

    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Self-assembly and sensing-group graft of pre-modified CNTs on resonant micro-cantilevers for specific detection of volatile organic compound vapors

    Science.gov (United States)

    Xu, Pengcheng; Li, Xinxin; Yu, Haitao; Liu, Min; Li, Jungang

    2010-11-01

    This paper reports MWCNT (multi-wall carbon nano-tube)-modified resonant micro-cantilever chemical sensors for detection of trinitrotoluene (TNT) vapor. The MWCNTs are pre-modified and then area-selectively self-assembled at the free-end gold pad of a micro-cantilever, in which a resonance-exciting heater and a signal-readout piezoresistive Wheatstone bridge are integrated. Featuring a high specific surface area, the MWCNTs are further functionalized with TNT-sensitive groups by grafting onto the sidewalls of the MWCNTs. To lower the non-specific absorption of water and other small organic molecules, the SiO2 surface of the micro-cantilever was also pre-treated for hydrophobicity and oleophobicity by self-assembling a monolayer of heptadecafluorodecyltrimethoxysilane. The results of our sensing experiments have shown a capability to rapidly detect ppb-level TNT vapor, and a high specificity of the functionalized groups to TNT molecules. The experiment has also confirmed a good long-term stability in detecting sensitivity.

  3. Changes in protein expression profiles between a low phytic acid rice ( Oryza sativa L. Ssp. japonica) line and its parental line: a proteomic and bioinformatic approach.

    Science.gov (United States)

    Emami, Kaveh; Morris, Nicholas J; Cockell, Simon J; Golebiowska, Gabriela; Shu, Qing-Yao; Gatehouse, Angharad M R

    2010-06-09

    The seed proteome of a low phytic acid (lpa) rice line (Os-lpa-XS110-1), developed as a novel food source, was compared to that of its parental line, Xiushui 110 (XS-110). Analysis by surfaced enhanced laser desorption ionization-time-of-flight mass spectrometry (SELDI-TOF MS) and two-dimensional gel electrophoresis (2-DE) allowed the detection of a potential low molecular weight biomarker and identification of 23 differentially expressed proteins that include stress-related proteins, storage proteins, and potential allergens. Bioinformatic analyses revealed that triose phosphate isomerase (TPI) and fructose bisphosphatealdolase (FBA), two major differentially expressed proteins, are involved in myo-inositol metabolism. Accumulation of globulin was also significantly decreased in the lpa line. This study demonstrates the potential of proteomic and bioinformatic profiling techniques for safety assessment of novel foods. Furthermore, these techniques provide powerful tools for studying functional genomics due to the possibility of identifying genes related to the mutated traits.

  4. Bioinformatics Identification of Modules of Transcription Factor Binding Sites in Alzheimer's Disease-Related Genes by In Silico Promoter Analysis and Microarrays

    Directory of Open Access Journals (Sweden)

    Regina Augustin

    2011-01-01

    Full Text Available The molecular mechanisms and genetic risk factors underlying Alzheimer's disease (AD pathogenesis are only partly understood. To identify new factors, which may contribute to AD, different approaches are taken including proteomics, genetics, and functional genomics. Here, we used a bioinformatics approach and found that distinct AD-related genes share modules of transcription factor binding sites, suggesting a transcriptional coregulation. To detect additional coregulated genes, which may potentially contribute to AD, we established a new bioinformatics workflow with known multivariate methods like support vector machines, biclustering, and predicted transcription factor binding site modules by using in silico analysis and over 400 expression arrays from human and mouse. Two significant modules are composed of three transcription factor families: CTCF, SP1F, and EGRF/ZBPF, which are conserved between human and mouse APP promoter sequences. The specific combination of in silico promoter and multivariate analysis can identify regulation mechanisms of genes involved in multifactorial diseases.

  5. "Broadband" Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP): Educational Model for Upliftment and Sustainable Development.

    Science.gov (United States)

    Chimusa, Emile R; Mbiyavanga, Mamana; Masilela, Velaphi; Kumuthini, Judit

    2015-11-01

    A shortage of practical skills and relevant expertise is possibly the primary obstacle to social upliftment and sustainable development in Africa. The "omics" fields, especially genomics, are increasingly dependent on the effective interpretation of large and complex sets of data. Despite abundant natural resources and population sizes comparable with many first-world countries from which talent could be drawn, countries in Africa still lag far behind the rest of the world in terms of specialized skills development. Moreover, there are serious concerns about disparities between countries within the continent. The multidisciplinary nature of the bioinformatics field, coupled with rare and depleting expertise, is a critical problem for the advancement of bioinformatics in Africa. We propose a formalized matchmaking system, which is aimed at reversing this trend, by introducing the Knowledge Transfer Programme (KTP). Instead of individual researchers travelling to other labs to learn, researchers with desirable skills are invited to join African research groups for six weeks to six months. Visiting researchers or trainers will pass on their expertise to multiple people simultaneously in their local environments, thus increasing the efficiency of knowledge transference. In return, visiting researchers have the opportunity to develop professional contacts, gain industry work experience, work with novel datasets, and strengthen and support their ongoing research. The KTP develops a network with a centralized hub through which groups and individuals are put into contact with one another and exchanges are facilitated by connecting both parties with potential funding sources. This is part of the PLOS Computational Biology Education collection.

  6. Automatic vehicle detection based on automatic histogram-based fuzzy C-means algorithm and perceptual grouping using very high-resolution aerial imagery and road vector data

    Science.gov (United States)

    Ghaffarian, Saman; Gökaşar, Ilgın

    2016-01-01

    This study presents an approach for the automatic detection of vehicles using very high-resolution images and road vector data. Initially, road vector data and aerial images are integrated to extract road regions. Then, the extracted road/street region is clustered using an automatic histogram-based fuzzy C-means algorithm, and edge pixels are detected using the Canny edge detector. In order to automatically detect vehicles, we developed a local perceptual grouping approach based on fusion of edge detection and clustering outputs. To provide the locality, an ellipse is generated using characteristics of the candidate clusters individually. Then, ratio of edge pixels to nonedge pixels in the corresponding ellipse is computed to distinguish the vehicles. Finally, a point-merging rule is conducted to merge the points that satisfy a predefined threshold and are supposed to denote the same vehicles. The experimental validation of the proposed method was carried out on six very high-resolution aerial images that illustrate two highways, two shadowed roads, a crowded narrow street, and a street in a dense urban area with crowded parked vehicles. The evaluation of the results shows that our proposed method performed 86% and 83% in overall correctness and completeness, respectively.

  7. Detection of Babesia Sp. EU1 and members of spotted fever group rickettsiae in ticks collected from migratory birds at Curonian Spit, North-Western Russia.

    Science.gov (United States)

    Movila, Alexandru; Reye, Anna L; Dubinina, Helen V; Tolstenkov, Oleg O; Toderas, Ion; Hübschen, Judith M; Muller, Claude P; Alekseev, Andrey N

    2011-01-01

    To reveal the prevalence of spotted fever group (SFG) rickettsiae and Babesia sp. in Ixodes ricinus (L.) ticks from migratory birds, 236 specimens represented 8 species of Passeriformes and were collected at Curonian Spit in Kaliningrad enclave of North-Western Russia. The ticks (total 126) being detached from four bird species, Turdus philomelos, Fringilla coelebs, Parus major, and Sturnus vulgaris, were investigated by PCR using the primers Rp CS.877p/Rp CS.1258n for the detection of Rickettsia and BJ1/BN2 for Babesia spp. Babesia spp. were detected in 2 of 126 (1.6%) ticks. The partial sequence of 18S rDNA had 100% similarity to human pathogenic Babesia sp. EU1. The SFG rickettsiae were detected in 19 of 126 (15.1%) ticks collected from the above-mentioned bird species. BLAST analysis of SFG rickettsia gltA assigned sequences to human pathogenic Rickettsia helvetica (10.3%), Rickettsia monacensis (3.9%), and Rickettsia japonica (0.8%) with 98%-100% sequence similarity. The SFG rickettsiae and Babesia sp. EU1 in ticks collected from the passerines in Russia were detected for the first time. The survey indicates that migratory birds may become a reservoir for Babesia spp. and SFG rickettsiae. Future investigations need to characterize the role of birds in the epidemiology of these human pathogens in the region.

  8. Diversity of group A rotavirus genes detected in the Triângulo Mineiro region, Minas Gerais, Brazil

    Directory of Open Access Journals (Sweden)

    Ana Carolina Bernardes Dulgheroff

    Full Text Available ABSTRACT Group A rotaviruses are the main causative agent of infantile gastroenteritis. The segmented nature of the viral genome allows reassortment of genome segments, which can generate genetic variants. In this study, we characterized the diversity of the VP7, VP4 (VP8*, VP6, NSP4, and NSP5 genes of the rotaviruses that circulated from 2005 to 2011 in the Triângulo Mineiro (TM region of Brazil. Samples with genotypes G2 (sublineages IVa-1 and IVa-3, G1 (sublineage I-A, G9 (lineage III, G12 (lineages II and III, G8 (lineage II, G3 (lineage III, P[4] (sublineages IVa and IVb, P[8] (sublineages P[8]-3.6, P[8]-3.3, and P[8]-3.1, I2 (lineage VII, E2 (lineages VI, XII, and X, and H2 (lineage III were identified. The associations found in the samples were G1, G9, or G12 with P[8]-I1-E1-H1; G2 or G8 with P[4]-I2-E2-H2; G12 with I3-E3-H6; and G3 with P[4]-I2-E3-H3 (previously unreported combination. Reassortment events in G2P[4] strains and an apparent pattern of temporal segregation within the lineages were observed. Five TM samples contained genes that exhibited high nucleotide and amino acid identities with strains of animal origin. The present study includes a period of pre- and post-introduction of rotavirus vaccination in all Brazilian territories, thereby serving as a basis for monitoring changes in the genetic constitution of rotaviruses. The results also contribute to the understanding of the diversity and evolution of rotaviruses in a global context.

  9. Multicenter clinical evaluation of the Xpert GBS LB assay for detection of group B Streptococcus in prenatal screening specimens.

    Science.gov (United States)

    Buchan, Blake W; Faron, Matthew L; Fuller, DeAnna; Davis, Thomas E; Mayne, Donna; Ledeboer, Nathan A

    2015-02-01

    Neonatal infection with Streptococcus agalactiae (group B Streptococcus [GBS]) is a leading cause of sepsis and meningitis in newborns. Recent guidelines have recommended universal screening of all pregnant women to identify those colonized with GBS and administration of peripartum prophylaxis to those identified as carriers to reduce the risk of early-onset GBS disease in neonates. Enriched culture methods are the current standard for prenatal GBS screening; however, the implementation of more sensitive molecular diagnostic tests may be able to further reduce the risk of early-onset GBS infection. We report a clinical evaluation of the Xpert GBS LB assay, a molecular diagnostic test for the identification of GBS from broth-enriched vaginal/rectal specimens obtained during routine prenatal screening. A total of 826 specimens were collected from women undergoing prenatal screening (35 to 37 weeks' gestation) and tested at one of three clinical centers. Each swab specimen was tested directly prior to enrichment using the Xpert GBS assay. Following 18 to 24 h of broth enrichment, each specimen was tested using the Xpert GBS LB assay and the FDA-cleared Smart GBS assay as a molecular diagnostic comparator. Results obtained using all three molecular tests were compared to those for broth-enriched culture as the gold standard. The sensitivity and specificity of the Xpert GBS LB assay were 99.0% and 92.4%, respectively, compared to those for the gold standard culture. The Smart GBS molecular test demonstrated sensitivity and specificity of 96.8% and 95.5%, respectively. The sensitivities of the two broth-enriched molecular methods were superior to those for direct testing of specimens using the Xpert GBS assay, which demonstrated sensitivity and specificity of 85.7% and 96.2%, respectively. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. Cloning, bioinformatics analysis, and expression of the dust mite allergen Der f 5 of Dermatophagoides farinae

    Directory of Open Access Journals (Sweden)

    Yubao Cui

    2012-08-01

    Full Text Available Crude extracts of house dust mites are used clinically for diagnosis and immunotherapy of allergic diseases, including bronchial asthma, perennial rhinitis, and atopic dermatitis. However, crude extracts are complexes with non-allergenic antigens and lack effective concentrations of important allergens, resulting in several side effects. Dermatophagoides farinae (Hughes; Acari: Pyroglyphidae is one of the predominant sources of dust mite allergens, which has more than 30 groups of allergen. The cDNA coding for the group 5 allergen of D. farinae from China was cloned, sequenced and expressed. According to alignment using the VECTOR NTI 9.0 software, there were eight mismatched nucleotides in five cDNA clones resulting in seven incompatible amino acid residues, suggesting that the Der f 5 allergen might have sequence polymorphism. Bioinformatics analysis revealed that the matured Der f 5 allergen has a molecular mass of 13604.03 Da, a theoretical pI of 5.43 and is probably hydrophobic and cytoplasmic. Similarities in amino acid sequences between Der f 5 and allergens of other domestic mite species, viz. Der p 5, Blo t 5, Sui m 5, and Lep d 5, were 79, 48, 53, and 37%, respectively. Phylogenetic analysis indicated that Der f 5 and Der p 5 clustered together. Blo t 5 and Ale o 5 also clustered together, although Blomia tropicalis and Aleuroglyphus ovatus belong to different mite families, viz. Echimyopodidae and Acaridae, respectively.

  11. Proteomic and bioinformatics analysis of human saliva for the dental-risk assessment

    Directory of Open Access Journals (Sweden)

    Laputková Galina

    2017-10-01

    Full Text Available Background: Dental caries disease is a dynamic process with a multi-factorial etiology. It is manifested by demineralization of enamel followed by damage spreading into the tooth inner structure. Successful early diagnosis could identify caries-risk and improve dental screening, providing a baseline for evaluating personalized dental treatment and prevention strategies. Methodology:\tSalivary proteome of the whole unstimulated saliva (WUS samples was assessed in caries-free and caries-susceptible individuals of older adolescent age with permanent dentition using a nano-HPLC and MALDI-TOF/TOF mass spectrometry. Results: 554 proteins in the caries-free and 695 proteins in the caries-susceptible group were identified. Assessment using bioinformatics tools and Gene Ontology (GO term enrichment analysis revealed qualitative differences between these two proteomes. Members of the caries-susceptible group exhibited a branch of cytokine binding gene products responsible for the regulation of immune and inflammatory responses to infections. Inspection of molecular functions and biological processes of caries-susceptible saliva samples revealed significant categories predominantly related to the activity of proteolytic peptidases, and the regulation of metabolic and catabolic processes of carbohydrates. Conclusions: Proteomic analysis of the whole saliva revealed information about potential risk factors associated with the development of caries-susceptibility and provides a better understanding of tooth protection mechanisms.

  12. Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis.

    Science.gov (United States)

    Philippe, Florian; Pelloux, Jérôme; Rayon, Catherine

    2017-06-08

    Pectins are plant cell wall polysaccharides that can be acetylated on C2 and/or C3 of galacturonic acid residues. The degree of acetylation of pectin can be modulated by pectin acetylesterase (EC 3.1.1.6, PAE). The function and structure of plant PAEs remain poorly understood and the role of the fine-tuning of pectin acetylation on cell wall properties has not yet been elucidated. In the present study, a bioinformatic approach was used on 72 plant PAEs from 16 species among 611 plant PAEs available in plant genomic databases. An overview of plant PAE proteins, particularly Arabidopsis thaliana PAEs, based on phylogeny analysis, protein motif identification and modeled 3D structure is presented. A phylogenetic tree analysis using protein sequences clustered the plant PAEs into five clades. AtPAEs clustered in four clades in the plant kingdom PAE tree while they formed three clades when a phylogenetic tree was performed only on Arabidopsis proteins, due to isoform AtPAE9. Primitive plants that display a smaller number of PAEs clustered into two clades, while in higher plants, the presence of multiple members of PAE genes indicated a diversification of AtPAEs. 3D homology modeling of AtPAE8 from clade 2 with a human Notum protein showed an α/β hydrolase structure with the hallmark Ser-His-Asp of the active site. A 3D model of AtPAE4 from clade 1 and AtPAE10 from clade 3 showed a similar shape suggesting that the diversification of AtPAEs is unlikely to arise from the shape of the protein. Primary structure prediction analysis of AtPAEs showed a specific motif characteristic of each clade and identified one major group of AtPAEs with a signal peptide and one group without a signal peptide. A multiple sequence alignment of the putative plant PAEs revealed consensus sequences with important putative catalytic residues: Ser, Asp, His and a pectin binding site. Data mining of gene expression profiles of AtPAE revealed that genes from clade 2 including AtPAE7, AtPAE8 and

  13. Molecular surveillance of spotted fever group rickettsioses in wildlife and detection of Rickettsia sibirica in a Topi (Damaliscus lunatus ssp. jimela in Kenya

    Directory of Open Access Journals (Sweden)

    David Ndeereh

    2017-01-01

    Full Text Available Spotted fever group rickettsioses are a group of tick-borne zoonotic diseases caused by intracellular bacteria of the genus Rickettsia. The diseases are widely reported amongst international travellers returning from most sub-Saharan Africa with fever, yet their importance in local populations largely remains unknown. Although this has started to change and recently there have been increasing reports of the diseases in livestock, ticks and humans in Kenya, they have not been investigated in wildlife. We examined the presence, prevalence and species of Rickettsia present in wildlife in two regions of Kenya with a unique human–wildlife–livestock interface. For this purpose, 79 wild animals in Laikipia County and 73 in Maasai Mara National Reserve were sampled. DNA extracted from blood was tested using the polymerase chain reaction (PCR to amplify the intergenic spacer rpmE-tRNAfMet and the citrate synthase-encoding gene gltA. Rickettsial DNA was detected in 2 of the 79 (2.5% animals in Laikipia and 4 of the 73 (5.5% in Maasai Mara. The PCR-positive amplicons of the gltA gene were sequenced to determine the detected Rickettsia species. This revealed Rickettsia sibirica in a Topi (Damaliscus lunatus ssp. jimela. This is the first report of spotted fever group rickettsioses in wildlife and the first to report R. sibirica in Kenya. The finding demonstrates the potential role of wild animals in the circulation of the diseases.

  14. Sensitivity of physiological measures for detecting systematic variations in cognitive demand from a working memory task: an on-road study across three age groups.

    Science.gov (United States)

    Mehler, Bruce; Reimer, Bryan; Coughlin, Joseph F

    2012-06-01

    To assess the sensitivity of two physiological measures for discriminating between levels of cognitive demand under driving conditions across different age groups. Previous driving research presents a mixed picture concerning the sensitivity of physiological measures for differentiating tasks with presumed differences in mental workload. A total of 108 relatively healthy drivers balanced by gender and across three age groups (20-29, 40-49, 60-69) engaged in three difficulty levels of an auditory presentation-verbal response working memory task. Heart rate and skin conductance level (SCL) both increased in a statistically significant fashion with each incremental increase in cognitive demand, whereas driving performance measures did not provide incremental discrimination. SCL was lower in the 40s and 60s age groups; however, the pattern of incremental increase with higher demand was consistent for heart rate and SCL across all age groups. Although each measure was quite sensitive at the group level, considering both SCL and heart rate improved detection of periods of heightened cognitive demand at the individual level. The data provide clear evidence that two basic physiological measures can be utilized under field conditions to differentiate multiple levels of objectively defined changes in cognitive demand. Methodological considerations, including task engagement, may account for some of the inconsistencies in previous research. These findings increase the confidence with which these measures may be applied to assess relative differences in mental workload when developing and optimizing human machine interface (HMI) designs and in exploring their potential role in advanced workload detection and augmented cognition systems.

  15. Pay-as-you-go data integration for bio-informatics

    NARCIS (Netherlands)

    Wanders, B.

    2012-01-01

    Scientific research in bio-informatics is often data-driven and supported by numerous biological databases. A biological database contains factual information collected from scientific experiments and computational analyses about areas including genomics, proteomics, metabolomics, microarray gene

  16. Fundamentals of bioinformatics and computational biology methods and exercises in matlab

    CERN Document Server

    Singh, Gautam B

    2015-01-01

    This book offers comprehensive coverage of all the core topics of bioinformatics, and includes practical examples completed using the MATLAB bioinformatics toolbox™. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics. This chapter will enable physical science students to fully understand and appreciate the ultimate goals of applying the principles of information technology to challenges in biological data management, sequence analysis, and systems biology. The first part of the book also includes a survey of existing biological databases, tools that have become essential in today’s biotechnology research. The second part of the book covers methodologies for retrieving biological information, including fundamental algorithms for sequence compar...

  17. Biopython: freely available Python tools for computational molecular biology and bioinformatics

    DEFF Research Database (Denmark)

    Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T

    2009-01-01

    SUMMARY: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments...

  18. Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools

    Directory of Open Access Journals (Sweden)

    Daisuke Kihara

    2006-01-01

    Full Text Available The immensely popular fields of cancer research and bioinformatics overlap in many different areas, e.g. large data repositories that allow for users to analyze data from many experiments (data handling, databases, pattern mining, microarray data analysis, and interpretation of proteomics data. There are many newly available resources in these areas that may be unfamiliar to most cancer researchers wanting to incorporate bioinformatics tools and analyses into their work, and also to bioinformaticians looking for real data to develop and test algorithms. This review reveals the interdependence of cancer research and bioinformatics, and highlight the most appropriate and useful resources available to cancer researchers. These include not only public databases, but general and specific bioinformatics tools which can be useful to the cancer researcher. The primary foci are function and structure prediction tools of protein genes. The result is a useful reference to cancer researchers and bioinformaticians studying cancer alike.

  19. Comparison of acceleration techniques forselected low-level bioinformatics operations

    Directory of Open Access Journals (Sweden)

    Daniel eLangenkaemper

    2016-02-01

    Full Text Available Within the recent years clock rates of modern processors stagnated while the demand for computing power continued to grow. This applied particularly for the fields of life sciences and bioinformatics, where new technologies keep on creating rapidly growing piles of raw data with increasing speed. The number of cores per processor increased in an attempt to compensate for slight increments of clock rates. This technological shift demands changes in software development, especially in the field of high performance computing where parallelization techniques are gaining in importance due to the pressing issue of large sized datasets generated by e.g. modern genomics.This paper presents an overview of state-of-the-art manual and automatic acceleration techniques and lists some applications employing these in different areas of sequence informatics. Furthermore we provide examples for automatic acceleration of two use cases to show typical problems and gains of transforming a serial application to a parallel one. The paper should aid the reader in deciding for a certain techniques for the problem at hand.We compare four different state-of-the-art automatic acceleration approaches (OpenMP, PluTo-SICA, PPCG, and OpenACC. Their performance as well as their applicability for selected use cases is discussed. While optimizations targeting the CPU worked better in the complex k-mer use case, optimizers for Graphics Processing Units (GPUs performed better in the matrix multiplication example. But performance is only superior at a certain problem size due to data migration overhead.We show that automatic code parallelization is feasible with current compiler software and yields significant increases in execution speed. Automatic optimizers for CPU are mature and usually

  20. What can bioinformatics do for Natural History museums?

    Directory of Open Access Journals (Sweden)

    Becerra, José María

    2003-06-01

    Full Text Available We propose the founding of a Natural History bioinformatics framework, which would solve one of the main problems in Natural History: data which is scattered around in many incompatible systems (not only computer systems, but also paper ones. This framework consists of computer resources (hardware and software, methodologies that ease the circulation of data, and staff expert in dealing with computers, who will develop software solutions to the problems encountered by naturalists. This system is organized in three layers: acquisition, data and analysis. Each layer is described, and an account of the elements that constitute it given.

    Se presentan las bases de una estructura bioinformática para Historia Natural, que trata de resolver uno de los principales problemas en ésta: la presencia de datos distribuidos a lo largo de muchos sistemas incompatibles entre sí (y no sólo hablamos de sistemas informáticos, sino también en papel. Esta estructura se sustenta en recursos informáticos (en sus dos vertientes: hardware y software, en metodologías que permitan la fácil circulación de los datos, y personal experto en el uso de ordenadores que se encargue de desarrollar soluciones software a los problemas que plantean los naturalistas. Este sistema estaría organizado en tres capas: de adquisición, de datos y de análisis. Cada una de estas capas se describe, indicando los elementos que la componen.