WorldWideScience

Sample records for bioinformatics resource center

  1. 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

    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...... 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...

  2. ENVIRONMENTAL BIOINFORMATICS AND COMPUTATIONAL TOXICOLOGY CENTER

    Science.gov (United States)

    The Center activities focused on integrating developmental efforts from the various research projects of the Center, and collaborative applications involving scientists from other institutions and EPA, to enhance research in critical areas. A representative sample of specif...

  3. A Survey of the Availability of Primary Bioinformatics Web Resources

    Institute of Scientific and Technical Information of China (English)

    Trias Thireou; George Spyrou; Vassilis Atlamazoglou

    2007-01-01

    The explosive growth of the bioinformatics field has led to a large amount of data and software applications publicly available as web resources. However, the lack of persistence of web references is a barrier to a comprehensive shared access. We conducted a study of the current availability and other features of primary bioinformatics web resources (such as software tools and databases). The majority (95%) of the examined bioinformatics web resources were found running on UNIX/Linux operating systems, and the most widely used web server was found to be Apache (or Apache-related products). Of the overall 1,130 Uniform Resource Locators (URLs) examined, 91% were highly available (more than 90% of the time), while only 4% showed low accessibility (less than 50% of the time) during the survey. Furthermore, the most common URL failure modes are presented and analyzed.

  4. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

    DEFF Research Database (Denmark)

    Babbitt, Patricia C.; Bagos, Pantelis G.; Bairoch, Amos;

    2015-01-01

    During 11–12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from...... protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication...

  5. CryptoDB: a Cryptosporidium bioinformatics resource update

    OpenAIRE

    Heiges, Mark; Wang, Haiming; Robinson, Edward; Aurrecoechea, Cristina; Gao, Xin; Kaluskar, Nivedita; Rhodes, Philippa; Wang, Sammy; He, Cong-Zhou; Su, Yanqi; Miller, John; Kraemer, Eileen; Kissinger, Jessica C

    2005-01-01

    The database, CryptoDB (), is a community bioinformatics resource for the AIDS-related apicomplexan-parasite, Cryptosporidium. CryptoDB integrates whole genome sequence and annotation with expressed sequence tag and genome survey sequence data and provides supplemental bioinformatics analyses and data-mining tools. A simple, yet comprehensive web interface is available for mining and visualizing the data. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded...

  6. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

    Science.gov (United States)

    Babbitt, Patricia C; Bagos, Pantelis G; Bairoch, Amos; Bateman, Alex; Chatonnet, Arnaud; Chen, Mark Jinan; Craik, David J; Finn, Robert D; Gloriam, David; Haft, Daniel H; Henrissat, Bernard; Holliday, Gemma L; Isberg, Vignir; Kaas, Quentin; Landsman, David; Lenfant, Nicolas; Manning, Gerard; Nagano, Nozomi; Srinivasan, Narayanaswamy; O'Donovan, Claire; Pruitt, Kim D; Sowdhamini, Ramanathan; Rawlings, Neil D; Saier, Milton H; Sharman, Joanna L; Spedding, Michael; Tsirigos, Konstantinos D; Vastermark, Ake; Vriend, Gerrit

    2015-01-01

    During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue. PMID:26284514

  7. Bioinformatics

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren

    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 as a...

  8. 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…

  9. Metadata Description Framework for Integration of Bioinformatics Information Resources: A Case of iBIRA

    Directory of Open Access Journals (Sweden)

    Shri Ram,

    2014-09-01

    Full Text Available Bioinformatics emerged as a new discipline dedicated to the answer the queries about life science using computational approaches. The basic aim of bioinformatics is to create databases, analyse data sets and managing data generated through large-scale projects such as Human Genome project (HGP. It covers a wide variety of traditional computer science domains, such as data modeling, data retrieval, data mining, data integration, data managing, data warehousing, and simulation of biological information generated through laboratory and field experiments. Due to varied form, nature, and activities in the field of bioinformatics, presenting the information in cohesive fashion is major challenge. The bioinformatics information resources are heterogeneous in nature. Integration and interoperability of information is one of the biggest challenges in this field. Bioinformatics, as an emerging field, needs attention towards metadata application for resource discovery. This paper discusses the metadata element set description framework for integration of various information resources related to the field of bioinformatics available over internet. A web-based tool iBIRA: Integrated Bioinformatics Information Resources Access has been designed and developed for integration of bioinformatics information resources. Dublin Core metadata element set has been used for description of information resources and XML schema has been used for interoperability of information resources with others. A database has been designed using structure query language (SQL–database management system and hypertext preprocessor (PHP–as web programming languages for integration of bioinformatics resources. The database is designated to categorise various resources into biological database, institutions, journals, patents, software tools, web-servers, etc., and the search result is presented in the form of ‘tree view’. Each of these categories of the resources has been analysed

  10. The European Bioinformatics Institute’s data resources

    OpenAIRE

    Brooksbank, Catherine; Cameron, Graham; Thornton, Janet

    2009-01-01

    The wide uptake of next-generation sequencing and other ultra-high throughput technologies by life scientists with a diverse range of interests, spanning fundamental biological research, medicine, agriculture and environmental science, has led to unprecedented growth in the amount of data generated. It has also put the need for unrestricted access to biological data at the centre of biology. The European Bioinformatics Institute (EMBL-EBI) is unique in Europe and is one of only two organisati...

  11. 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.

  12. CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus

    Science.gov (United States)

    The Rhipicephalus microplus genome is large and complex in structure, making a genome sequence difficult to assemble and costly to resource the required bioinformatics. In light of this, a consortium of international collaborators was formed to pool resources to begin sequencing this genome. We have...

  13. G2LC: Resources Autoscaling for Real Time Bioinformatics Applications in IaaS

    Directory of Open Access Journals (Sweden)

    Rongdong Hu

    2015-01-01

    Full Text Available Cloud computing has started to change the way how bioinformatics research is being carried out. Researchers who have taken advantage of this technology can process larger amounts of data and speed up scientific discovery. The variability in data volume results in variable computing requirements. Therefore, bioinformatics researchers are pursuing more reliable and efficient methods for conducting sequencing analyses. This paper proposes an automated resource provisioning method, G2LC, for bioinformatics applications in IaaS. It enables application to output the results in a real time manner. Its main purpose is to guarantee applications performance, while improving resource utilization. Real sequence searching data of BLAST is used to evaluate the effectiveness of G2LC. Experimental results show that G2LC guarantees the application performance, while resource is saved up to 20.14%.

  14. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

    DEFF Research Database (Denmark)

    Babbitt, Patricia C.; Bagos, Pantelis G.; Bairoch, Amos; Bateman, Alex; Chatonnet, Arnaud; Chen, Mark Jinan; Craik, David J.; Finn, Robert D.; Gloriam, David; Haft, Daniel H.; Henrissat, Bernard; Holliday, Gemma L.; Isberg, Vignir; Kaas, Quentin; Landsman, David; Lenfant, Nicolas; Manning, Gerard; Nagano, Nozomi; Srinivasan, Narayanaswamy; O’Donovan, Claire; Pruitt, Kim D.; Sowdhamini, Ramanathan; Rawlings, Neil D.; Saier, Milton H.; Sharman, Joanna L.; Spedding, Michael; Tsirigos, Konstantinos D.; Vastermark, Ake; Vriend, Gerrit

    2015-01-01

    During 11–12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from ...

  15. Resource Centered Store

    OpenAIRE

    Heese, Ralf

    2016-01-01

    Mit dem Resource Description Framework (RDF) können Eigenschaften von und die Beziehungen zwischen Ressourcen maschinenverarbeitbar beschrieben werden. Dadurch werden diese Daten für Maschinen zugänglicher und können unter anderem automatisch Daten zu einer Ressource lokalisieren und verarbeiten, unterschiedliche Bedeutungen einer Zeichenkette erkennen und implizite Informationen ableiten. Das Datenmodell von RDF und der zugehörigen Anfragesprache SPARQL basiert auf gerichteten und beschrifte...

  16. AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome

    OpenAIRE

    Legeai, Fabrice; Shigenobu, Shuji; Gauthier, Jean-Pierre; Colbourne, John; Rispe, Claude; Collin, Olivier; Richards, Stephen; Wilson, Alex C. C.; Tagu, Denis

    2010-01-01

    AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search c...

  17. Tools and data services registry: a community effort to document bioinformatics resources.

    Science.gov (United States)

    Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé; Kalaš, Matúš; Rydza, Emil; Chmura, Piotr; Anthon, Christian; Beard, Niall; Berka, Karel; Bolser, Dan; Booth, Tim; Bretaudeau, Anthony; Brezovsky, Jan; Casadio, Rita; Cesareni, Gianni; Coppens, Frederik; Cornell, Michael; Cuccuru, Gianmauro; Davidsen, Kristian; Vedova, Gianluca Della; Dogan, Tunca; Doppelt-Azeroual, Olivia; Emery, Laura; Gasteiger, Elisabeth; Gatter, Thomas; Goldberg, Tatyana; Grosjean, Marie; Grüning, Björn; Helmer-Citterich, Manuela; Ienasescu, Hans; Ioannidis, Vassilios; Jespersen, Martin Closter; Jimenez, Rafael; Juty, Nick; Juvan, Peter; Koch, Maximilian; Laibe, Camille; Li, Jing-Woei; Licata, Luana; Mareuil, Fabien; Mičetić, Ivan; Friborg, Rune Møllegaard; Moretti, Sebastien; Morris, Chris; Möller, Steffen; Nenadic, Aleksandra; Peterson, Hedi; Profiti, Giuseppe; Rice, Peter; Romano, Paolo; Roncaglia, Paola; Saidi, Rabie; Schafferhans, Andrea; Schwämmle, Veit; Smith, Callum; Sperotto, Maria Maddalena; Stockinger, Heinz; Vařeková, Radka Svobodová; Tosatto, Silvio C E; de la Torre, Victor; Uva, Paolo; Via, Allegra; Yachdav, Guy; Zambelli, Federico; Vriend, Gert; Rost, Burkhard; Parkinson, Helen; Løngreen, Peter; Brunak, Søren

    2016-01-01

    Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools. PMID:26538599

  18. National Sexual Violence Resource Center (NSVRC)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The National Sexual Violence Resource Center (NSVRC) is a national information and resource hub relating to all aspects of sexual violence. NSVRC staff collect and...

  19. 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...

  20. Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource

    OpenAIRE

    Schuette, Scott; Piatkowski, Brian; Corley, Aaron; Lang, Daniel; Geisler, Matt

    2015-01-01

    Background Physcomitrella patens, a haploid dominant plant, is fast becoming a useful molecular genetics and bioinformatics tool due to its key phylogenetic position as a bryophyte in the post-genomic era. Genome sequences from select reference species were compared bioinformatically to Physcomitrella patens using reciprocal blasts with the InParanoid software package. A reference protein interaction database assembled using MySQL by compiling BioGrid, BIND, DIP, and Intact databases was quer...

  1. Applications and Methods Utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for Bioinformatics Resource Discovery and Disparate Data and Service Integration

    Science.gov (United States)

    Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of scientific data between information resources difficu...

  2. Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community

    OpenAIRE

    Yun Zhang; Klem, Edward B.; Wei Jen; Richard H. Scheuermann; Larsen, Christopher N.; Sam Zaremba; Sanjeev Kumar; Pickett, Brett E; Greer, Douglas S.; Zhiping Gu; Guangyu Sun; Liwei Zhou; Lucy Stewart

    2012-01-01

    Several viruses within the Coronaviridae family have been categorized as either emerging or re-emerging human pathogens, with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) being the most well known. The NIAID-sponsored Virus Pathogen Database and Analysis Resource (ViPR, www.viprbrc.org) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses, including the entire Coronaviridae family. ViPR provides access to sequence records, gene and...

  3. Self-Access Centers: Maximizing Learners’ Access to Center Resources

    Directory of Open Access Journals (Sweden)

    Mark W. Tanner

    2010-09-01

    Full Text Available Originally published in TESL-EJ March 2009, Volume 12, Number 4 (http://tesl-ej.org/ej48/a2.html. Reprinted with permission from the authors.Although some students have discovered how to use self-access centers effectively, the majority appear to be unaware of available resources. A website and database of materials were created to help students locate materials and use the Self-Access Study Center (SASC at Brigham Young University’s English Language Center (ELC more effectively. Students took two surveys regarding their use of the SASC. The first survey was given before the website and database were made available. A second survey was administered 12 weeks after students had been introduced to the resource. An analysis of the data shows that students tend to use SASC resources more autonomously as a result of having a web-based database. The survey results suggest that SAC managers can encourage more autonomous use of center materials by provided a website and database to help students find appropriate materials to use to learn English.

  4. Missouri Career Education. Career Resource Center Bibliography.

    Science.gov (United States)

    Jones, Linda C.

    This bibliography contains a listing of 1276 materials in the Career Education Resource Center available for preview or short-term loan to Missouri educators. The first six sections classify materials by Elementary, Junior High, Senior High, Professional, Stereotyping, and Special Needs. Within each section materials are listed alphabetically by…

  5. Illinois trauma centers and community violence resources

    Directory of Open Access Journals (Sweden)

    Bennet Butler

    2014-01-01

    Full Text Available Background: Elder abuse and neglect (EAN, intimate partner violence (IPV, and street-based community violence (SBCV are significant public health problems, which frequently lead to traumatic injury. Trauma centers can provide an effective setting for intervention and referral, potentially interrupting the cycle of violence. Aims: To assess existing institutional resources for the identification and treatment of violence victims among patients presenting with acute injury to statewide trauma centers. Settings and Design: We used a prospective, web-based survey of trauma medical directors at 62 Illinois trauma centers. Nonresponders were contacted via telephone to complete the survey. Materials and Methods: This survey was based on a survey conducted in 2004 assessing trauma centers and IPV resources. We modified this survey to collect data on IPV, EAN, and SBCV. Statistical Analysis: Univariate and bivariate statistics were performed using STATA statistical software. Results: We found that 100% of trauma centers now screen for IPV, an improvement from 2004 (P = 0.007. Screening for EAN (70% and SBCV (61% was less common (P < 0.001, and hospitals thought that resources for SBCV in particular were inadequate (P < 0.001 and fewer resources were available for these patients (P = 0.02. However, there was lack of uniformity of screening, tracking, and referral practices for victims of violence throughout the state. Conclusion: The multiplicity of strategies for tracking and referring victims of violence in Illinois makes it difficult to assess screening and tracking or form generalized policy recommendations. This presents an opportunity to improve care delivered to victims of violence by standardizing care and referral protocols.

  6. Illinois trauma centers and community violence resources

    OpenAIRE

    Bennet Butler; Ogo Agubuzu; Luke Hansen; Marie Crandall

    2014-01-01

    Background: Elder abuse and neglect (EAN), intimate partner violence (IPV), and street-based community violence (SBCV) are significant public health problems, which frequently lead to traumatic injury. Trauma centers can provide an effective setting for intervention and referral, potentially interrupting the cycle of violence. Aims: To assess existing institutional resources for the identification and treatment of violence victims among patients presenting with acute injury to statewide traum...

  7. Marshall Space Flight Center Telescience Resource Kit

    Science.gov (United States)

    Wade, Gina

    2016-01-01

    Telescience Resource Kit (TReK) is a suite of software applications that can be used to monitor and control assets in space or on the ground. The Telescience Resource Kit was originally developed for the International Space Station program. Since then it has been used to support a variety of NASA programs and projects including the WB-57 Ascent Vehicle Experiment (WAVE) project, the Fast Affordable Science and Technology Satellite (FASTSAT) project, and the Constellation Program. The Payloads Operations Center (POC), also known as the Payload Operations Integration Center (POIC), provides the capability for payload users to operate their payloads at their home sites. In this environment, TReK provides local ground support system services and an interface to utilize remote services provided by the POC. TReK provides ground system services for local and remote payload user sites including International Partner sites, Telescience Support Centers, and U.S. Investigator sites in over 40 locations worldwide. General Capabilities: Support for various data interfaces such as User Datagram Protocol, Transmission Control Protocol, and Serial interfaces. Data Services - retrieve, process, record, playback, forward, and display data (ground based data or telemetry data). Command - create, modify, send, and track commands. Command Management - Configure one TReK system to serve as a command server/filter for other TReK systems. Database - databases are used to store telemetry and command definition information. Application Programming Interface (API) - ANSI C interface compatible with commercial products such as Visual C++, Visual Basic, LabVIEW, Borland C++, etc. The TReK API provides a bridge for users to develop software to access and extend TReK services. Environments - development, test, simulations, training, and flight. Includes standalone training simulators.

  8. MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease.

    Science.gov (United States)

    Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T; van Oven, Mannis; Wallace, Douglas C; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F; Attimonelli, Marcella; Zuchner, Stephan; Falk, Marni J; Gai, Xiaowu

    2016-06-01

    MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources. PMID:26919060

  9. Virtualized cloud data center networks issues in resource management

    CERN Document Server

    Tsai, Linjiun

    2016-01-01

    This book discusses the characteristics of virtualized cloud networking, identifies the requirements of cloud network management, and illustrates the challenges in deploying virtual clusters in multi-tenant cloud data centers. The book also introduces network partitioning techniques to provide contention-free allocation, topology-invariant reallocation, and highly efficient resource utilization, based on the Fat-tree network structure. Managing cloud data center resources without considering resource contentions among different cloud services and dynamic resource demands adversely affects the performance of cloud services and reduces the resource utilization of cloud data centers. These challenges are mainly due to strict cluster topology requirements, resource contentions between uncooperative cloud services, and spatial/temporal data center resource fragmentation. Cloud data center network resource allocation/reallocation which cope well with such challenges will allow cloud services to be provisioned with ...

  10. Virtual Resources Centers and Their Role in Small Rural Schools.

    Science.gov (United States)

    Freitas, Candido Varela de; Silva, Antonio Pedro da

    Virtual resources centers have been considered a pedagogical tool since the increasing development of electronic means allowed for the storage of huge amounts of information and its easy retrieval. Bearing in mind the need for enhancing the appearance of those centers, a discipline of "Management of Resources Centers" was included in a specialized…

  11. SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

    Science.gov (United States)

    Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

    2011-01-01

    SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/ PMID:22120661

  12. Tools and data services registry: a community effort to document bioinformatics resources

    OpenAIRE

    Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé; Kalaš, Matúš; Rydza, Emil; Chmura, Piotr; Anthon, Christian; Beard, Niall; Berka, Karel; Bolser, Dan; Booth, Tim; Bretaudeau, Anthony; Brezovsky, Jan; Casadio, Rita; Cesareni, Gianni

    2016-01-01

    Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is ...

  13. Tools and data services registry: a community effort to document bioinformatics resources

    OpenAIRE

    Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé; Kalaš, Matúš; Rydza, Emil Karol; Chmura, Piotr Jaroslaw; Anthon, Christian; Beard, Niall; Berka, Karel; Bolser, Dan; Booth, Tim; Bretaudeau, Anthony; Brezovsky, Jan; Casadio, Rita; Cesareni, Gianni

    2015-01-01

    Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is ...

  14. Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics

    OpenAIRE

    Tennis Joseph T; Good Benjamin M; Wilkinson Mark D

    2009-01-01

    Abstract Background Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags) and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need f...

  15. SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

    OpenAIRE

    Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

    2011-01-01

    SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST s...

  16. The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications

    Directory of Open Access Journals (Sweden)

    Schmid Amy K

    2007-11-01

    Full Text Available Abstract Background Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. Results The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV, and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. Conclusion The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the

  17. Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV.

    Science.gov (United States)

    Kawano, Shin; Ono, Hiromasa; Takagi, Toshihisa; Bono, Hidemasa

    2012-03-01

    In recent years, biological web resources such as databases and tools have become more complex because of the enormous amounts of data generated in the field of life sciences. Traditional methods of distributing tutorials include publishing textbooks and posting web documents, but these static contents cannot adequately describe recent dynamic web services. Due to improvements in computer technology, it is now possible to create dynamic content such as video with minimal effort and low cost on most modern computers. The ease of creating and distributing video tutorials instead of static content improves accessibility for researchers, annotators and curators. This article focuses on online video repositories for educational and tutorial videos provided by resource developers and users. It also describes a project in Japan named TogoTV (http://togotv.dbcls.jp/en/) and discusses the production and distribution of high-quality tutorial videos, which would be useful to viewer, with examples. This article intends to stimulate and encourage researchers who develop and use databases and tools to distribute how-to videos as a tool to enhance product usability. PMID:21803786

  18. Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics

    Directory of Open Access Journals (Sweden)

    Tennis Joseph T

    2009-09-01

    Full Text Available Abstract Background Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need for metadata to enhance its value, these repositories present a potentially valuable new resource for application developers. Here we characterize the current contents of two scientifically relevant metadata repositories created through social tagging. This investigation helps to establish how such socially constructed metadata might be used as it stands currently and to suggest ways that new social tagging systems might be designed that would yield better aggregate products. Results We assessed the metadata that users of CiteULike and Connotea associated with citations in PubMed with the following metrics: coverage of the document space, density of metadata (tags per document, rates of inter-annotator agreement, and rates of agreement with MeSH indexing. CiteULike and Connotea were very similar on all of the measurements. In comparison to PubMed, document coverage and per-document metadata density were much lower for the social tagging systems. Inter-annotator agreement within the social tagging systems and the agreement between the aggregated social tagging metadata and MeSH indexing was low though the latter could be increased through voting. Conclusion The most promising uses of metadata from current academic social tagging repositories will be those that find ways to utilize the novel relationships between users, tags, and documents exposed through these systems. For more traditional kinds of indexing-based applications (such as keyword-based search to

  19. Educator Resource Center for NASA Langley Research Center

    Science.gov (United States)

    Bridgford, Todd; Koltun, Nick R.

    2003-01-01

    The goal of the ERCN is to provide expertise and facilities to help educators access and utilize science, mathematics, and technology instructional products aligned with national standards and appropriate state frameworks and based on NASA s unique mission and results. The NASA Langley s Office of Education has established the service area for this ERC to be the five states of Kentucky, North Carolina, South Carolina, Virginia and West Virginia. This educational grant activity is associated with NASA s Mission to inspire the next generation of explorers.. .as only NASA can. The communication of NASA s knowledge is the prime role of this ERC. Functioning as a dissemination system of instructional materials and support for pre-college education programs we have met the NASA Education ERCN Program's goal. The following ERCN objectives have been accomplished: Demonstrate and facilitate the use of NASA educational products and technologies in print, video and web based formats. Examples include but are not limited to NASA approved Educator s Guides with Activities based on national standards for appropriate subjects and grade levels. We have demonstrated the use videotape series in analogue format and the new digital video instructional systems along with the use of NASA TV. The promotion of web page based resources such as the new NASA Portal web and the ability to download print resources is continuously facilitated in workshops. This objective has been completed by educator contacts that include on-site visits, phone requests, postal mail requests, e-mail requests, fax requests and workshops offered.

  20. Creating a Resource Center for Homeschoolers: The Impact of Technology.

    Science.gov (United States)

    Javid, Mahnaz A.

    1998-01-01

    Summarizes the findings of a two-month case study of Edmonds Cyberschool (Washington), a resource center for homeschoolers. The study focused on the impact of technology on students' learning as indicated in three areas: attitude toward technology, the use of technology, and value of technology versus other available resources. (Author/LRW)

  1. Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it

    OpenAIRE

    Swainston Neil; Griffiths Tony; Hedeler Cornelia; Garwood Christopher; Garwood Kevin; Oliver Stephen G; Paton Norman W

    2006-01-01

    Abstract Background The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated i...

  2. Nursing Reference Center: a point-of-care resource.

    Science.gov (United States)

    Vardell, Emily; Paulaitis, Gediminas Geddy

    2012-01-01

    Nursing Reference Center is a point-of-care resource designed for the practicing nurse, as well as nursing administrators, nursing faculty, and librarians. Users can search across multiple resources, including topical Quick Lessons, evidence-based care sheets, patient education materials, practice guidelines, and more. Additional features include continuing education modules, e-books, and a new iPhone application. A sample search and comparison with similar databases were conducted. PMID:22559182

  3. Building an Information Resource Center for Competitive Intelligence.

    Science.gov (United States)

    Martin, J. Sperling

    1992-01-01

    Outlines considerations in the design of a Competitive Intelligence Information Resource Center (CIIRC), which is needed by business organizations for effective strategic decision making. Discussed are user needs, user participation, information sources, technology and interface design, operational characteristics, and planning for implementation.…

  4. Electronic Commerce Resource Centers. An Industry--University Partnership.

    Science.gov (United States)

    Gulledge, Thomas R.; Sommer, Rainer; Tarimcilar, M. Murat

    1999-01-01

    Electronic Commerce Resource Centers focus on transferring emerging technologies to small businesses through university/industry partnerships. Successful implementation hinges on a strategic operating plan, creation of measurable value for customers, investment in customer-targeted training, and measurement of performance outputs. (SK)

  5. 76 FR 53885 - Patent and Trademark Resource Centers Metrics

    Science.gov (United States)

    2011-08-30

    ..., Public Search Services Division, Office of the Chief Information Officer, United States Patent and... United States Patent and Trademark Office Patent and Trademark Resource Centers Metrics ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark Office (USPTO), as part of...

  6. Agrigenomics for microalgal biofuel production: an overview of various bioinformatics resources and recent studies to link OMICS to bioenergy and bioeconomy.

    Science.gov (United States)

    Misra, Namrata; Panda, Prasanna Kumar; Parida, Bikram Kumar

    2013-11-01

    Microalgal biofuels offer great promise in contributing to the growing global demand for alternative sources of renewable energy. However, to make algae-based fuels cost competitive with petroleum, lipid production capabilities of microalgae need to improve substantially. Recent progress in algal genomics, in conjunction with other "omic" approaches, has accelerated the ability to identify metabolic pathways and genes that are potential targets in the development of genetically engineered microalgal strains with optimum lipid content. In this review, we summarize the current bioeconomic status of global biofuel feedstocks with particular reference to the role of "omics" in optimizing sustainable biofuel production. We also provide an overview of the various databases and bioinformatics resources available to gain a more complete understanding of lipid metabolism across algal species, along with the recent contributions of "omic" approaches in the metabolic pathway studies for microalgal biofuel production. PMID:24044362

  7. Annotated Resource List of Peace Education Resources Available from Wilmington College Peace Resource Center, Hiroshima/Nagasaki Memorial Collection.

    Science.gov (United States)

    Wilmington Coll., OH. Peace Resource Center.

    Over 130 print and nonprint peace education resources for use with adult groups and elementary, secondary, and college students are described. Audiovisuals may be rented and books may be purchased from the Wilmington College (Ohio) Peace Resource Center. Audiovisuals, including slides, videotapes and videotape cassettes, and 16mm films, are…

  8. Database resources of the National Center for Biotechnology Information

    OpenAIRE

    . .

    2012-01-01

    In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, H...

  9. Database resources of the National Center for Biotechnology

    OpenAIRE

    Wheeler, David L.; Church, Deanna M.; Federhen, Scott; Lash, Alex E.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M; Sequeira, Edwin; Tatusova, Tatiana A.; Wagner, Lukas

    2003-01-01

    In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGe...

  10. Amarillo National Resource Center for Plutonium 1999 plan

    International Nuclear Information System (INIS)

    The purpose of the Amarillo National Resource Center for Plutonium is to serve the Texas Panhandle, the State of Texas and the US Department of Energy by: conducting scientific and technical research; advising decision makers; and providing information on nuclear weapons materials and related environment, safety, health, and nonproliferation issues while building academic excellence in science and technology. This paper describes the electronic resource library which provides the national archives of technical, policy, historical, and educational information on plutonium. Research projects related to the following topics are described: Environmental restoration and protection; Safety and health; Waste management; Education; Training; Instrumentation development; Materials science; Plutonium processing and handling; and Storage

  11. Amarillo National Resource Center for Plutonium 1999 plan

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-01-30

    The purpose of the Amarillo National Resource Center for Plutonium is to serve the Texas Panhandle, the State of Texas and the US Department of Energy by: conducting scientific and technical research; advising decision makers; and providing information on nuclear weapons materials and related environment, safety, health, and nonproliferation issues while building academic excellence in science and technology. This paper describes the electronic resource library which provides the national archives of technical, policy, historical, and educational information on plutonium. Research projects related to the following topics are described: Environmental restoration and protection; Safety and health; Waste management; Education; Training; Instrumentation development; Materials science; Plutonium processing and handling; and Storage.

  12. 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.

  13. The ESRC: A Web-based Environmental Satellite Resource Center

    Science.gov (United States)

    Abshire, W. E.; Guarente, B.; Dills, P. N.

    2009-12-01

    The COMET® Program has developed an Environmental Satellite Resource Center (known as the ESRC), a searchable, database-driven Website that provides easy access to a wide range of useful information training materials on polar-orbiting and geostationary satellites. Primarily sponsored by the NPOESS Program and NOAA, the ESRC is a tool for users seeking reliable sources of satellite information, training, and data. First published in September 2008, and upgraded in April 2009, the site is freely available at: http://www.meted.ucar.edu/esrc. Additional contributions to the ESRC are sought and made on an ongoing basis. The ESRC was created in response to a broad community request first made in May 2006. The COMET Program was asked to develop the site to consolidate and simplify access to reliable, current, and diverse information, training materials, and data associated with environmental satellites. The ESRC currently includes over 400 significant resources from NRL, CIMSS, CIRA, NASA, VISIT, NESDIS, and EUMETSAT, and improves access to the numerous satellite resources available from COMET’s MetEd Website. The ESRC is designed as a community site where organizations and individuals around the globe can easily submit their resources via online forms by providing a small set of metadata. The ESRC supports languages other than English and multi-lingual character sets have been tested. COMET’s role is threefold: 1) maintain the site, 2) populate it with our own materials, including smaller, focused learning objects derived from our larger training modules, and 3) provide the necessary quality assurance and monitoring to ensure that all resources are appropriate and well described before being made available. Our presentation will demonstrate many of the features and functionality of searching for resources using the ESRC, and will outline the steps for users to make their own submissions. For the site to reach its full potential, submissions representing diverse

  14. NASA's Meteorologist Center: Online Resources to Promote Climate Literacy

    Science.gov (United States)

    Jackson, R.; Tenenbaum, L. F.; Witte, J.

    2012-12-01

    In a recent survey by George Mason University, a significant number of meteorologists and weathercasters in America cited lack of access to appropriate visuals and graphics as a basic impediment to reporting the reality of anthropogenic climate change. To address this need, NASA's Global Climate Change Website, climate.nasa.gov, has developed an online Meteorologist Center, stocked with high quality graphics and animations, public education materials, and a list of credible online resources. The goal of the project is to provide weathercasters with a "one-stop shop" for broadcast-ready materials that can be used to report on global climate change and to educate audiences.;

  15. Aquaculture, husbandry, and shipping at the Zebrafish International Resource Center.

    Science.gov (United States)

    Varga, Z M

    2016-01-01

    This chapter provides an overview of the Zebrafish International Resource Center (ZIRC) aquaculture systems, husbandry, and live fish shipping methods. The ZIRC has a recirculating water system with mechanical and biological filtration in its main fish facility, and a flow-through water system for its quarantine room. I describe basic husbandry methods for breeding, rearing larvae, feeding and shipping of fish. Whereas the procedures presented here are merely an overview and only the most essential methods are included, they offer starting points to set up, develop, refine, or troubleshoot methods in other fish facilities. PMID:27443942

  16. Aquaculture and husbandry at the zebrafish international resource center.

    Science.gov (United States)

    Varga, Zoltán M

    2011-01-01

    This chapter provides an overview of the aquaculture system and the husbandry methods used at the Zebrafish International Resource Center (ZIRC). ZIRC employs a recirculating water system with mechanical and biological filtration for its main facility, and a flow-through water system for its quarantine room. I describe basic husbandry methods for breeding, rearing larvae, and feeding and the extensive in-house health surveillance for the biosafety of the fish population. Whereas the description of these procedures is merely an overview and only the most essential methods are included, it offers several starting points to set up, refine, or troubleshoot other fish facilities. PMID:21924177

  17. GALT Protein Database, a Bioinformatics Resource for the Manage-ment and Analysis of Structural Features of a Galactosemia-related Protein and Its Mutants

    Institute of Scientific and Technical Information of China (English)

    Antonio d'Acierno; Angelo Facchiano; Anna Marabotti

    2009-01-01

    We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type Ⅰ. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.

  18. Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration

    Science.gov (United States)

    2010-01-01

    Background Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap") offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS]) used SSWAP to semantically describe selected data and web services. Methods We selected high-priority Quantitative Trait Locus (QTL), genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL), Resource Description Framework (RDF) and eXtensible Markup Language (XML) documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info. Results A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST). Conclusions The need for semantic integration technologies has preceded available solutions. We

  19. Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP for bioinformatics resource discovery and disparate data and service integration

    Directory of Open Access Journals (Sweden)

    Nelson Rex T

    2010-06-01

    Full Text Available Abstract Background Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap" offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS] used SSWAP to semantically describe selected data and web services. Methods We selected high-priority Quantitative Trait Locus (QTL, genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL, Resource Description Framework (RDF and eXtensible Markup Language (XML documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info. Results A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST. Conclusions The need for semantic integration technologies has preceded

  20. Eukaryotic Pathogen Database Resources (EuPathDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with...

  1. Database resources of the National Center for Biotechnology Information.

    Science.gov (United States)

    2016-01-01

    The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:26615191

  2. AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies

    Directory of Open Access Journals (Sweden)

    Shankavaram Uma

    2006-04-01

    Full Text Available Abstract Background Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein lysate arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop precise information on the genes that encode their antigens. Translation among the various protein and gene identifier types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody, protein, and gene information, we initially developed a relational database in Filemaker for our own use. When it became apparent that the information would be useful to many other researchers faced with the need to choose or characterize antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed in Java. Description AbMiner is a user-friendly, web-based relational database of information on > 600 commercially available antibodies that we validated by Western blot for protein microarray studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety of other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our quality-control data against a pool of 60 diverse cancer cell types (the NCI-60 and also protein expression levels for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection of the listed antibodies. Some other available database resources give information on antibody specificity for one or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in a pool of 60 diverse cell types from nine different

  3. Fluor Hanford ALARA Center is a D and D Resource

    International Nuclear Information System (INIS)

    II. The ALARA Center staff routinely researches and tests new technology, sponsor vendor demonstrations, and redistribute tools, equipment and temporary shielding that may not be needed at one facility to another facility that needs it. The ALARA Center staff learns about new technology in several ways. This includes past radiological work experience, interaction with vendors, lessons learned, networking with other DOE sites, visits to the Hanford Technical Library, attendance at off-site conferences and ALARA Workshops. Personnel that contact the ALARA Center for assistance report positive results when they implement the tools, equipment and work practices recommended by the ALARA Center staff. This has translated to reduced exposure for workers and reduced the risk of contamination spread. For example: using a hydraulic shear on one job saved 16 Rem of exposure that would have been received if workers had used saws-all tools to cut piping in twenty-nine locations. Currently, the ALARA Center staff is emphasizing D and D techniques on size-reducing materials, decontamination techniques, use of remote tools/video equipment, capture ventilation, fixatives, using containments and how to find lessons learned. The ALARA Center staff issues a weekly report that discusses their interaction with the workforce and any new work practices, tools and equipment being used by the Hanford contractors. Distribution of this weekly report is to about 130 personnel on site and 90 personnel off site. This effectively spreads the word about ALARA throughout the DOE Complex. DOE EM-23, in conjunction with the D and D and Environmental Restoration work group of the Energy Facility Contractors Organization (EFCOG) established the Hanford ALARA Center as the D and D Hotline for companies who have questions about how D and D work is accomplished. The ALARA Center has become a resource to the nuclear industry and routinely helps contractors at other DOE Sites, power reactors, DOD sites, and

  4. Uso da bioinformática na diferenciação molecular da Entamoeba histolytica e Entamoeba díspar = Molecular discrimination of Entamoeba histolytica and Entamoeba dispar by bioinformatics resources

    Directory of Open Access Journals (Sweden)

    Eliane Gasparino

    2008-07-01

    Full Text Available Amebíase invasiva, causada por Entamoeba histolytica, é microscopicamente indistinguível da espécie não-patogênica Entamoeba dispar. Com auxílio de ferramentas de bioinformática, objetivou-se diferenciar Entamoeba histolytica e Entamoeba dispar por técnicasmoleculares. A análise foi realizada a partir do banco de dados da National Center for Biotechnology Information; pela pesquisa de similaridade de sequências, elegeu-se o gene da cisteína sintase. Um par de primer foi desenhado (programa Web Primer e foi selecionada a enzima de restrição TaqI (programa Web Cutter. Após a atuação da enzima, o fragmento foi dividido em dois, um com 255 pb e outro com 554 pb, padrão característico da E. histolytica. Na ausência de corte, o fragmento apresentou o tamanho de 809 pb, referente à E. dispar.Under microscopic conditions, the invasive Entamoeba histolytica is indistinguishable from the non-pathogenic species Entamoeba dispar. In this way, the present study was carried out to determine a molecular strategy for discriminating both species by the mechanisms of bioinformatics. The gene cysteine synthetase was consideredfor such a purpose by using the resources of the National Center for Biotechnology Information data bank in the search for similarities in the gene sequence. In this way, a primer pair was designed by the Web Primer program and the restriction enzyme TaqI was selected by the Web Cutter software program. The DNA fragment had a size of 809 bpbefore cutting, which is consistent with E. dispar. The gene fragment was partitioned in a first fragment with 255 bp and a second one with 554 bp, which is similar to the genetic characteristics of E. histolytica.

  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. Bioinformatic tools for studying post-transcriptional gene regulation : The UAlbany TUTR collection and other informatic resources.

    Science.gov (United States)

    Doyle, Francis; Zaleski, Christopher; George, Ajish D; Stenson, Erin K; Ricciardi, Adele; Tenenbaum, Scott A

    2008-01-01

    The untranslated regions (UTRs) of many mRNAs contain sequence and structural motifs that are used to regulate the stability, localization, and translatability of the mRNA. It should be possible to discover previously unidentified RNA regulatory motifs by examining many related nucleotide sequences, which are assumed to contain a common motif. This is a general practice for discovery of DNA-based sequence-based patterns, in which alignment tools are heavily exploited. However, because of the complexity of sequential and structural components of RNA-based motifs, simple-alignment tools are frequently inadequate. The consensus sequences they find frequently have the potential for significant variability at any given position and are only loosely characterized. The development of RNA-motif discovery tools that infer and integrate structural information into motif discovery is both necessary and expedient. Here, we provide a selected list of existing web-accessible algorithms for the discovery of RNA motifs, which, although not exhaustive, represents the current state of the art. To facilitate the development, evaluation, and training of new software programs that identify RNA motifs, we created the UAlbany training UTR (TUTR) database, which is a collection of validated sets of sequences containing experimentally defined regulatory motifs. Presently, eleven training sets have been generated with associated indexes and "answer sets" provided that identify where the previously characterized RNA motif [the iron responsive element (IRE), AU-rich class-2 element (ARE), selenocysteine insertion sequence (SECIS), etc.] resides in each sequence. The UAlbany TUTR collection is a shared resource that is available to researchers for software development and as a research aid. PMID:18369974

  7. An Introduction to Bioinformatics

    Institute of Scientific and Technical Information of China (English)

    SHENGQi-zheng; DeMoorBart

    2004-01-01

    As a newborn interdisciplinary field, bioinformatics is receiving increasing attention from biologists, computer scientists, statisticians, mathematicians and engineers. This paper briefly introduces the birth, importance, and extensive applications of bioinformatics in the different fields of biological research. A major challenge in bioinformatics - the unraveling of gene regulation - is discussed in detail.

  8. Argonne Laboratory Computing Resource Center - FY2004 Report.

    Energy Technology Data Exchange (ETDEWEB)

    Bair, R.

    2005-04-14

    In the spring of 2002, Argonne National Laboratory founded the Laboratory Computing Resource Center, and in April 2003 LCRC began full operations with Argonne's first teraflops computing cluster. The LCRC's driving mission is to enable and promote computational science and engineering across the Laboratory, primarily by operating computing facilities and supporting application use and development. This report describes the scientific activities, computing facilities, and usage in the first eighteen months of LCRC operation. In this short time LCRC has had broad impact on programs across the Laboratory. The LCRC computing facility, Jazz, is available to the entire Laboratory community. In addition, the LCRC staff provides training in high-performance computing and guidance on application usage, code porting, and algorithm development. All Argonne personnel and collaborators are encouraged to take advantage of this computing resource and to provide input into the vision and plans for computing and computational analysis at Argonne. Steering for LCRC comes from the Computational Science Advisory Committee, composed of computing experts from many Laboratory divisions. The CSAC Allocations Committee makes decisions on individual project allocations for Jazz.

  9. 34 CFR 464.1 - What is the State Literacy Resource Centers Program?

    Science.gov (United States)

    2010-07-01

    ... purpose of sharing information, data, research, and expertise and literacy resources. (Authority: 20 U.S.C... 34 Education 3 2010-07-01 2010-07-01 false What is the State Literacy Resource Centers Program...) OFFICE OF VOCATIONAL AND ADULT EDUCATION, DEPARTMENT OF EDUCATION STATE LITERACY RESOURCE CENTERS...

  10. 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

    2016-03-01

    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. PMID:26851671

  11. L-025: EPR-First Responders: Resource Coordinator and National Center for Emergency Operations

    International Nuclear Information System (INIS)

    This conference cover the importance of resource coordinator and the national Center for Emergency Operations which provides a stable environment installation and a valuable aid in the radiological emergency situation.The resources coordinator maintains the registers and resources located in general as well as the National Center for Emergency Operations is the ideal place for the public information Center. Both roles provide support and encourage the efforts to respond to the incident Command

  12. Amarillo National Resource Center for Plutonium. Quarterly technical progress report, May 1, 1997--July 31, 1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-09-01

    Progress summaries are provided from the Amarillo National Center for Plutonium. Programs include the plutonium information resource center, environment, public health, and safety, education and training, nuclear and other material studies.

  13. Agile parallel bioinformatics workflow management using Pwrake

    OpenAIRE

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

    2011-01-01

    Abstract 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 environm...

  14. Deep Learning in Bioinformatics

    OpenAIRE

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2016-01-01

    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 res...

  15. The Right Stuff: Essential Resources for Managing Your Middle School Media Center.

    Science.gov (United States)

    Manczuk, Suzanne

    1999-01-01

    Describes the following resources for managing a middle school media center: literature bibliographies with on-target middle school recommendations and useful annotations; resources for teaching primary sources; resources on censorship and banned books; basic Internet guides; copyright-law resources; information-literacy standards; and…

  16. Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

    Directory of Open Access Journals (Sweden)

    Tilton Susan C

    2012-11-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p Conclusions BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis generation tool for systems biology. The miRNA workflow in BRM allows for efficient processing of multiple miRNA and mRNA datasets in a single

  17. An Instructional Resource Center in a Senior Dental Clinic.

    Science.gov (United States)

    Berrong, Joseph M.; And Others

    1982-01-01

    Development of an instructional materials center and self-instructional materials on clinical dental procedures is described. The center is located near students' operatories and the student-tested programs were developed cost-effectively and relatively quickly. (MSE)

  18. Bioinformatics as a pedagogical resource for the biology course in the State University of Ceara - UECE - Fortaleza, Ceará State - doi: 10.4025/actascieduc.v34i1.14584

    Directory of Open Access Journals (Sweden)

    Howard Lopes Ribeiro Junior

    2012-05-01

    Full Text Available The objective of this study was to evaluate and apply the Bioinformatics theoretical contents and practical for the course students in Biological Sciences Degree Fully enrolled in the disciplines of General Genetics and Molecular Biology, State University of Ceara in 2010. The theoretical approach previously tested (RIBEIRO JUNIOR, 2011 consisted of a presentation of historical concepts, basic and specific to current advances in research involved the areas of molecular biology. The practice of "Building a Molecular Phylogeny in Silico" is designed to become functional in practice the concepts presented above, using the database of the National Center for Biotechnology Information, NCBI, and their sequence alignment tool, the BLASTp (Basic Local Alignment Search Tool Protein-Protein. positive results obtained with the application of the lecture Introduction to Bioinformatics and practical activities were highlighted with the characterizations of molecular phylogenies of the sequences hypothetical proposals for the implementation of the alignments and the statements of students mentioned above. These activities were seen as essential so that students could experience step by step to a better understanding of the emerging field of life sciences: the Bioinformatics

  19. Introduction to Bioinformatics

    OpenAIRE

    Thampi, Sabu M.

    2009-01-01

    Bioinformatics is a new discipline that addresses the need to manage and interpret the data that in the past decade was massively generated by genomic research. This discipline represents the convergence of genomics, biotechnology and information technology, and encompasses analysis and interpretation of data, modeling of biological phenomena, and development of algorithms and statistics. This article presents an introduction to bioinformatics

  20. 34 CFR 669.1 - What is the Language Resource Centers Program?

    Science.gov (United States)

    2010-07-01

    ... improving the nation's capacity for teaching and learning foreign languages effectively. (Authority: 20 U.S... 34 Education 3 2010-07-01 2010-07-01 false What is the Language Resource Centers Program? 669.1... POSTSECONDARY EDUCATION, DEPARTMENT OF EDUCATION LANGUAGE RESOURCE CENTERS PROGRAM General § 669.1 What is...

  1. Natural Resource Program Center FY 2011 Annual Report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This annual report describes implementation of the Natural Resource Program Center’s Inventory and Monitoring (I&M) program during FY 2011. The introduction...

  2. RESOURCES CENTERS IN THE FIELD OF SOCIAL ECONOMY IN ROMANIA

    OpenAIRE

    Mihaela Pitea

    2013-01-01

    This article briefly presents the eligible initiatives of the Sectorial Operational Program “Human Resources Development 2007 – 2013” Invest in People! (POSDRU) on the Priority Axis nr. 6: Promotion Social Inclusion, Intervention Field 6.1 Developing social economy. POSDRU has supported the set-up of the Resources Centres for Social Economy that proved in time to be useful by providing information and offering support to the communities. This article describes the centres that made their a...

  3. Chemistry in Bioinformatics

    OpenAIRE

    Mitchell John; Murray-Rust Peter; Rzepa Henry

    2005-01-01

    Abstract Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the auth...

  4. Earth Resources Observation and Science (EROS) Center's Landsat State Mosaics Gallery

    Data.gov (United States)

    National Aeronautics and Space Administration — The Earth Resources Observation and Science (EROS) Center manages the this gallery of images of the 50 U.S. states plus Puerto Rico as derived by Landsat data.

  5. Earth Resources Observation and Science (EROS) Center's Earth as Art Image Gallery 3

    Data.gov (United States)

    National Aeronautics and Space Administration — The Earth Resources Observation and Science (EROS) Center manages the Earth as Art Three exhibit, which provides fresh and inspiring glimpses of different parts of...

  6. Natural Resource Program Center Inventory and Monitoring Fiscal Year 2012 Annual Work Plan

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The Natural Resource Program Center annual work plan discusses the goals and objectives of the Inventory and Monitoring IM program for fiscal year 2012. The...

  7. Earth Resources Observation and Science (EROS) Center's Earth as Art Image Gallery 2

    Data.gov (United States)

    National Aeronautics and Space Administration — The Earth Resources Observation and Science (EROS) Center manages this collection of forty-five new scenes developed for their aesthetic beauty, rather than for...

  8. Amarillo National Resource Center for Plutonium quarterly technical progress report, August 1--October 31, 1998

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-11-01

    This paper describes activities of the Center under the following topical sections: Electronic resource library; Environmental restoration and protection; Health and safety; Waste management; Communication program; Education program; Training; Analytical development; Materials science; Plutonium processing and handling; and Storage.

  9. Earth Resources Observation and Science (EROS) Center's Journey of Lewis and Clark Gallery

    Data.gov (United States)

    National Aeronautics and Space Administration — The Earth Resources Observation and Science (EROS) Center manages the this gallery of Landsat-derived images of one of the most remarkable and productive scientific...

  10. Amarillo National Resource Center for Plutonium. Quarterly technical progress report, February 1, 1998--April 30, 1998

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-06-01

    Activities from the Amarillo National Resource Center for Plutonium are described. Areas of work include materials science of nuclear and explosive materials, plutonium processing and handling, robotics, and storage.

  11. Information resources at the National Center for Biotechnology Information.

    OpenAIRE

    Woodsmall, R M; Benson, D A

    1993-01-01

    The National Center for Biotechnology Information (NCBI), part of the National Library of Medicine, was established in 1988 to perform basic research in the field of computational molecular biology as well as build and distribute molecular biology databases. The basic research has led to new algorithms and analysis tools for interpreting genomic data and has been instrumental in the discovery of human disease genes for neurofibromatosis and Kallmann syndrome. The principal database responsibi...

  12. Nuclear Energy Center Site Survey, 1975. Part V. Resource availability and site screening

    International Nuclear Information System (INIS)

    Resource requirements for nuclear energy centers are discussed and the large land areas which meet these requirements and may contain potential sites for a nuclear energy center (NEC) are identified. Maps of the areas are included that identify seismic zones, river flow rates, and population density

  13. Using Language Corpora to Develop a Virtual Resource Center for Business English

    Science.gov (United States)

    Ngo, Thi Phuong Le

    2015-01-01

    A Virtual Resource Center (VRC) has been brought into use since 2008 as an integral part of a task-based language teaching and learning program for Business English courses at Nantes University, France. The objective of the center is to enable students to work autonomously and individually on their language problems so as to improve their language…

  14. Amarillo National Resource Center for Plutonium quarterly technical progress report, February 1--April 30, 1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-06-01

    This report contains short summaries of the activities carried out under the umbrella of the Amarillo National Resource Center for Plutonium. Studies are related to the Plutonium Information Resource; advisory functions; environmental, public health and safety; communication, education, and training; and nuclear and other material studies. Approximately 40 report summaries are presented. Several detailed reports are also included.

  15. Amarillo National Resource Center for Plutonium quarterly technical progress report, August 1, 1997--October 31, 1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-31

    This report summarizes activities of the Amarillo National Resource Center for Plutonium during the quarter. The report describes the Electronic Resource Library; DOE support activities; current and future environmental health and safety programs; pollution prevention and pollution avoidance; communication, education, training, and community involvement programs; and nuclear and other material studies, including plutonium storage and disposition studies.

  16. Chemistry in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Mitchell John

    2005-06-01

    Full Text Available Abstract Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.

  17. Assessment of water resources for nuclear energy centers

    International Nuclear Information System (INIS)

    Maps of the conterminous United States showing the rivers with sufficient flow to be of interest as potential sites for nuclear energy centers are presented. These maps show the rivers with (1) mean annual flows greater than 3000 cfs, with the flow rates identified for ranges of 3000 to 6000, 6000 to 12,000, 12,000 to 24,000, and greater than 24,000 cfs; (2) monthly, 20-year low flows greater than 1500 cfs, with the flow rates identified for ranges of 1500 to 3000, 3000 to 6000, 6000 to 12,000, and greater than 12,000 cfs; and (3) annual, 20-year low flows greater than 1500 cfs, with the flow rates identified for ranges of 1500 to 3000, 3000 to 6000, 6000 to 12,000, and greater than 12,000 cfs. Criteria relating river flow rates required for various size generating stations both for sites located on reservoirs and for sites without local storage of cooling water are discussed. These criteria are used in conjunction with plant water consumption rates (based on both instantaneous peak and annual average usage rates) to estimate the installed generating capacity that may be located at one site or within a river basin. Projections of future power capacity requirements, future demand for water (both withdrawals and consumption), and regions of expected water shortages are also presented. Regional maps of water availability, based on annual, 20-year low flows, are also shown. The feasibility of locating large energy centers in these regions is discussed

  18. 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.…

  19. The MMS Science Data Center: Operations, Capabilities, and Resource.

    Science.gov (United States)

    Larsen, K. W.; Pankratz, C. K.; Giles, B. L.; Kokkonen, K.; Putnam, B.; Schafer, C.; Baker, D. N.

    2015-12-01

    The Magnetospheric MultiScale (MMS) constellation of satellites completed their six month commissioning period in August, 2015 and began science operations. Science operations for the Solving Magnetospheric Acceleration, Reconnection, and Turbulence (SMART) instrument package occur at the Laboratory for Atmospheric and Space Physics (LASP). The Science Data Center (SDC) at LASP is responsible for the data production, management, distribution, and archiving of the data received. The mission will collect several gigabytes per day of particles and field data. Management of these data requires effective selection, transmission, analysis, and storage of data in the ground segment of the mission, including efficient distribution paths to enable the science community to answer the key questions regarding magnetic reconnection. Due to the constraints on download volume, this includes the Scientist-in-the-Loop program that identifies high-value science data needed to answer the outstanding questions of magnetic reconnection. Of particular interest to the community is the tools and associated website we have developed to provide convenient access to the data, first by the mission science team and, beginning March 1, 2016, by the entire community. This presentation will demonstrate the data and tools available to the community via the SDC and discuss the technologies we chose and lessons learned.

  20. Bioinformatics and School Biology

    Science.gov (United States)

    Dalpech, Roger

    2006-01-01

    The rapidly changing field of bioinformatics is fuelling the need for suitably trained personnel with skills in relevant biological "sub-disciplines" such as proteomics, transcriptomics and metabolomics, etc. But because of the complexity--and sheer weight of data--associated with these new areas of biology, many school teachers feel…

  1. Addressing underutilization of consumer health information resource centers: a formative study*

    Science.gov (United States)

    Kennedy, May G.; Kiken, Laura; Shipman, Jean P.

    2008-01-01

    Problem: Four consumer health information centers in Richmond, Virginia, provide one-on-one assistance in accessing health information. Because they may not be fully utilized at present, an exploratory marketing study of factors affecting usage of the centers was conducted. Method: Observers counted center passers-by and tracked their paths. Also, brief intercept interviews were conducted with people who had just used a center, people nearby who could have used one but did not, and people on the street. Finally, in-depth individual interviews were conducted with key informants. Results: There was a high degree of satisfaction with the centers among users. Nonusers universally endorsed the center concept. However, most passers-by did not even glance at the centers, and intercept interviewees suggested better signage and promoting the resource centers through various media channels. Key informants added suggestions about interpersonal strategies (e.g., physician referrals) for center usage promotion but cautioned that a large increase in traffic could not be accommodated without increasing staff size or shifting from a model of individualized service. Conclusions: Triangulating findings from multiple data collection methods can provide useful guidance for efforts to promote center utilization. At minimum, steps should be taken to make the largest centers more noticeable. Because center utilization is not only associated with consumer satisfaction with hospitals, but may also foster health literacy, both hospital-based and community-based usage promotion strategies may be warranted. All such promotional strategies should be audience-tested before they are adopted. PMID:18219380

  2. ATLAS Tier-2 at the Compute Resource Center GoeGrid in Göttingen

    CERN Document Server

    Meyer, J; The ATLAS collaboration; Weber, P

    2010-01-01

    GoeGrid is a grid resource center located in Goettingen, Germany. The resources are commonly used, funded, and maintained by communities doing research in the fields grid development, computer science, biomedicine, high energy physics, theoretical physics, astrophysics, and the humanities. For the high energy physics community GoeGrid serves as a Tier-2 center for the ATLAS experiment as part of the world-wide LHC computing grid (WLCG). The status and performance of the Tier-2 center will be presented with a focus on the interdisciplinary setup and administration of the cluster. Given the various requirements of the different communities on the hardware and software setup the challenge of the common operation of the cluster will be detailed. The benefits are an efficient use of computer and manpower resources. Further interdisciplinary projects are commonly organized courses for students of all fields to support education on grid-computing.

  3. ATLAS Tier-2 at the Compute Resource Center GoeGrid in Gettingen

    International Nuclear Information System (INIS)

    GoeGrid is a grid resource center located in Gettingen, Germany. The resources are commonly used, funded, and maintained by communities doing research in the fields of grid development, computer science, biomedicine, high energy physics, theoretical physics, astrophysics, and the humanities. For the high energy physics community, GoeGrid serves as a Tier-2 center for the ATLAS experiment as part of the world-wide LHC computing grid (WLCG). The status and performance of the Tier-2 center is presented with a focus on the interdisciplinary setup and administration of the cluster. Given the various requirements of the different communities on the hardware and software setup the challenge of the common operation of the cluster is detailed. The benefits are an efficient use of computer and personpower resources.

  4. ATLAS Tier-2 at the Compute Resource Center GoeGrid in Goettingen

    CERN Document Server

    Meyer, J; The ATLAS collaboration; Weber, P

    2011-01-01

    GoeGrid is a grid resource center located in G¨ottingen, Germany. The resources are commonly used, funded, and maintained by communities doing research in the fields grid development, computer science, biomedicine, high energy physics, theoretical physics, astrophysics, and the humanities. For the high energy physics community GoeGrid serves as a Tier-2 center for the ATLAS experiment as part of the world-wide LHC computing grid (WLCG). The status and performance of the Tier-2 center is presented with a focus on the interdisciplinary setup and administration of the cluster. Given the various requirements of the different communities on the hardware and software setup the challenge of the common operation of the cluster is detailed. The benefits are an efficient use of computer and manpower resources.

  5. ThalInd, a β-thalassemia and hemoglobinopathies database for India: defining a model country-specific and disease-centric bioinformatics resource.

    Science.gov (United States)

    Sinha, Sujata; Black, Michael L; Agarwal, Sarita; Das, Reena; Bittles, Alan H; Bellgard, Matthew

    2011-08-01

    Web-based informatics resources for genetic disorders have evolved from genome-wide databases like OMIM and HGMD to Locus Specific databases (LSDBs) and National and Ethnic Mutation Databases (NEMDBs). However, with the increasing amenability of genetic disorders to diagnosis and better management, many previously underreported conditions are emerging as disorders of public health significance. In turn, the greater emphasis on noncommunicable disorders has generated a demand for comprehensive and relevant disease-based information from end-users, including clinicians, patients, genetic epidemiologists, health administrators and policymakers. To accommodate these demands, country-specific and disease-centric resources are required to complement the existing LSDBs and NEMDBs. Currently available preconfigured Web-based software applications can be customized for this purpose. The present article describes the formulation and construction of a Web-based informatics resource for β-thalassemia and other hemoglobinopathies, initially for use in India, a multiethnic, multireligious country with a population approaching 1,200 million. The resource ThalInd (http://ccg.murdoch.edu.au/thalind) has been created using the LOVD system, an open source platform-independent database system. The system has been customized to incorporate and accommodate data pertinent to molecular genetics, population genetics, genotype-phenotype correlations, disease burden, and infrastructural assessment. Importantly, the resource also has been aligned with the administrative health system and demographic resources of the country. PMID:21520336

  6. Data availability and the role of the earth resources observation systems data center

    Science.gov (United States)

    Watkins, A. H.

    1975-01-01

    With the launch of LANDSAT-1 in July 1972, and the follow-on launch of LANDSAT-2 in January of this year, routine availability of satellite imagery and electronic data of the earth's resources has become a reality. Federal data centers provide LANDSAT data to resource managers and the general public. These data centers have to date provided almost 500,000 frames of LANDSAT data at a cost of more than $2,000,000. Data from the LANDSAT satellite program, along with data and information from the Skylab manned program, are available over any location to anyone for the cost of reproduction.

  7. 2011 Year in review--Earth Resources Observation and Science Center

    Science.gov (United States)

    Johnson, Rebecca, (compiler)

    2012-01-01

    The USGS Earth Resources Observation and Science (EROS) Center's 2011 Year in Review is an annual report recounting the broad scope of the Center's 2011 accomplishments. The report covers preparations for the Landsat Data Continuity Mission (LDCM) launch, the ever-increasing use of free Landsat data, monitoring the effects of natural hazards, and more to emphasize the importance of innovation in using satellite data to study change over time.

  8. In the Spotlight: Bioinformatics

    Science.gov (United States)

    Wang, May Dongmei

    2016-01-01

    During 2012, next generation sequencing (NGS) has attracted great attention in the biomedical research community, especially for personalized medicine. Also, third generation sequencing has become available. Therefore, state-of-art sequencing technology and analysis are reviewed in this Bioinformatics spotlight on 2012. Next-generation sequencing (NGS) is high-throughput nucleic acid sequencing technology with wide dynamic range and single base resolution. The full promise of NGS depends on the optimization of NGS platforms, sequence alignment and assembly algorithms, data analytics, novel algorithms for integrating NGS data with existing genomic, proteomic, or metabolomic data, and quantitative assessment of NGS technology in comparing to more established technologies such as microarrays. NGS technology has been predicated to become a cornerstone of personalized medicine. It is argued that NGS is a promising field for motivated young researchers who are looking for opportunities in bioinformatics. PMID:23192635

  9. 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.

  10. Bioinformatics big data processing

    OpenAIRE

    Cohen-Boulakia, Sarah; Valduriez, Patrick

    2016-01-01

    The volumes of bioinformatics data available on the Web are constantly increasing.Access and joint exploitation of these highly distributed data (i.e, available in distributed Webdata sources) and highly heterogeneous (in text or tabulated les including images, in dierentformats, described with dierent levels of detail and dierent levels of quality ...) is essential forthe biological knowledge to progress. The purpose of this short report is to present in a simpleway the problems of the joint...

  11. 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.

  12. Resources

    Science.gov (United States)

    ... palate - resources Colon cancer - resources Cystic fibrosis - resources Depression - resources Diabetes - resources Digestive disease - resources Drug abuse - resources Eating disorders - resources Elder care - resources Epilepsy - resources Family troubles - ...

  13. Resources

    Science.gov (United States)

    ... Depression - resources Diabetes - resources Digestive disease - resources Drug abuse - resources Eating disorders - resources Elder care - resources Epilepsy - resources Family troubles - resources Gastrointestinal disorders - resources Hearing impairment - resources ...

  14. 34 CFR 656.3 - What activities define a comprehensive or undergraduate National Resource Center?

    Science.gov (United States)

    2010-07-01

    ... basis; (d) Maintains linkages with overseas institutions of higher education and other organizations... 34 Education 3 2010-07-01 2010-07-01 false What activities define a comprehensive or undergraduate National Resource Center? 656.3 Section 656.3 Education Regulations of the Offices of the Department...

  15. Measuring Malaysia School Resource Centers' Standards through iQ-PSS: An Online Management Information System

    Science.gov (United States)

    Zainudin, Fadzliaton; Ismail, Kamarulzaman

    2010-01-01

    The Ministry of Education has come up with an innovative way to monitor the progress of 9,843 School Resource Centers (SRCs) using an online management information system called iQ-PSS (Quality Index of SRC). This paper aims to describe the data collection method and analyze the current state of SRCs in Malaysia and explain how the results can be…

  16. Personal Resources and Homelessness in Early Life: Predictors of Depression in Consumers of Homeless Multiservice Centers

    Science.gov (United States)

    DeForge, Bruce R.; Belcher, John R.; O'Rourke, Michael; Lindsey, Michael A.

    2008-01-01

    This study explored the relationship between personal resources and previous adverse life events such as homelessness and depression. Participants were recruited from two church sponsored multisite social service centers in Anne Arundel County, Maryland. The interview included demographics and several standardized scales to assess history of…

  17. Using the PubMatrix literature-mining resource to accelerate student-centered learning in a veterinary problem-based learning curriculum.

    Science.gov (United States)

    David, John; Irizarry, Kristopher J L

    2009-01-01

    Problem-based learning (PBL) creates an atmosphere in which veterinary students must take responsibility for their own education. Unlike a traditional curriculum where students receive discipline-specific information by attending formal lectures, PBL is designed to elicit self-directed, student-centered learning such that each student determines (1) what he/she does not know (learning issues), (2) what he/she needs to learn, (3) how he/she will learn it, and (4) what resources he/she will use. One of the biggest challenges facing students in a PBL curriculum is efficient time management while pursuing learning issues. Bioinformatics resources, such as the PubMatrix literature-mining tool, allow access to tremendous amounts of information almost instantaneously. To accelerate student-centered learning it is necessary to include resources that enhance the rate at which students can process biomedical information. Unlike using the PubMed interface directly, the PubMatrix tool enables users to automate queries, allowing up to 1,000 distinct PubMed queries to be executed per single PubMatrix submission. Users may submit multiple PubMatrix queries per session, resulting in the ability to execute tens of thousands of PubMed queries in a single day. The intuitively organized results, which remain accessible from PubMatrix user accounts, enable students to rapidly assimilate and process hundreds of thousands of individual publication records as they relate to the student's specific learning issues and query terms. Subsequently, students can explore substantially more of the biomedical publication landscape per learning issue and spend a greater fraction of their time actively engaged in resolving their learning issues. PMID:19625669

  18. Bioinformatic methods in protein characterization

    OpenAIRE

    Kallberg, Yvonne

    2002-01-01

    Bioinformatics is an emerging interdisciplinary research field in which mathematics. computer science and biology meet. In this thesis. bioinformatic methods for analysis of functional and structural properties among proteins will be presented. I have developed and applied bioinformatic methods on the enzyme superfamily of short-chain dehydrogenases/reductases (SDRs), coenzyme-binding enzymes of the Rossmann fold type, and amyloid-forming proteins and peptides. The basis...

  19. The Role of Human Resource Management in Iranian SMEs; in the Case of Medical Imaging Centers

    Directory of Open Access Journals (Sweden)

    Amirhossein Akhavan

    2010-05-01

    Full Text Available Human Resource Management (HRM faces difficulties in small businesses which derive from the small size and absence of adequate financial resources. Many authors have investigated the changed version of HRM in small enterprises which is some deal different with HRM in large enterprises. But in Iran researches are not interested in investigating human resource management in the field of small businesses and this encouraged me to perform this research. At first, this study has reviewed HRM policies and practices in small and medium enterprises (SMEs in the world. Then Iranian medical imaging centers have been selected as knowledge SMEs and some related managerial information has been collected from them by observation and interview. The obtained findings are about the role that HRM plays in today Iranian SMEs in the case of medical imaging centers. In this chapter the type of Human Resource Management which is accomplished in medical imaging enterprises in Iran is discovered and you can find the mistakes performed by their managers. These findings are analyzed based on literatures. In the conclusion part, some differences between western and Iranian models are proved and the study concludes that most of the owner managers in medical imaging centers in Iran could not execute HRM practices, even if they knew them or not. At last, some key points are presented as final recommendations to Iranian medical imaging SMEs in order to help them to improve their efficiency in the future.

  20. Bioinformatics and genomic medicine.

    Science.gov (United States)

    Kim, Ju Han

    2002-01-01

    Bioinformatics is a rapidly emerging field of biomedical research. A flood of large-scale genomic and postgenomic data means that many of the challenges in biomedical research are now challenges in computational science. Clinical informatics has long developed methodologies to improve biomedical research and clinical care by integrating experimental and clinical information systems. The informatics revolution in both bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics, and prognostics. Postgenome informatics, powered by high-throughput technologies and genomic-scale databases, is likely to transform our biomedical understanding forever, in much the same way that biochemistry did a generation ago. This paper describes how these technologies will impact biomedical research and clinical care, emphasizing recent advances in biochip-based functional genomics and proteomics. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine-learning algorithms are discussed. Use of integrative biochip informatics technologies, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and the integrated management of biomolecular databases, are also discussed. PMID:12544491

  1. Agile parallel bioinformatics workflow management using Pwrake

    Directory of Open Access Journals (Sweden)

    Tanaka Masahiro

    2011-09-01

    Full Text Available Abstract 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

  2. Establishing a health outcomes and economics center in radiology: strategies and resources required

    International Nuclear Information System (INIS)

    To describe the resources and strategies required to establish a health outcomes and economics center in radiology.Methods. Human and nonhuman resources required to perform sound outcomes and economics studies in radiology are reviewed.Results. Human resources needed include skilled medical and nonmedical staff. Nonhuman resources required are: (1) communication and information network; (2) education tools and training programs; (3) budgetary strategies; and (4) sources of income. Effective utilization of these resources allows the performance of robust operational and clinical research projects in decision analysis, cost-effectiveness, diagnostic performance (sensitivity, specificity, and ROC curves), and clinical analytical and experimental studies.Conclusion. As new radiologic technology and techniques are introduced in medicine, society is increasingly demanding sound clinical studies that will determine the impact of radiologic studies on patient outcome. Health-care funding is scarce, and therefore third-party payers and hospitals are demanding more efficiency and productivity from radiologic service providers. To meet these challenges, radiology departments could establish health outcomes and economics centers to study the clinical effectiveness of imaging and its impact on patient outcome. (orig.)

  3. Amarillo National Resource Center for Plutonium. Quarterly technical progress report, November 1, 1997--January 31, 1998

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-03-01

    This report provides information on projects conducted by the Amarillo National Resource Center for Plutonium, a consortium of Texas A&M University, Texas Tech University, and the University of Texas. Progress is reported for four major areas: (1) plutonium information resource; (2) environmental, safety, and health; (3) communication, education, training, and community involvement; and (4) nuclear and other material studies. Environmental, safety, and health projects reported include a number of studies on high explosives. Progress reported for nuclear material studies includes storage and waste disposal investigations.

  4. Bioinformatics and Computational Core Technology Center

    Data.gov (United States)

    Federal Laboratory Consortium — SERVICES PROVIDED BY THE COMPUTER CORE FACILITY Evaluation, purchase, set up, and maintenance of the computer hardware and network for the 170 users in the research...

  5. Uso da bioinformática na diferenciação molecular da Entamoeba histolytica e Entamoeba díspar - DOI: 10.4025/actascihealthsci.v30i2.2375 Molecular discrimination of Entamoeba histolytica and Entamoeba dispar by bioinformatics resources - DOI: 10.4025/actascihealthsci.v30i2.2375

    Directory of Open Access Journals (Sweden)

    Débora Sommer

    2008-12-01

    Full Text Available Amebíase invasiva, causada por Entamoeba histolytica, é microscopicamente indistinguível da espécie não-patogênica Entamoeba dispar. Com auxílio de ferramentas de bioinformática, objetivou-se diferenciar Entamoeba histolytica e Entamoeba dispar por técnicas moleculares. A análise foi realizada a partir do banco de dados da National Center for Biotechnology Information; pela pesquisa de similaridade de sequências, elegeu-se o gene da cisteína sintase. Um par de primer foi desenhado (programa Web Primer e foi selecionada a enzima de restrição TaqI (programa Web Cutter. Após a atuação da enzima, o fragmento foi dividido em dois, um com 255 pb e outro com 554 pb, padrão característico da E. histolytica. Na ausência de corte, o fragmento apresentou o tamanho de 809 pb, referente à E. dispar.Under microscopic conditions, the invasive Entamoeba histolytica is indistinguishable from the non-pathogenic species Entamoeba dispar. In this way, the present study was carried out to determine a molecular strategy for discriminating both species by the mechanisms of bioinformatics. The gene cysteine synthetase was considered for such a purpose by using the resources of the National Center for Biotechnology Information data bank in the search for similarities in the gene sequence. In this way, a primer pair was designed by the Web Primer program and the restriction enzyme TaqI was selected by the Web Cutter software program. The DNA fragment had a size of 809 bp before cutting, which is consistent with E. dispar. The gene fragment was partitioned in a first fragment with 255 bp and a second one with 554 bp, which is similar to the genetic characteristics of E. histolytica.

  6. The Criticality Safety Information Resource Center at Los Alamos National Laboratory

    International Nuclear Information System (INIS)

    The mission of the Criticality Safety Information Resource Center (CSIRC) at Los Alamos National Laboratory (LANL) is the preservation of primary documentation supporting criticality safety. In many cases, but not all, this primary documentation consists of experimentalists' logbooks. Experience has shown that the logbooks and other primary information are vulnerable to being discarded. Destruction of these logbooks results in a permanent loss to the criticality safety community

  7. Bioinformatics analyses for signal transduction networks

    Institute of Scientific and Technical Information of China (English)

    LIU Wei; LI Dong; ZHU YunPing; HE FuChu

    2008-01-01

    Research in signaling networks contributes to a deeper understanding of organism living activities. With the development of experimental methods in the signal transduction field, more and more mechanisms of signaling pathways have been discovered. This paper introduces such popular bioin-formatics analysis methods for signaling networks as the common mechanism of signaling pathways and database resource on the Internet, summerizes the methods of analyzing the structural properties of networks, including structural Motif finding and automated pathways generation, and discusses the modeling and simulation of signaling networks in detail, as well as the research situation and tendency in this area. Now the investigation of signal transduction is developing from small-scale experiments to large-scale network analysis, and dynamic simulation of networks is closer to the real system. With the investigation going deeper than ever, the bioinformatics analysis of signal transduction would have immense space for development and application.

  8. Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics

    DEFF Research Database (Denmark)

    Kouskoumvekaki, Irene; Shublaq, Nour; Brunak, Søren

    2014-01-01

    access to user-friendly solutions to navigate, integrate and extract information out of biological databases, as well as to combine tools and data resources in bioinformatics workflows. In this review, we present services that assist biomedical scientists in incorporating bioinformatics tools...... that facilitate the integration of biomedical ontologies and bioinformatics tools in computational workflows....

  9. 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…

  10. Engineering BioInformatics

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ With the completion of human genome sequencing, a new era of bioinformatics st arts. On one hand, due to the advance of high throughput DNA microarray technol ogies, functional genomics such as gene expression information has increased exp onentially and will continue to do so for the foreseeable future. Conventional m eans of storing, analysing and comparing related data are already overburdened. Moreover, the rich information in genes , their functions and their associated wide biological implication requires new technologies of analysing data that employ sophisticated statistical and machine learning algorithms, powerful com puters and intensive interaction together different data sources such as seque nce data, gene expression data, proteomics data and metabolic pathway informati on to discover complex genomic structures and functional patterns with other bi ological process to gain a comprehensive understanding of cell physiology.

  11. 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...

  12. Renewable Resources: a national catalog of model projects. Volume 3. Southern Solar Energy Center Region

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-07-01

    This compilation of diverse conservation and renewable energy projects across the United States was prepared through the enthusiastic participation of solar and alternate energy groups from every state and region. Compiled and edited by the Center for Renewable Resources, these projects reflect many levels of innovation and technical expertise. In many cases, a critique analysis is presented of how projects performed and of the institutional conditions associated with their success or failure. Some 2000 projects are included in this compilation; most have worked, some have not. Information about all is presented to aid learning from these experiences. The four volumes in this set are arranged in state sections by geographic region, coinciding with the four Regional Solar Energy Centers. The table of contents is organized by project category so that maximum cross-referencing may be obtained. This volume includes information on the Southern Solar Energy Center Region. (WHK)

  13. Renewable Resources: a national catalog of model projects. Volume 1. Northeast Solar Energy Center Region

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-07-01

    This compilation of diverse conservation and renewable energy projects across the United States was prepared through the enthusiastic participation of solar and alternate energy groups from every state and region. Compiled and edited by the Center for Renewable Resources, these projects reflect many levels of innovation and technical expertise. In many cases, a critique analysis is presented of how projects performed and of the institutional conditions associated with their success or failure. Some 2000 projects are included in this compilation; most have worked, some have not. Information about all is presented to aid learning from these experiences. The four volumes in this set are arranged in state sections by geographic region, coinciding with the four Regional Solar Energy Centers. The table of contents is organized by project category so that maximum cross-referencing may be obtained. This volume includes information on the Northeast Solar Energy Center Region. (WHK).

  14. Nuclear Regulatory Commission programs are supported by the technology resources of the Engineering Physics Information Centers

    International Nuclear Information System (INIS)

    The Engineering Physics Information Centers (EPIC) at Oak Ridge National Laboratory have two activities which support NRC Programs, the Radiation Shielding Information Center (RSIC) and the Technical Data Management Center (TDMC). The older of the two, RSIC, was established in 1963 as an Information Analysis Center in the general field of radiation shielding, transport, and protection. It has multiple agency funding to acquire, evaluate, organize, and distribute information (including computing technology and numerical data) relevant to its field. The TDMC was established in 1978 to perform work for NRC in fields not related to RSIC's subject coverage and to perform tasks beyond the normal level of activity for RSIC. The two centers share administrative functions, physical premises, specialists skills, and computing resources. The NRC/ADM/TIDC monitors the cosponsorship of RSIC for coverage of agency-wide interests and plans, directs, and coordinates the work of the TDMC, including the establishment of TDMC as the agency-wide repository for packaged computer-related technical information products. The contract monitor is Myrna L. Steele

  15. Translational bioinformatics in psychoneuroimmunology: methods and applications.

    Science.gov (United States)

    Yan, Qing

    2012-01-01

    Translational bioinformatics plays an indispensable role in transforming psychoneuroimmunology (PNI) into personalized medicine. It provides a powerful method to bridge the gaps between various knowledge domains in PNI and systems biology. Translational bioinformatics methods at various systems levels can facilitate pattern recognition, and expedite and validate the discovery of systemic biomarkers to allow their incorporation into clinical trials and outcome assessments. Analysis of the correlations between genotypes and phenotypes including the behavioral-based profiles will contribute to the transition from the disease-based medicine to human-centered medicine. Translational bioinformatics would also enable the establishment of predictive models for patient responses to diseases, vaccines, and drugs. In PNI research, the development of systems biology models such as those of the neurons would play a critical role. Methods based on data integration, data mining, and knowledge representation are essential elements in building health information systems such as electronic health records and computerized decision support systems. Data integration of genes, pathophysiology, and behaviors are needed for a broad range of PNI studies. Knowledge discovery approaches such as network-based systems biology methods are valuable in studying the cross-talks among pathways in various brain regions involved in disorders such as Alzheimer's disease. PMID:22933157

  16. 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. PMID:25050811

  17. BOD: a customizable bioinformatics on demand system accommodating multiple steps and parallel tasks

    OpenAIRE

    Qiao, Li-An; Zhu, Jing; Liu, Qingyan; Zhu, Tao; Song, Chi; Lin, Wei; Wei, Guozhu; Mu, Lisen; Tao, Jiang; Zhao, Nanming; Yang, Guangwen; Liu, Xiangjun

    2004-01-01

    The integration of bioinformatics resources worldwide is one of the major concerns of the biological community. We herein established the BOD (Bioinformatics on demand) system to use Grid computing technology to set up a virtual workbench via a web-based platform, to assist researchers performing customized comprehensive bioinformatics work. Users will be able to submit entire search queries and computation requests, e.g. from DNA assembly to gene prediction and finally protein folding, from ...

  18. String Mining in Bioinformatics

    Science.gov (United States)

    Abouelhoda, Mohamed; Ghanem, Moustafa

    Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word "data-mining" is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

  19. 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! PMID:27471065

  20. Global computing for bioinformatics.

    Science.gov (United States)

    Loewe, Laurence

    2002-12-01

    Global computing, the collaboration of idle PCs via the Internet in a SETI@home style, emerges as a new way of massive parallel multiprocessing with potentially enormous CPU power. Its relations to the broader, fast-moving field of Grid computing are discussed without attempting a review of the latter. This review (i) includes a short table of milestones in global computing history, (ii) lists opportunities global computing offers for bioinformatics, (iii) describes the structure of problems well suited for such an approach, (iv) analyses the anatomy of successful projects and (v) points to existing software frameworks. Finally, an evaluation of the various costs shows that global computing indeed has merit, if the problem to be solved is already coded appropriately and a suitable global computing framework can be found. Then, either significant amounts of computing power can be recruited from the general public, or--if employed in an enterprise-wide Intranet for security reasons--idle desktop PCs can substitute for an expensive dedicated cluster. PMID:12511066

  1. 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. PMID:25996054

  2. ASD: a bioinformatics resource on alternative splicing

    OpenAIRE

    Stamm, Stefan; Riethoven, Jean-Jack; Le Texier, Vincent; Gopalakrishnan, Chellappa; Kumanduri, Vasudev; Tang, Yesheng; Barbosa-Morais, Nuno L.; Thanaraj, Thangavel Alphonse

    2005-01-01

    Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. We present the continuation and upgrade of the ASD [T. A. Thanaraj, S. Stamm, F. Clark, J. J. Riethoven, V. Le Texier, J. Muilu (2004) Nucleic Acids Res. 32, D64–D69] that consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database...

  3. The Resource Configuration Method with Lower Energy Consumption Based on Prediction in Cloud Data Center

    Directory of Open Access Journals (Sweden)

    Quan Liang

    2014-07-01

    Full Text Available The cloud computing data center have numerous hosts as well as application requests. In future, the short response time and user Qos are required, and the lower electricity power consumption to build the low-carbon green network is an irrevocable trend. The paper first puts forward a reconfiguration framework based on the request prediction of Double Exponential Smoothing, On the basis, work out in advance the allocation scheme which can improve the resource utilization ratio as well as lower energy consumption. The paper also present a concept of Utility Ratio Matrix (URM to represent allocations of hosts and Virtual Machines (VMs and a reconfiguration algorithm. The algorithm can separate the reconfiguration computing from the real allocation so that it can avoid a time delay, and can also reduce the energy consumption in data center. The corresponding analysis and experimental results show the feasibility of the reconfiguration algorithm in this paper.

  4. Inbound Call Centers and Emotional Dissonance in the Job Demands – Resources Model

    Science.gov (United States)

    Molino, Monica; Emanuel, Federica; Zito, Margherita; Ghislieri, Chiara; Colombo, Lara; Cortese, Claudio G.

    2016-01-01

    Background: Emotional labor, defined as the process of regulating feelings and expressions as part of the work role, is a major characteristic in call centers. In particular, interacting with customers, agents are required to show certain emotions that are considered acceptable by the organization, even though these emotions may be different from their true feelings. This kind of experience is defined as emotional dissonance and represents a feature of the job especially for call center inbound activities. Aim: The present study was aimed at investigating whether emotional dissonance mediates the relationship between job demands (workload and customer verbal aggression) and job resources (supervisor support, colleague support, and job autonomy) on the one hand, and, on the other, affective discomfort, using the job demands-resources model as a framework. The study also observed differences between two different types of inbound activities: customer assistance service (CA) and information service. Method: The study involved agents of an Italian Telecommunication Company, 352 of whom worked in the CA and 179 in the information service. The hypothesized model was tested across the two groups through multi-group structural equation modeling. Results: Analyses showed that CA agents experience greater customer verbal aggression and emotional dissonance than information service agents. Results also showed, only for the CA group, a full mediation of emotional dissonance between workload and affective discomfort, and a partial mediation of customer verbal aggression and job autonomy, and affective discomfort. Conclusion: This study’s findings contributed both to the emotional labor literature, investigating the mediational role of emotional dissonance in the job demands-resources model, and to call center literature, considering differences between two specific kinds of inbound activities. Suggestions for organizations and practitioners emerged in order to identify

  5. Clustering Techniques in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Muhammad Ali Masood

    2015-01-01

    Full Text Available Dealing with data means to group information into a set of categories either in order to learn new artifacts or understand new domains. For this purpose researchers have always looked for the hidden patterns in data that can be defined and compared with other known notions based on the similarity or dissimilarity of their attributes according to well-defined rules. Data mining, having the tools of data classification and data clustering, is one of the most powerful techniques to deal with data in such a manner that it can help researchers identify the required information. As a step forward to address this challenge, experts have utilized clustering techniques as a mean of exploring hidden structure and patterns in underlying data. Improved stability, robustness and accuracy of unsupervised data classification in many fields including pattern recognition, machine learning, information retrieval, image analysis and bioinformatics, clustering has proven itself as a reliable tool. To identify the clusters in datasets algorithm are utilized to partition data set into several groups based on the similarity within a group. There is no specific clustering algorithm, but various algorithms are utilized based on domain of data that constitutes a cluster and the level of efficiency required. Clustering techniques are categorized based upon different approaches. This paper is a survey of few clustering techniques out of many in data mining. For the purpose five of the most common clustering techniques out of many have been discussed. The clustering techniques which have been surveyed are: K-medoids, K-means, Fuzzy C-means, Density-Based Spatial Clustering of Applications with Noise (DBSCAN and Self-Organizing Map (SOM clustering.

  6. Teacher collaboration in a public school to set up language resource centers: portraying advantages, benefits, and challenges

    OpenAIRE

    Rojas Serrano, Javier Augusto

    2009-01-01

    In the present article, the author attempts to describe the benefits, challenges, advantages and disadvantages experienced by teachers in a public school when working collaboratively to implement a language resource center in their institution. Taking as a point of departure the development of a proposal to implement the resource center in their school, some teachers engaged in group work in order to attain the different objectives that were stated at the beginning of the process, thus encoun...

  7. Analysis of Metagenomics Next Generation Sequence Data for Fungal ITS Barcoding: Do You Need Advance Bioinformatics Experience?

    Science.gov (United States)

    Ahmed, Abdalla

    2016-01-01

    During the last few decades, most of microbiology laboratories have become familiar in analyzing Sanger sequence data for ITS barcoding. However, with the availability of next-generation sequencing platforms in many centers, it has become important for medical mycologists to know how to make sense of the massive sequence data generated by these new sequencing technologies. In many reference laboratories, the analysis of such data is not a big deal, since suitable IT infrastructure and well-trained bioinformatics scientists are always available. However, in small research laboratories and clinical microbiology laboratories the availability of such resources are always lacking. In this report, simple and user-friendly bioinformatics work-flow is suggested for fast and reproducible ITS barcoding of fungi. PMID:27507959

  8. Analysis of Metagenomics Next Generation Sequence Data for Fungal ITS Barcoding: Do You Need Advance Bioinformatics Experience?

    Science.gov (United States)

    Ahmed, Abdalla

    2016-01-01

    During the last few decades, most of microbiology laboratories have become familiar in analyzing Sanger sequence data for ITS barcoding. However, with the availability of next-generation sequencing platforms in many centers, it has become important for medical mycologists to know how to make sense of the massive sequence data generated by these new sequencing technologies. In many reference laboratories, the analysis of such data is not a big deal, since suitable IT infrastructure and well-trained bioinformatics scientists are always available. However, in small research laboratories and clinical microbiology laboratories the availability of such resources are always lacking. In this report, simple and user-friendly bioinformatics work-flow is suggested for fast and reproducible ITS barcoding of fungi.

  9. Application Of Data Mining In Bioinformatics

    OpenAIRE

    KHALID RAZA

    2012-01-01

    This article highlights some of the basic concepts of bioinformatics and data mining. The major research areas of bioinformatics are highlighted. The application of data mining in the domain of bioinformatics is explained. It also highlights some of the current challenges and opportunities of data mining in bioinformatics.

  10. Performance evaluation of data center service localization based on virtual resource migration in software defined elastic optical network.

    Science.gov (United States)

    Yang, Hui; Zhang, Jie; Ji, Yuefeng; Tan, Yuanlong; Lin, Yi; Han, Jianrui; Lee, Young

    2015-09-01

    Data center interconnection with elastic optical network is a promising scenario to meet the high burstiness and high-bandwidth requirements of data center services. In our previous work, we implemented cross stratum optimization of optical network and application stratums resources that allows to accommodate data center services. In view of this, this study extends the data center resources to user side to enhance the end-to-end quality of service. We propose a novel data center service localization (DCSL) architecture based on virtual resource migration in software defined elastic data center optical network. A migration evaluation scheme (MES) is introduced for DCSL based on the proposed architecture. The DCSL can enhance the responsiveness to the dynamic end-to-end data center demands, and effectively reduce the blocking probability to globally optimize optical network and application resources. The overall feasibility and efficiency of the proposed architecture are experimentally verified on the control plane of our OpenFlow-based enhanced SDN testbed. The performance of MES scheme under heavy traffic load scenario is also quantitatively evaluated based on DCSL architecture in terms of path blocking probability, provisioning latency and resource utilization, compared with other provisioning scheme. PMID:26368410

  11. The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers

    OpenAIRE

    Fox, Joanne A.; Butland, Stefanie L.; McMillan, Scott; Campbell, Graeme; Ouellette, B. F. Francis

    2005-01-01

    The Bioinformatics Links Directory is an online community resource that contains a directory of freely available tools, databases, and resources for bioinformatics and molecular biology research. The listing of the servers published in this and previous issues of Nucleic Acids Research together with other useful tools and websites represents a rich repository of resources that are openly provided to the research community using internet technologies. The 166 servers highlighted in the 2005 We...

  12. Providing Curriculum Support in the School Library Media Center: Resource Alignment, or How To Eat an Elephant.

    Science.gov (United States)

    Lowe, Karen

    2003-01-01

    Discusses the process of weeding, updating, and building a school library media collection that supports the state curriculum. Explains resource alignment, a process for using the shelf list as a tool to analyze and align media center resources to state curricula, and describes a five-year plan and its usefulness for additional funding. (LRW)

  13. 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…

  14. An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

    Science.gov (United States)

    The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee (MASC) and the North American Arabidopsis Steering C...

  15. Performance evaluation of multi-stratum resources integrated resilience for software defined inter-data center interconnect.

    Science.gov (United States)

    Yang, Hui; Zhang, Jie; Zhao, Yongli; Ji, Yuefeng; Wu, Jialin; Lin, Yi; Han, Jianrui; Lee, Young

    2015-05-18

    Inter-data center interconnect with IP over elastic optical network (EON) is a promising scenario to meet the high burstiness and high-bandwidth requirements of data center services. In our previous work, we implemented multi-stratum resources integration among IP networks, optical networks and application stratums resources that allows to accommodate data center services. In view of this, this study extends to consider the service resilience in case of edge optical node failure. We propose a novel multi-stratum resources integrated resilience (MSRIR) architecture for the services in software defined inter-data center interconnect based on IP over EON. A global resources integrated resilience (GRIR) algorithm is introduced based on the proposed architecture. The MSRIR can enable cross stratum optimization and provide resilience using the multiple stratums resources, and enhance the data center service resilience responsiveness to the dynamic end-to-end service demands. The overall feasibility and efficiency of the proposed architecture is experimentally verified on the control plane of our OpenFlow-based enhanced SDN (eSDN) testbed. The performance of GRIR algorithm under heavy traffic load scenario is also quantitatively evaluated based on MSRIR architecture in terms of path blocking probability, resilience latency and resource utilization, compared with other resilience algorithms. PMID:26074588

  16. Argonne's Laboratory Computing Resource Center 2009 annual report.

    Energy Technology Data Exchange (ETDEWEB)

    Bair, R. B. (CLS-CI)

    2011-05-13

    Now in its seventh year of operation, the Laboratory Computing Resource Center (LCRC) continues to be an integral component of science and engineering research at Argonne, supporting a diverse portfolio of projects for the U.S. Department of Energy and other sponsors. The LCRC's ongoing mission is to enable and promote computational science and engineering across the Laboratory, primarily by operating computing facilities and supporting high-performance computing application use and development. This report describes scientific activities carried out with LCRC resources in 2009 and the broad impact on programs across the Laboratory. The LCRC computing facility, Jazz, is available to the entire Laboratory community. In addition, the LCRC staff provides training in high-performance computing and guidance on application usage, code porting, and algorithm development. All Argonne personnel and collaborators are encouraged to take advantage of this computing resource and to provide input into the vision and plans for computing and computational analysis at Argonne. The LCRC Allocations Committee makes decisions on individual project allocations for Jazz. Committee members are appointed by the Associate Laboratory Directors and span a range of computational disciplines. The 350-node LCRC cluster, Jazz, began production service in April 2003 and has been a research work horse ever since. Hosting a wealth of software tools and applications and achieving high availability year after year, researchers can count on Jazz to achieve project milestones and enable breakthroughs. Over the years, many projects have achieved results that would have been unobtainable without such a computing resource. In fiscal year 2009, there were 49 active projects representing a wide cross-section of Laboratory research and almost all research divisions.

  17. Generations of interdisciplinarity in bioinformatics

    Science.gov (United States)

    Bartlett, Andrew; Lewis, Jamie; Williams, Matthew L.

    2016-01-01

    Bioinformatics, a specialism propelled into relevance by the Human Genome Project and the subsequent -omic turn in the life science, is an interdisciplinary field of research. Qualitative work on the disciplinary identities of bioinformaticians has revealed the tensions involved in work in this “borderland.” As part of our ongoing work on the emergence of bioinformatics, between 2010 and 2011, we conducted a survey of United Kingdom-based academic bioinformaticians. Building on insights drawn from our fieldwork over the past decade, we present results from this survey relevant to a discussion of disciplinary generation and stabilization. Not only is there evidence of an attitudinal divide between the different disciplinary cultures that make up bioinformatics, but there are distinctions between the forerunners, founders and the followers; as inter/disciplines mature, they face challenges that are both inter-disciplinary and inter-generational in nature. PMID:27453689

  18. Mars Atmospheric In Situ Resource Utilization Projects at the Kennedy Space Center

    Science.gov (United States)

    Muscatello, Anthony; Hintze, Paul; Meier, Anne; Bayliss, Jon; Karr, Laurel; Paley, Steve; Marone, Matt; Gibson, Tracy; Surma, Jan; Mansell, Matt; Lunn, Griffin; Devor, Robert; Berggren, Mark

    2016-01-01

    The atmosphere of Mars, which is 96 percent carbon dioxide (CO2), is a rich resource for the human exploration of the red planet, primarily by the production of rocket propellants and oxygen for life support. Three recent projects led by NASAs Kennedy Space Center have been investigating the processing of CO2. The first project successfully demonstrated the Mars Atmospheric Processing Module (APM), which freezes CO2 with cryocoolers and combines sublimated CO2 with hydrogen to make methane and water. The second project absorbs CO2 with Ionic Liquids and electrolyzes it with water to make methane and oxygen, but with limited success so far. A third project plans to recover up to 100 of the oxygen in spacecraft respiratory CO2. A combination of the Reverse Water Gas Shift reaction and the Boudouard reaction eventually fill the reactor up with carbon, stopping the process. A system to continuously remove and collect carbon has been tested with encouraging results.

  19. The Criticality Safety Information Resource Center (CSIRC) at Los Alamos National Laboratory

    International Nuclear Information System (INIS)

    The Criticality Safety Information Resource Center (CSIRC) at Los Alamos National Laboratory (LANL) is a program jointly funded by the U.S. Department of Energy (DOE) and the U.S. Nuclear Regulatory Commission (NRC) in conjunction with the Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 97-2. The goal of CSIRC is to preserve primary criticality safety documentation from U.S. critical experimental sites and to make this information available for the benefit of the technical community. Progress in archiving criticality safety primary documents at the LANL archives as well as efforts to make this information available to researchers are discussed. The CSIRC project has a natural linkage to the International Criticality Safety Benchmark Evaluation Project (ICSBEP). This paper raises the possibility that the CSIRC project will evolve in a fashion similar to the ICSBEP. Exploring the implications of linking the CSIRC to the international criticality safety community is the motivation for this paper

  20. Update on Genomic Databases and Resources at the National Center for Biotechnology Information.

    Science.gov (United States)

    Tatusova, Tatiana

    2016-01-01

    The National Center for Biotechnology Information (NCBI), as a primary public repository of genomic sequence data, collects and maintains enormous amounts of heterogeneous data. Data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domains are integrated with the analytical, search, and retrieval resources through the NCBI website, text-based search and retrieval system, provides a fast and easy way to navigate across diverse biological databases.Comparative genome analysis tools lead to further understanding of evolution processes quickening the pace of discovery. Recent technological innovations have ignited an explosion in genome sequencing that has fundamentally changed our understanding of the biology of living organisms. This huge increase in DNA sequence data presents new challenges for the information management system and the visualization tools. New strategies have been designed to bring an order to this genome sequence shockwave and improve the usability of associated data. PMID:27115625

  1. Community Coordinated Modeling Center: A Powerful Resource in Space Science and Space Weather Education

    Science.gov (United States)

    Chulaki, A.; Kuznetsova, M. M.; Rastaetter, L.; MacNeice, P. J.; Shim, J. S.; Pulkkinen, A. A.; Taktakishvili, A.; Mays, M. L.; Mendoza, A. M. M.; Zheng, Y.; Mullinix, R.; Collado-Vega, Y. M.; Maddox, M. M.; Pembroke, A. D.; Wiegand, C.

    2015-12-01

    Community Coordinated Modeling Center (CCMC) is a NASA affiliated interagency partnership with the primary goal of aiding the transition of modern space science models into space weather forecasting while supporting space science research. Additionally, over the past ten years it has established itself as a global space science education resource supporting undergraduate and graduate education and research, and spreading space weather awareness worldwide. A unique combination of assets, capabilities and close ties to the scientific and educational communities enable this small group to serve as a hub for raising generations of young space scientists and engineers. CCMC resources are publicly available online, providing unprecedented global access to the largest collection of modern space science models (developed by the international research community). CCMC has revolutionized the way simulations are utilized in classrooms settings, student projects, and scientific labs and serves hundreds of educators, students and researchers every year. Another major CCMC asset is an expert space weather prototyping team primarily serving NASA's interplanetary space weather needs. Capitalizing on its unrivaled capabilities and experiences, the team provides in-depth space weather training to students and professionals worldwide, and offers an amazing opportunity for undergraduates to engage in real-time space weather monitoring, analysis, forecasting and research. In-house development of state-of-the-art space weather tools and applications provides exciting opportunities to students majoring in computer science and computer engineering fields to intern with the software engineers at the CCMC while also learning about the space weather from the NASA scientists.

  2. Drug targets for lymphatic filariasis: A bioinformatics approach

    Directory of Open Access Journals (Sweden)

    Om Prakash Sharma

    2013-08-01

    Full Text Available This review article discusses the current scenario of the national and international burden due to lymphatic filariasis (LF and describes the active elimination programmes for LF and their achievements to eradicate this most debilitating disease from the earth. Since, bioinformatics is a rapidly growing field of biological study, and it has an increasingly significant role in various fields of biology. We have reviewed its leading involvement in the filarial research using different approaches of bioinformatics and have summarized available existing drugs and their targets to re-examine and to keep away from the resisting conditions. Moreover, some of the novel drug targets have been assembled for further study to design fresh and better pharmacological therapeutics. Various bioinformatics-based web resources, and databases have been discussed, which may enrich the filarial research.

  3. 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...

  4. Visualising "Junk" DNA through Bioinformatics

    Science.gov (United States)

    Elwess, Nancy L.; Latourelle, Sandra M.; Cauthorn, Olivia

    2005-01-01

    One of the hottest areas of science today is the field in which biology, information technology,and computer science are merged into a single discipline called bioinformatics. This field enables the discovery and analysis of biological data, including nucleotide and amino acid sequences that are easily accessed through the use of computers. As…

  5. 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...

  6. 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…

  7. 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. PMID:24792157

  8. Argonne's Laboratory Computing Resource Center : 2005 annual report.

    Energy Technology Data Exchange (ETDEWEB)

    Bair, R. B.; Coghlan, S. C; Kaushik, D. K.; Riley, K. R.; Valdes, J. V.; Pieper, G. P.

    2007-06-30

    Argonne National Laboratory founded the Laboratory Computing Resource Center in the spring of 2002 to help meet pressing program needs for computational modeling, simulation, and analysis. The guiding mission is to provide critical computing resources that accelerate the development of high-performance computing expertise, applications, and computations to meet the Laboratory's challenging science and engineering missions. The first goal of the LCRC was to deploy a mid-range supercomputing facility to support the unmet computational needs of the Laboratory. To this end, in September 2002, the Laboratory purchased a 350-node computing cluster from Linux NetworX. This cluster, named 'Jazz', achieved over a teraflop of computing power (10{sup 12} floating-point calculations per second) on standard tests, making it the Laboratory's first terascale computing system and one of the fifty fastest computers in the world at the time. Jazz was made available to early users in November 2002 while the system was undergoing development and configuration. In April 2003, Jazz was officially made available for production operation. Since then, the Jazz user community has grown steadily. By the end of fiscal year 2005, there were 62 active projects on Jazz involving over 320 scientists and engineers. These projects represent a wide cross-section of Laboratory expertise, including work in biosciences, chemistry, climate, computer science, engineering applications, environmental science, geoscience, information science, materials science, mathematics, nanoscience, nuclear engineering, and physics. Most important, many projects have achieved results that would have been unobtainable without such a computing resource. The LCRC continues to improve the computational science and engineering capability and quality at the Laboratory. Specific goals include expansion of the use of Jazz to new disciplines and Laboratory initiatives, teaming with Laboratory infrastructure

  9. Argonne's Laboratory computing resource center : 2006 annual report.

    Energy Technology Data Exchange (ETDEWEB)

    Bair, R. B.; Kaushik, D. K.; Riley, K. R.; Valdes, J. V.; Drugan, C. D.; Pieper, G. P.

    2007-05-31

    Argonne National Laboratory founded the Laboratory Computing Resource Center (LCRC) in the spring of 2002 to help meet pressing program needs for computational modeling, simulation, and analysis. The guiding mission is to provide critical computing resources that accelerate the development of high-performance computing expertise, applications, and computations to meet the Laboratory's challenging science and engineering missions. In September 2002 the LCRC deployed a 350-node computing cluster from Linux NetworX to address Laboratory needs for mid-range supercomputing. This cluster, named 'Jazz', achieved over a teraflop of computing power (10{sup 12} floating-point calculations per second) on standard tests, making it the Laboratory's first terascale computing system and one of the 50 fastest computers in the world at the time. Jazz was made available to early users in November 2002 while the system was undergoing development and configuration. In April 2003, Jazz was officially made available for production operation. Since then, the Jazz user community has grown steadily. By the end of fiscal year 2006, there were 76 active projects on Jazz involving over 380 scientists and engineers. These projects represent a wide cross-section of Laboratory expertise, including work in biosciences, chemistry, climate, computer science, engineering applications, environmental science, geoscience, information science, materials science, mathematics, nanoscience, nuclear engineering, and physics. Most important, many projects have achieved results that would have been unobtainable without such a computing resource. The LCRC continues to foster growth in the computational science and engineering capability and quality at the Laboratory. Specific goals include expansion of the use of Jazz to new disciplines and Laboratory initiatives, teaming with Laboratory infrastructure providers to offer more scientific data management capabilities, expanding Argonne staff

  10. Engaging Community Stakeholders to Evaluate the Design, Usability, and Acceptability of a Chronic Obstructive Pulmonary Disease Social Media Resource Center

    OpenAIRE

    Stellefson, Michael; Chaney, Beth; Chaney, Don; Paige, Samantha; Payne-Purvis, Caroline; Tennant, Bethany; Walsh-Childers, Kim; Sriram, PS; Alber, Julia

    2015-01-01

    Background Patients with chronic obstructive pulmonary disease (COPD) often report inadequate access to comprehensive patient education resources. Objective The purpose of this study was to incorporate community-engagement principles within a mixed-method research design to evaluate the usability and acceptability of a self-tailored social media resource center for medically underserved patients with COPD. Methods A multiphase sequential design (qual → QUANT → quant + QUAL) was incorporated i...

  11. Impact of the Development of a Light Microscopy Shared Resource for the University of Rochester Medical Center: A Quantitative Assessment

    OpenAIRE

    Jepson, M.; Jordan, P.; Kasischke, K.; Brown, E.; Reed, A; Lentine, M.; Bushnell, T.; Puzas, E.; Callahan, L.M.

    2014-01-01

    The University of Rochester Medical Center (URMC) determined the need for a shared Light Microscopy facility to support researchers requiring high-end light microscopy for their research programs. URMC Shared Resource Laboratories (SRLs) represent a strategic investment in technology, targeted expertise, and space administration to systematically support and advance the research mission of the institution. Recognizing the need for centralized light microscopy resources to support the Universi...

  12. Application of bioinformatics in tropical medicine

    Institute of Scientific and Technical Information of China (English)

    Wiwanitkit V

    2008-01-01

    Bioinformatics is a usage of information technology to help solve biological problems by designing novel and in-cisive algorithms and methods of analyses.Bioinformatics becomes a discipline vital in the era of post-genom-ics.In this review article,the application of bioinformatics in tropical medicine will be presented and dis-cussed.

  13. The International Center for Integrated Water Resources Management (ICIWaRM): The United States' Contribution to UNESCO IHP's Global Network of Water Centers

    Science.gov (United States)

    Logan, W. S.

    2015-12-01

    The concept of a "category 2 center"—i.e., one that is closely affiliated with UNESCO, but not legally part of UNESCO—dates back many decades. However, only in the last decade has the concept been fully developed. Within UNESCO, the International Hydrological Programme (IHP) has led the way in creating a network of regional and global water-related centers.ICIWaRM—the International Center for Integrated Water Resources Management—is one member of this network. Approved by UNESCO's General Conference, the center has been operating since 2009. It was designed to fill a niche in the system for a center that was backed by an institution with on-the-ground water management experience, but that also had strong connections to academia, NGOs and other governmental agencies. Thus, ICIWaRM is hosted by the US Army Corps of Engineers' Institute for Water Resources (IWR), but established with an internal network of partner institutions. Three main factors have contributed to any success that ICIWaRM has achieved in its global work: A focus on practical science and technology which can be readily transferred. This includes the Corps' own methodologies and models for planning and water management, and those of our university and government partners. Collaboration with other UNESCO Centers on joint applied research, capacity-building and training. A network of centers needs to function as a network, and ICIWaRM has worked together with UNESCO-affiliated centers in Chile, Brazil, Paraguay, the Dominican Republic, Japan, China, and elsewhere. Partnering with and supporting existing UNESCO-IHP programs. ICIWaRM serves as the Global Technical Secretariat for IHP's Global Network on Water and Development Information in Arid Lands (G-WADI). In addition to directly supporting IHP, work through G-WADI helps the center to frame, prioritize and integrate its activities. With the recent release of the United Nation's 2030 Agenda for Sustainable Development, it is clear that

  14. The Bone Marrow Transplantation Center of the National Cancer Institute - its resources to assist patients with bone marrow failure

    International Nuclear Information System (INIS)

    This paper describes the bone marrow transplantation center of the brazilian National Cancer Institute, which is responsible for the cancer control in Brazil. The document also describes the resources available in the Institute for assisting patients presenting bone marrow failures. The Center provides for allogeneic and autologous bone marrow transplants, peripheral stem cell transplants, umbilical cord collections and transplants, and a small experience with unrelated bone marrow transplants. The Center receives patient from all over the country and provides very sophisticated medical care at no direct cost to the patients

  15. Lessons Learned from Creating the Public Earthquake Resource Center at CERI

    Science.gov (United States)

    Patterson, G. L.; Michelle, D.; Johnston, A.

    2004-12-01

    The Center for Earthquake Research and Information (CERI) at the University of Memphis opened the Public Earthquake Resource Center (PERC) in May 2004. The PERC is an interactive display area that was designed to increase awareness of seismology, Earth Science, earthquake hazards, and earthquake engineering among the general public and K-12 teachers and students. Funding for the PERC is provided by the US Geological Survey, The NSF-funded Mid America Earthquake Center, and the University of Memphis, with input from the Incorporated Research Institutions for Seismology. Additional space at the facility houses local offices of the US Geological Survey. PERC exhibits are housed in a remodeled residential structure at CERI that was donated by the University of Memphis and the State of Tennessee. Exhibits were designed and built by CERI and US Geological Survey staff and faculty with the help of experienced museum display subcontractors. The 600 square foot display area interactively introduces the basic concepts of seismology, real-time seismic information, seismic network operations, paleoseismology, building response, and historical earthquakes. Display components include three 22" flat screen monitors, a touch sensitive monitor, 3 helicorder elements, oscilloscope, AS-1 seismometer, life-sized liquefaction trench, liquefaction shake table, and building response shake table. All displays include custom graphics, text, and handouts. The PERC website at www.ceri.memphis.edu/perc also provides useful information such as tour scheduling, ask a geologist, links to other institutions, and will soon include a virtual tour of the facility. Special consideration was given to address State science standards for teaching and learning in the design of the displays and handouts. We feel this consideration is pivotal to the success of any grass roots Earth Science education and outreach program and represents a valuable lesson that has been learned at CERI over the last several

  16. Establishing bioinformatics research in the Asia Pacific

    OpenAIRE

    Tammi Martti; Ranganathan Shoba; Gribskov Michael; Tan Tin Wee

    2006-01-01

    Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-...

  17. Selecting Diverse Resources of Native American Perspective for the Curriculum Center: Children's Literature, Leveled Readers, and Social Studies Curriculum

    Science.gov (United States)

    Meyer, Nadean

    2011-01-01

    Biased and inaccurate information about Native Americans continue in children's resources and remain in many of today's curriculum centers. While Native American students remain a minority in schools, accurate information is vital for understanding contemporary society and our history by both Native and non-Native students. Many states including…

  18. The Amarillo National Resource Center for Plutonium. Quarterly progress detailed report, 1 November 1996--31 January 1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    Progress for this quarter is given for each of the following Center programs: (1) plutonium information resource; (2) advisory function (DOE and state support); (3) environmental, public health and safety; (3) communication, education, and training; and (4) nuclear and other material studies. Both summaries of the activities and detailed reports are included.

  19. 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.

  20. Development of Russian's industrial and technological resources required to produce PET center equipment

    International Nuclear Information System (INIS)

    Positron emission tomography (PET) is one of the most sensitive and promising methods of nuclear medicine. During the last 10-15 years positron-emission tomography (PET) has developed into a routine clinical diagnostics approach used in oncology, cardiology, neurology, psychiatry and pharmacokinetics applications. Present broad application of PET is associated with the use of not only very short-lived ''bio-isotopes'', but also of other, longer-lived positron emitters and generator systems. At present, PET technique is becoming increasingly important in clinical functional diagnostics. Considering the growing demand from domestic medical institutions in PET diagnostic equipment, the task of providing the national clinics with such instruments becomes not only topical, but vital. Although to present days major medical institutions in Moscow and in St. Petersburg have started procuring imported instruments for their PET, Russia's industrial and technological resources required to produce PET center equipment are already enough developed. Research and development efforts that have been underway at Institute for Theoretical and Experimental Physics (ITEP), Efremov Scientific Research Institute of Electrophysical Apparatus (NIIEFA) with participation of Central Scientific Research Roentgen-Radiological Institute (CNIRRI) and Bakulev Cardiovascular Surgery Scientific Center (BCSSC) engendered a theoretical, technical and technological foundation for design and production of the equipment required to implement PET technique in the Russian clinical environment. A several cyclotrons with target systems for PET-radionuclide production has been constructed and manufactured. The line of this cyclotrons including negative ion cyclotron CC-18/9 with vertical magnet and simultaneous dual beam extraction for accelerating 18 MeV protons 100 μA extracted beam current and 9 MeV deuterons 50 μA extracted beam current and negative ion cyclotron CC-12 with vertical magnet and

  1. A Survey of Bioinformatics Database and Software Usage through Mining the Literature

    Science.gov (United States)

    Nenadic, Goran; Filannino, Michele; Brass, Andy; Robertson, David L.; Stevens, Robert

    2016-01-01

    Computer-based resources are central to much, if not most, biological and medical research. However, while there is an ever expanding choice of bioinformatics resources to use, described within the biomedical literature, little work to date has provided an evaluation of the full range of availability or levels of usage of database and software resources. Here we use text mining to process the PubMed Central full-text corpus, identifying mentions of databases or software within the scientific literature. We provide an audit of the resources contained within the biomedical literature, and a comparison of their relative usage, both over time and between the sub-disciplines of bioinformatics, biology and medicine. We find that trends in resource usage differs between these domains. The bioinformatics literature emphasises novel resource development, while database and software usage within biology and medicine is more stable and conservative. Many resources are only mentioned in the bioinformatics literature, with a relatively small number making it out into general biology, and fewer still into the medical literature. In addition, many resources are seeing a steady decline in their usage (e.g., BLAST, SWISS-PROT), though some are instead seeing rapid growth (e.g., the GO, R). We find a striking imbalance in resource usage with the top 5% of resource names (133 names) accounting for 47% of total usage, and over 70% of resources extracted being only mentioned once each. While these results highlight the dynamic and creative nature of bioinformatics research they raise questions about software reuse, choice and the sharing of bioinformatics practice. Is it acceptable that so many resources are apparently never reused? Finally, our work is a step towards automated extraction of scientific method from text. We make the dataset generated by our study available under the CC0 license here: http://dx.doi.org/10.6084/m9.figshare.1281371. PMID:27331905

  2. A Survey of Bioinformatics Database and Software Usage through Mining the Literature.

    Science.gov (United States)

    Duck, Geraint; Nenadic, Goran; Filannino, Michele; Brass, Andy; Robertson, David L; Stevens, Robert

    2016-01-01

    Computer-based resources are central to much, if not most, biological and medical research. However, while there is an ever expanding choice of bioinformatics resources to use, described within the biomedical literature, little work to date has provided an evaluation of the full range of availability or levels of usage of database and software resources. Here we use text mining to process the PubMed Central full-text corpus, identifying mentions of databases or software within the scientific literature. We provide an audit of the resources contained within the biomedical literature, and a comparison of their relative usage, both over time and between the sub-disciplines of bioinformatics, biology and medicine. We find that trends in resource usage differs between these domains. The bioinformatics literature emphasises novel resource development, while database and software usage within biology and medicine is more stable and conservative. Many resources are only mentioned in the bioinformatics literature, with a relatively small number making it out into general biology, and fewer still into the medical literature. In addition, many resources are seeing a steady decline in their usage (e.g., BLAST, SWISS-PROT), though some are instead seeing rapid growth (e.g., the GO, R). We find a striking imbalance in resource usage with the top 5% of resource names (133 names) accounting for 47% of total usage, and over 70% of resources extracted being only mentioned once each. While these results highlight the dynamic and creative nature of bioinformatics research they raise questions about software reuse, choice and the sharing of bioinformatics practice. Is it acceptable that so many resources are apparently never reused? Finally, our work is a step towards automated extraction of scientific method from text. We make the dataset generated by our study available under the CC0 license here: http://dx.doi.org/10.6084/m9.figshare.1281371. PMID:27331905

  3. The retention of health human resources in primary healthcare centers in Lebanon: a national survey

    Directory of Open Access Journals (Sweden)

    Alameddine Mohamad

    2012-11-01

    Full Text Available Abstract Background Critical shortages of health human resources (HHR, associated with high turnover rates, have been a concern in many countries around the globe. Of particular interest is the effect of such a trend on the primary healthcare (PHC sector; considered a cornerstone in any effective healthcare system. This study is a rare attempt to investigate PHC HHR work characteristics, level of burnout and likelihood to quit as well as the factors significantly associated with staff retention at PHC centers in Lebanon. Methods A cross-sectional design was utilized to survey all health providers at 81 PHC centers dispersed in all districts of Lebanon. The questionnaire consisted of four sections: socio-demographic/ professional background, organizational/institutional characteristics, likelihood to quit and level of professional burnout (using the Maslach-Burnout Inventory. A total of 755 providers completed the questionnaire (60.5% response rate. Bivariate analyses and multinomial logistic regression were used to determine factors associated with likelihood to quit. Results Two out of five respondents indicated likelihood to quit their jobs within the next 1–3 years and an additional 13.4% were not sure about quitting. The top three reasons behind likelihood to quit were poor salary (54.4%, better job opportunities outside the country (35.1% and lack of professional development (33.7%. A U-shaped relationship was observed between age and likelihood to quit. Regression analysis revealed that high levels of burnout, lower level of education and low tenure were all associated with increased likelihood to quit. Conclusions The study findings reflect an unstable workforce and are not conducive to supporting an expanded role for PHC in the Lebanese healthcare system. While strategies aiming at improving staff retention would be important to develop and implement for all PHC HHR; targeted retention initiatives should focus on the young-new recruits

  4. Annual report of Nuclear Human Resource Development Center. April 1, 2012 - March 31, 2013

    International Nuclear Information System (INIS)

    This annual report summarizes the activities of Nuclear Human Resource Development Center (NuHRDeC) of Japan Atomic Energy Agency (JAEA) in the fiscal year 2012. In this fiscal year, we flexibly designed training courses corresponding with the needs from outside, while organizing the annually scheduled training programs, and also actively addressed the challenging issues on human resource development, such as to enhance the collaboration with academia and to organize international training for Asian countries. The number of trainees who completed the domestic training courses in 2012 was increased to 525, which is 30 percent more than the previous year. And also, in order to respond to the Tokyo Electric Power Company (TEPCO)'s Fukushima No.1 nuclear power plant accident, we also organized the special training courses on radiation survey for the subcontracting companies working with TEPCO, and the training courses on decontamination work for the construction companies in Fukushima prefecture. The total number of attendees in these special courses was more than 4,000 persons. JAEA continued its cooperative activities with universities. In respect of the cooperation with graduate school of University of Tokyo, we accepted 14 students and cooperatively conducted practical exercises for nuclear major. Furthermore, we also actively continued cooperation on practical exercises for students of universities which were signed in Nuclear HRD Program. In terms of the collaboration network with universities, the joint course was held with six universities through utilizing the remote education system. Furthermore, the intensive course at Okayama University, Fukui University, and practical exercise at Nuclear Fuel Cycle Engineering Laboratories of JAEA were also conducted. In respect of International training, NuHRDeC continuously implemented the Instructor Training Program (ITP) by receiving the annual sponsorship from MEXT. In fiscal year 2012, eight countries (i

  5. Annual report of Nuclear Human Resource Development Center. April 1, 2010 - March 31, 2011

    International Nuclear Information System (INIS)

    This annual report summarizes the activities of Nuclear Human Resource Development Center (NuHRDeC) of Japan Atomic Energy Agency (JAEA) in the fiscal year 2010. In this fiscal year, NuHRDeC flexibly designed and conducted as need training courses upon requests while conducting the annually scheduled training programs, and actively addressed the challenge of human resource development, such as to enhance the collaboration with academia and to expand the number of participating countries for international training. The number of trainees who completed the domestic training courses in 2010 was slightly increased to 340, which is 6 percent more than the previous year. The number of those who completed the staff technical training courses was 879 in 2010, which is 12 percent more than the previous year. As a result, the total number of trainees during this period is about 10 percent more than the previous year. In order to correspond with the needs from outside of JAEA, four temporary courses were held upon the request from Nuclear and Industrial Safety Agency (NISA), Ministry of Economy, Trade and Industry (METI). JAEA continued its cooperative activities with universities; cooperation with graduate school of University of Tokyo, and the cooperative graduate school program was enlarged to cooperate with totally 19 graduate schools, one faculty of undergraduate school, and one technical college, including the newly joined 1 graduate school in 2010. JAEA also continued cooperative activities with Nuclear HRD Program initiated by MEXT and METI in 2007. The joint course has continued networking with six universities through utilizing the remote education system, Japan Nuclear Education Network (JNEN), and special lectures, summer and winter practice were also conducted. In respect of International training, NuHRDeC continuously implemented the Instructor Training Program (ITP) by receiving the annual sponsorship from MEXT. In fiscal year 2010, four countries (Bangladesh

  6. Annual report of Nuclear Human Resource Development Center. April 1, 2013 - March 31, 2014

    International Nuclear Information System (INIS)

    This annual report summarizes the activities of Nuclear Human Resource Development Center (NuHRDeC) of Japan Atomic Energy Agency (JAEA) in the FY2013. In FY2013, we flexibly designed special training courses corresponding with the outside training needs, while organizing the annually scheduled regular training programs. We also actively addressed the challenging issues on human resource development, such as to enhance the collaboration with academia and to organize international training for Asian countries. The number of trainees who participated in the domestic regular training courses in 2013 was more than 300 persons. Besides these regular courses, we also organized the special training courses based on the outside needs, e.g. the training courses on radiation survey and decontamination work in Fukushima prefecture for the subcontracting companies of the Tokyo Electric Power Company (TEPCO) working to respond to the TEPCO's Fukushima Daiichi nuclear power station accident. JAEA continued its cooperative activities with universities. In respect of the cooperation with graduate school of University of Tokyo, we accepted nuclear major students and cooperatively conducted lectures and practical exercises for one year. In terms of the collaboration network with universities, the joint course was successfully held with six universities through utilizing the remote education system. Furthermore, the intensive course at Okayama University, University of Fukui, and practical exercise at Nuclear Fuel Cycle Engineering Laboratories of JAEA were also conducted. In respect of International training, we continuously implemented the Instructor Training Program (ITP) by receiving the annual sponsorship from Ministry of Education, Culture, Sports, Science and Technology. In fiscal year 2013, eight countries (i.e. Bangladesh, Indonesia, Kazakhstan, Malaysia, Mongolia, Philippines, Thailand, Vietnam) joined this Instructor training courses. Furthermore, we organized nuclear

  7. Annual report of Nuclear Human Resource Development Center. April 1, 2011 - March 31, 2012

    International Nuclear Information System (INIS)

    This annual report summarizes the activities of Nuclear Human Resource Development Center (NuHRDeC) of Japan Atomic Energy Agency (JAEA) in the fiscal year 2011. In this fiscal year, we flexibly designed and conducted training courses corresponding with the needs from outside, while conducting the annually scheduled training programs, and also actively addressed the challenge of human resource development, such as to enhance the collaboration with academia and to organize international training for Asian countries. The number of trainees who completed the domestic training courses in 2011 was increased to 387, which is 14 percent more than the previous year. And also, in order to respond to the Tokyo Electric Power Company (TEPCO)'s Fukushima No.1 nuclear power plant accident, we also newly designed and organized the special training courses on radiation survey for the subcontracting companies working with TEPCO, and the training courses on decontamination work for the construction companies in Fukushima prefecture. The total number of attendees in these special courses was 3,800 persons. JAEA continued its cooperative activities with universities. In respect of the cooperation with graduate school of University of Tokyo, we accepted 17 students and cooperatively conducted practical exercises for nuclear major. Furthermore, we also actively continued cooperation on practical exercises for students of universities which were signed in Nuclear HRD Program. In terms of the collaboration network with universities, the joint course was held with six universities through utilizing the remote education system. Furthermore, the intensive course at Okayama University and practical exercise at Nuclear Fuel Cycle Engineering Laboratories of JAEA were also conducted. In respect of International training, NuHRDeC continuously implemented the Instructor Training Program (ITP) by receiving the annual sponsorship from MEXT. In fiscal year 2011, seven countries (i.e. Bangladesh

  8. Best practices in bioinformatics training for life scientists

    DEFF Research Database (Denmark)

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik;

    2013-01-01

    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......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...... 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...

  9. Using registries to integrate bioinformatics tools and services into workbench environments

    DEFF Research Database (Denmark)

    Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer;

    2015-01-01

    within convenient, integrated “workbench” environments. Resource descriptions are the core element of registry and workbench systems, which are used to both help the user find and comprehend available software tools, data resources, and Web Services, and to localise, execute and combine them......The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand increasingly usable and integrated ways to access and analyse data, especially......, a software component that will ease the integration of bioinformatics resources in a workbench environment, using their description provided by the existing ELIXIR Tools and Data Services Registry....

  10. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

    Science.gov (United States)

    Katayama, Toshiaki; Arakawa, Kazuharu; Nakao, Mitsuteru; Ono, Keiichiro; Aoki-Kinoshita, Kiyoko F; Yamamoto, Yasunori; Yamaguchi, Atsuko; Kawashima, Shuichi; Chun, Hong-Woo; Aerts, Jan; Aranda, Bruno; Barboza, Lord Hendrix; Bonnal, Raoul Jp; Bruskiewich, Richard; Bryne, Jan C; Fernández, José M; Funahashi, Akira; Gordon, Paul Mk; Goto, Naohisa; Groscurth, Andreas; Gutteridge, Alex; Holland, Richard; Kano, Yoshinobu; Kawas, Edward A; Kerhornou, Arnaud; Kibukawa, Eri; Kinjo, Akira R; Kuhn, Michael; Lapp, Hilmar; Lehvaslaiho, Heikki; Nakamura, Hiroyuki; Nakamura, Yasukazu; Nishizawa, Tatsuya; Nobata, Chikashi; Noguchi, Tamotsu; Oinn, Thomas M; Okamoto, Shinobu; Owen, Stuart; Pafilis, Evangelos; Pocock, Matthew; Prins, Pjotr; Ranzinger, René; Reisinger, Florian; Salwinski, Lukasz; Schreiber, Mark; Senger, Martin; Shigemoto, Yasumasa; Standley, Daron M; Sugawara, Hideaki; Tashiro, Toshiyuki; Trelles, Oswaldo; Vos, Rutger A; Wilkinson, Mark D; York, William; Zmasek, Christian M; Asai, Kiyoshi; Takagi, Toshihisa

    2010-01-01

    Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies. PMID:20727200

  11. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

    Directory of Open Access Journals (Sweden)

    Katayama Toshiaki

    2010-08-01

    Full Text Available Abstract Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS and Computational Biology Research Center (CBRC and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

  12. The Counseling Center: An Undervalued Resource in Recruitment, Retention, and Risk Management

    Science.gov (United States)

    Bishop, John B.

    2010-01-01

    A primary responsibility for directors of college and university counseling centers is to explain to various audiences the multiple ways such units are of value to their institutions. This article reviews the history of how counseling center directors have been encouraged to develop and describe the work of their centers. Often overlooked are the…

  13. Developing expertise in bioinformatics for biomedical research in Africa

    OpenAIRE

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

    2015-01-01

    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 help...

  14. Bioinformatics glossary based Database of Biological Databases: DBD

    OpenAIRE

    Siva Kiran RR; Setty MVN; Hanumatha Rao G

    2009-01-01

    Database of Biological/Bioinformatics Databases (DBD) is a collection of 1669 databases and online resources collected from NAR Database Summary Papers (http://www.oxfordjournals.org/nar/database/a/) & Internet search engines. The database has been developed based on 437 keywords (Glossary) available in http://falcon.roswellpark.org/labweb/glossary.html. Keywords with their relevant databases are arranged in alphabetic order which enables quick accession of databases by researchers. Dat...

  15. Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

    Science.gov (United States)

    Verheggen, Kenneth; Maddelein, Davy; Hulstaert, Niels; Martens, Lennart; Barsnes, Harald; Vaudel, Marc

    2016-03-01

    The use of proteomics bioinformatics substantially contributes to an improved understanding of proteomes, but this novel and in-depth knowledge comes at the cost of increased computational complexity. Parallelization across multiple computers, a strategy termed distributed computing, can be used to handle this increased complexity; however, setting up and maintaining a distributed computing infrastructure requires resources and skills that are not readily available to most research groups. Here we propose a free and open-source framework named Pladipus that greatly facilitates the establishment of distributed computing networks for proteomics bioinformatics tools. Pladipus is straightforward to install and operate thanks to its user-friendly graphical interface, allowing complex bioinformatics tasks to be run easily on a network instead of a single computer. As a result, any researcher can benefit from the increased computational efficiency provided by distributed computing, hence empowering them to tackle more complex bioinformatics challenges. Notably, it enables any research group to perform large-scale reprocessing of publicly available proteomics data, thus supporting the scientific community in mining these data for novel discoveries. PMID:26510693

  16. Resources to Support Ethical Practice in Evaluation: An Interview with the Director of the National Center for Research and Professional Ethics

    Science.gov (United States)

    Goodyear, Leslie

    2012-01-01

    Where do evaluators find resources on ethics and ethical practice? This article highlights a relatively new online resource, a centerpiece project of the National Center for Professional and Research Ethics (NCPRE), which brings together information on best practices in ethics in research, academia, and business in an online portal and center. It…

  17. Establishing bioinformatics research in the Asia Pacific

    Directory of Open Access Journals (Sweden)

    Tammi Martti

    2006-12-01

    Full Text Available Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet, Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand, Penang (Malaysia, Auckland (New Zealand and Busan (South Korea. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community.

  18. Energy-Efficient Management of Data Center Resources for Cloud Computing: A Vision, Architectural Elements, and Open Challenges

    CERN Document Server

    Buyya, Rajkumar; Abawajy, Jemal

    2010-01-01

    Cloud computing is offering utility-oriented IT services to users worldwide. Based on a pay-as-you-go model, it enables hosting of pervasive applications from consumer, scientific, and business domains. However, data centers hosting Cloud applications consume huge amounts of energy, contributing to high operational costs and carbon footprints to the environment. Therefore, we need Green Cloud computing solutions that can not only save energy for the environment but also reduce operational costs. This paper presents vision, challenges, and architectural elements for energy-efficient management of Cloud computing environments. We focus on the development of dynamic resource provisioning and allocation algorithms that consider the synergy between various data center infrastructures (i.e., the hardware, power units, cooling and software), and holistically work to boost data center energy efficiency and performance. In particular, this paper proposes (a) architectural principles for energy-efficient management of ...

  19. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

    Directory of Open Access Journals (Sweden)

    Baseler Michael W

    2007-11-01

    Full Text Available Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.

  20. 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.

  1. Best practices in bioinformatics training for life scientists.

    Science.gov (United States)

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik; Brazas, Michelle D; Brooksbank, Cath; Budd, Aidan; De Las Rivas, Javier; Dreyer, Jacqueline; Fernandes, Pedro L; van Gelder, Celia; Jacob, Joachim; Jimenez, Rafael C; Loveland, Jane; Moran, Federico; Mulder, Nicola; Nyrönen, Tommi; Rother, Kristian; Schneider, Maria Victoria; Attwood, Teresa K

    2013-09-01

    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. PMID:23803301

  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/. PMID:26882475

  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. Bioinformatics and Microarray Data Analysis on the Cloud.

    Science.gov (United States)

    Calabrese, Barbara; Cannataro, Mario

    2016-01-01

    High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data storage and computing power. Cloud computing offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and thus, it may represent the key technology for facing those issues. In fact, in the recent years it has been adopted for the deployment of different bioinformatics solutions and services both in academia and in the industry. Although this, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine. This chapter reviews main academic and industrial cloud-based bioinformatics solutions; with a special focus on microarray data analysis solutions and underlines main issues and problems related to the use of such platforms for the storage and analysis of patients data. PMID:25863787

  5. Incorporating a New Bioinformatics Component into Genetics at a Historically Black College: Outcomes and Lessons

    Science.gov (United States)

    Holtzclaw, J. David; Eisen, Arri; Whitney, Erika M.; Penumetcha, Meera; Hoey, J. Joseph; Kimbro, K. Sean

    2006-01-01

    Many students at minority-serving institutions are underexposed to Internet resources such as the human genome project, PubMed, NCBI databases, and other Web-based technologies because of a lack of financial resources. To change this, we designed and implemented a new bioinformatics component to supplement the undergraduate Genetics course at…

  6. Biology in 'silico': The Bioinformatics Revolution.

    Science.gov (United States)

    Bloom, Mark

    2001-01-01

    Explains the Human Genome Project (HGP) and efforts to sequence the human genome. Describes the role of bioinformatics in the project and considers it the genetics Swiss Army Knife, which has many different uses, for use in forensic science, medicine, agriculture, and environmental sciences. Discusses the use of bioinformatics in the high school…

  7. Fuzzy Logic in Medicine and Bioinformatics

    OpenAIRE

    Torres, Angela; Nieto, Juan J.

    2006-01-01

    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).

  8. 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 RLK) genetic…

  9. 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…

  10. 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.

  11. Rapid Development of Bioinformatics Education in China

    Science.gov (United States)

    Zhong, Yang; Zhang, Xiaoyan; Ma, Jian; Zhang, Liang

    2003-01-01

    As the Human Genome Project experiences remarkable success and a flood of biological data is produced, bioinformatics becomes a very "hot" cross-disciplinary field, yet experienced bioinformaticians are urgently needed worldwide. This paper summarises the rapid development of bioinformatics education in China, especially related undergraduate…

  12. 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.

  13. 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.

  14. 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.

  15. Website for avian flu information and bioinformatics

    Institute of Scientific and Technical Information of China (English)

    GAO; George; Fu

    2009-01-01

    Highly pathogenic influenza A virus H5N1 has spread out worldwide and raised the public concerns. This increased the output of influenza virus sequence data as well as the research publication and other reports. In order to fight against H5N1 avian flu in a comprehensive way, we designed and started to set up the Website for Avian Flu Information (http://www.avian-flu.info) from 2004. Other than the influenza virus database available, the website is aiming to integrate diversified information for both researchers and the public. From 2004 to 2009, we collected information from all aspects, i.e. reports of outbreaks, scientific publications and editorials, policies for prevention, medicines and vaccines, clinic and diagnosis. Except for publications, all information is in Chinese. Till April 15, 2009, the cumulative news entries had been over 2000 and research papers were approaching 5000. By using the curated data from Influenza Virus Resource, we have set up an influenza virus sequence database and a bioinformatic platform, providing the basic functions for the sequence analysis of influenza virus. We will focus on the collection of experimental data and results as well as the integration of the data from the geological information system and avian influenza epidemiology.

  16. Website for avian flu information and bioinformatics

    Institute of Scientific and Technical Information of China (English)

    LIU Di; LIU Quan-He; WU Lin-Huan; LIU Bin; WU Jun; LAO Yi-Mei; LI Xiao-Jing; GAO George Fu; MA Jun-Cai

    2009-01-01

    Highly pathogenic influenza A virus H5N1 has spread out worldwide and raised the public concerns. This increased the output of influenza virus sequence data as well as the research publication and other reports. In order to fight against H5N1 avian flu in a comprehensive way, we designed and started to set up the Website for Avian Flu Information (http://www.avian-flu.info) from 2004. Other than the influenza virus database available, the website is aiming to integrate diversified information for both researchers and the public. From 2004 to 2009, we collected information from all aspects, i.e. reports of outbreaks, scientific publications and editorials, policies for prevention, medicines and vaccines, clinic and diagnosis. Except for publications, all information is in Chinese. Till April 15, 2009, the cumulative news entries had been over 2000 and research papers were approaching 5000. By using the curated data from Influenza Virus Resource, we have set up an influenza virus sequence database and a bioin-formatic platform, providing the basic functions for the sequence analysis of influenza virus. We will focus on the collection of experimental data and results as well as the integration of the data from the geological information system and avian influenza epidemiology.

  17. The European Bioinformatics Institute in 2016: Data growth and integration.

    Science.gov (United States)

    Cook, Charles E; Bergman, Mary Todd; Finn, Robert D; Cochrane, Guy; Birney, Ewan; Apweiler, Rolf

    2016-01-01

    New technologies are revolutionising biological research and its applications by making it easier and cheaper to generate ever-greater volumes and types of data. In response, the services and infrastructure of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.uk) are continually expanding: total disk capacity increases significantly every year to keep pace with demand (75 petabytes as of December 2015), and interoperability between resources remains a strategic priority. Since 2014 we have launched two new resources: the European Variation Archive for genetic variation data and EMPIAR for two-dimensional electron microscopy data, as well as a Resource Description Framework platform. We also launched the Embassy Cloud service, which allows users to run large analyses in a virtual environment next to EMBL-EBI's vast public data resources. PMID:26673705

  18. 15 CFR 291.4 - National industry-specific pollution prevention and environmental compliance resource centers.

    Science.gov (United States)

    2010-01-01

    ..., external evaluation for assessing outcomes of the activity, and “customer satisfaction” measures of...) The center should assist the customer in choosing the most cost- effective, environmentally sound... for identifying those customer needs; and methodologies for continually improving the understanding...

  19. 75 FR 23319 - Notice of Funding Availability for the Small Business Transportation Resource Center Program

    Science.gov (United States)

    2010-05-03

    ... DOT-published marketing materials, such as STLP Program Information, Bonding Assistance information..., chamber of commerce, college or university, community college, and any other qualifying transportation... receive ample resources from the SBTRC, i.e., access to working capital, bonding assistance,...

  20. 78 FR 41817 - Notice of Funding Availability for the Small Business Transportation Resource Center Program

    Science.gov (United States)

    2013-07-11

    ... distribute DOT-published marketing materials, such as Short Term Lending Program (STLP) Information, Bonding... organization, transportation-related trade association, chamber of commerce, college or university, community... control group will receive ample resources from the SBTRC, i.e., access to working capital,...

  1. Yoga for Stress Management Program as a Complementary Alternative Counseling Resource in a University Counseling Center

    Science.gov (United States)

    Milligan, Colleen K.

    2006-01-01

    A Yoga for Stress Management Program (YSMP) that served as a complementary alternative therapy resource was successfully implemented at a midsize, predominantly undergraduate university. It was offered in addition to traditional treatments for student mental health. Counselors, Residence Life staff, and faculty found that the program was useful…

  2. Amarillo National Resource Center for Plutonium. Quarterly technical progress report, May 1--July 31, 1998

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-09-01

    Progress is reported on research projects related to the following: Electronic resource library; Environment, safety, and health; Communication, education, training, and community involvement; Nuclear and other materials; and Reporting, evaluation, monitoring, and administration. Technical studies investigate remedial action of high explosives-contaminated lands, radioactive waste management, nondestructive assay methods, and plutonium processing, handling, and storage.

  3. CoryneCenter – An online resource for the integrated analysis of corynebacterial genome and transcriptome data

    Directory of Open Access Journals (Sweden)

    Hüser Andrea T

    2007-11-01

    Full Text Available Abstract Background The introduction of high-throughput genome sequencing and post-genome analysis technologies, e.g. DNA microarray approaches, has created the potential to unravel and scrutinize complex gene-regulatory networks on a large scale. The discovery of transcriptional regulatory interactions has become a major topic in modern functional genomics. Results To facilitate the analysis of gene-regulatory networks, we have developed CoryneCenter, a web-based resource for the systematic integration and analysis of genome, transcriptome, and gene regulatory information for prokaryotes, especially corynebacteria. For this purpose, we extended and combined the following systems into a common platform: (1 GenDB, an open source genome annotation system, (2 EMMA, a MAGE compliant application for high-throughput transcriptome data storage and analysis, and (3 CoryneRegNet, an ontology-based data warehouse designed to facilitate the reconstruction and analysis of gene regulatory interactions. We demonstrate the potential of CoryneCenter by means of an application example. Using microarray hybridization data, we compare the gene expression of Corynebacterium glutamicum under acetate and glucose feeding conditions: Known regulatory networks are confirmed, but moreover CoryneCenter points out additional regulatory interactions. Conclusion CoryneCenter provides more than the sum of its parts. Its novel analysis and visualization features significantly simplify the process of obtaining new biological insights into complex regulatory systems. Although the platform currently focusses on corynebacteria, the integrated tools are by no means restricted to these species, and the presented approach offers a general strategy for the analysis and verification of gene regulatory networks. CoryneCenter provides freely accessible projects with the underlying genome annotation, gene expression, and gene regulation data. The system is publicly available at http://www.CoryneCenter.de.

  4. 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.

  5. 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. PMID:25856076

  6. Geological characteristics and resource potentials of oil shale in Ordos Basin, Center China

    Energy Technology Data Exchange (ETDEWEB)

    Yunlai, Bai; Yingcheng, Zhao; Long, Ma; Wu-jun, Wu; Yu-hu, Ma

    2010-09-15

    It has been shown that not only there are abundant oil, gas, coal, coal-bed gas, groundwater and giant uranium deposits but also there are abundant oil shale resources in Ordos basin. It has been shown also that the thickness of oil shale is, usually, 4-36m, oil-bearing 1.5%-13.7%, caloric value 1.66-20.98MJ/kg. The resource amount of oil shale with burial depth less than 2000 m is over 2000x108t (334). Within it, confirmed reserve is about 1x108t (121). Not only huge economic benefit but also precious experience in developing oil shale may be obtained in Ordos basin.

  7. The Sharjah Center for Astronomy and Space Sciences (SCASS 2015): Concept and Resources

    Science.gov (United States)

    Naimiy, Hamid M. K. Al

    2015-08-01

    The Sharjah Center for Astronomy and Space Sciences (SCASS) was launched this year 2015 at the University of Sharjah in the UAE. The center will serve to enrich research in the fields of astronomy and space sciences, promote these fields at all educational levels, and encourage community involvement in these sciences. SCASS consists of:The Planetarium: Contains a semi-circle display screen (18 meters in diameter) installed at an angle of 10° which displays high-definition images using an advanced digital display system consisting of seven (7) high-performance light-display channels. The Planetarium Theatre offers a 200-seat capacity with seats placed at highly calculated angles. The Planetarium also contains an enormous star display (Star Ball - 10 million stars) located in the heart of the celestial dome theatre.The Sharjah Astronomy Observatory: A small optical observatory consisting of a reflector telescope 45 centimeters in diameter to observe the galaxies, stars and planets. Connected to it is a refractor telescope of 20 centimeters in diameter to observe the sun and moon with highly developed astronomical devices, including a digital camera (CCD) and a high-resolution Echelle Spectrograph with auto-giving and remote calibration ports.Astronomy, space and physics educational displays for various age groups include:An advanced space display that allows for viewing the universe during four (4) different time periods as seen by:1) The naked eye; 2) Galileo; 3) Spectrographic technology; and 4) The space technology of today.A space technology display that includes space discoveries since the launching of the first satellite in 1940s until now.The Design Concept for the Center (450,000 sq. meters) was originated by HH Sheikh Sultan bin Mohammed Al Qasimi, Ruler of Sharjah, and depicts the dome as representing the sun in the middle of the center surrounded by planetary bodies in orbit to form the solar system as seen in the sky.

  8. The retention of health human resources in primary healthcare centers in Lebanon: a national survey

    OpenAIRE

    Alameddine Mohamad; Saleh Shadi; El-Jardali Fadi; Dimassi Hani; Mourad Yara

    2012-01-01

    Abstract Background Critical shortages of health human resources (HHR), associated with high turnover rates, have been a concern in many countries around the globe. Of particular interest is the effect of such a trend on the primary healthcare (PHC) sector; considered a cornerstone in any effective healthcare system. This study is a rare attempt to investigate PHC HHR work characteristics, level of burnout and likelihood to quit as well as the factors significantly associated with staff reten...

  9. 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...

  10. Challenge: A Multidisciplinary Degree Program in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Mudasser Fraz Wyne

    2006-06-01

    Full Text Available Bioinformatics is a new field that is poorly served by any of the traditional science programs in Biology, Computer science or Biochemistry. Known to be a rapidly evolving discipline, Bioinformatics has emerged from experimental molecular biology and biochemistry as well as from the artificial intelligence, database, pattern recognition, and algorithms disciplines of computer science. While institutions are responding to this increased demand by establishing graduate programs in bioinformatics, entrance barriers for these programs are high, largely due to the significant prerequisite knowledge which is required, both in the fields of biochemistry and computer science. Although many schools currently have or are proposing graduate programs in bioinformatics, few are actually developing new undergraduate programs. In this paper I explore the blend of a multidisciplinary approach, discuss the response of academia and highlight challenges faced by this emerging field.

  11. Amarillo National Resource Center for plutonium. Work plan progress report, November 1, 1995--January 31, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Cluff, D. [Texas Tech Univ., Lubbock, TX (United States)

    1996-04-01

    The Center operates under a cooperative agreement between DOE and the State of Texas and is directed and administered by an education consortium. Its programs include developing peaceful uses for the materials removed from dismantled weapons, studying effects of nuclear materials on environment and public health, remedying contaminated soils and water, studying storage, disposition, and transport of Pu, HE, and other hazardous materials removed from weapons, providing research and counsel to US in carrying out weapons reductions in cooperation with Russia, and conducting a variety of education and training programs.

  12. Fiscal year 1988 program report: Pennsylvania Center for Water Resources Research

    Energy Technology Data Exchange (ETDEWEB)

    McDonnell, A.J.

    1989-08-01

    Three projects and a program of technology transfer were conducted under the Pennsylvania Fiscal Year 1988 State Water Resources Research Grants Program (PL 98-242, Sect. 104). In a completed study focused on the protection of water supplies, mature slow sand filters were found to remove 100 percent of Cryptosporidium and Giardia cysts. A site specific study examined the behavior of sedimentary iron and manganese in an acid mine drainage wetland system. A study was initiated to link a comprehensive non-point source model, AGNPS with current GIS technology to enhance the models' utility for evaluating regional water quality problems related to non-point source agricultural pollution.

  13. Integrative Bioinformatics for Genomics and Proteomics

    OpenAIRE

    Wu, C.H.

    2011-01-01

    Systems integration is becoming the driving force for 21st century biology. Researchers are systematically tackling gene functions and complex regulatory processes by studying organisms at different levels of organization, from genomes and transcriptomes to proteomes and interactomes. To fully realize the value of such high-throughput data requires advanced bioinformatics for integration, mining, comparative analysis, and functional interpretation. We are developing a bioinformatics research ...

  14. Bioinformatics clouds for big data manipulation

    OpenAIRE

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

    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 a...

  15. No-boundary thinking in bioinformatics research

    OpenAIRE

    Huang, Xiuzhen; Bruce, Barry; Buchan, Alison; Congdon, Clare Bates; Cramer, Carole L.; Jennings, Steven F; Jiang, Hongmei; Li, Zenglu; McClure, Gail; McMullen, Rick; Moore, Jason H.; Nanduri, Bindu; Peckham, Joan; Perkins, Andy; Polson, Shawn W.

    2013-01-01

    Currently there are definitions from many agencies and research societies defining “bioinformatics” as deriving knowledge from computational analysis of large volumes of biological and biomedical data. Should this be the bioinformatics research focus? We will discuss this issue in this review article. We would like to promote the idea of supporting human-infrastructure (HI) with no-boundary thinking (NT) in bioinformatics (HINT).

  16. Bioinformatics for saffron (Crocus sativus L.) improvement

    OpenAIRE

    Ghulam A. PARRAY; Abdul G. Rather; Parvez Sofi; Shafiq A. Wani; Amjad M. Husaini; Asif B. Shikari; Javid I. Mir

    2009-01-01

    Saffron (Crocus sativus L.) is a sterile triploid plant and belongs to the Iridaceae (Liliales, Monocots). Its genome is of relatively large size and is poorly characterized. Bioinformatics can play an enormous technical role in the sequence-level structural characterization of saffron genomic DNA. Bioinformatics tools can also help in appreciating the extent of diversity of various geographic or genetic groups of cultivated saffron to infer relationships between groups and accessions. The ch...

  17. Design of SCADA water resource management control center by a bi-objective redundancy allocation problem and particle swarm optimization

    International Nuclear Information System (INIS)

    SCADA is an essential system to control critical facilities in big cities. SCADA is utilized in several sectors such as water resource management, power plants, electricity distribution centers, traffic control centers, and gas deputy. The failure of SCADA results in crisis. Hence, the design of SCADA system in order to serve a high reliability considering limited budget and other constraints is essential. In this paper, a bi-objective redundancy allocation problem (RAP) is proposed to design Tehran's SCADA water resource management control center. Reliability maximization and cost minimization are concurrently considered. Since the proposed RAP is a non-linear multi-objective mathematical programming so the exact methods cannot efficiently handle it. A multi-objective particle swarm optimization (MOPSO) algorithm is designed to solve it. Several features such as dynamic parameter tuning, efficient constraint handling and Pareto gridding are inserted in proposed MOPSO. The results of proposed MOPSO are compared with an efficient ε-constraint method. Several non-dominated designs of SCADA system are generated using both methods. Comparison metrics based on accuracy and diversity of Pareto front are calculated for both methods. The proposed MOPSO algorithm reports better performance. Finally, in order to choose the practical design, the TOPSIS algorithm is used to prune the Pareto front. - Highlights: • Multi-objective redundancy allocation problem (MORAP) is proposed to design SCADA system. • Multi-objective particle swarm optimization (MOPSO) is proposed to solve MORAP. • Efficient epsilon-constraint method is adapted to solve MORAP. • Non-dominated solutions are generated on Pareto front of MORAP by both methods. • Several multi-objective metrics are calculated to compare the performance of methods

  18. A Method for Determination of Resource Potantial of Cankırı Historical City Center

    Directory of Open Access Journals (Sweden)

    E. Erdogan

    2008-01-01

    Full Text Available The scope of this research, within the frame of Cankırı’s urban site area case, is to highlight the importance of urban landscape design in conservation of historical city centers in order to assure cultural continuity and their integration with modern living conditions to ensure their proper transfer to future generations as livable spaces. On the above mentioned extend, conservation of historical places, urban landscape design and development process of city centers in terms of space and history were touched upon. Besides, according to the findings obtained from preliminary works and analyses carried out in the research field, proposals were pronounced to maintain the sustainability of natural and cultural values in Cankırı’s urban site area. Additionally, existent maps covering the urban site under question were digitalized and computerized and by this way spatial data and attribute data were linked together and arranged in order to build up a reference data base for both city of Cankırı and similar studies.

  19. 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.

  20. The Biomedical Computing Technology Information Center. An international resource for technology sharing

    International Nuclear Information System (INIS)

    The expense of developing and maintaining special software and interfaces has been prohibitive to many clinical installations desiring to perform computer-assisted studies. Also, existing developmental groups have been economically unable to adequately transfer their work to such smaller installations. In response to this need and through the efforts of the Society of Nuclear Medicine Computer Committee, the US Energy Research and Development Administration (ERDA) has established the Biomedical Computing Technology Information Center (BCTIC) at the Oak Ridge National Laboratory (ORNL). BCTIC collects, organizes, evaluates and disseminates information on computing technology pertinent to biomedicine in general and nuclear medicine in particular, providing the needed routes of communication between installations and serving as a clearinghouse for the exchange of biomedical computing software, data and interface designs. BCTIC services are available to its sponsors and their contractors and to any individual or group willing to participate in mutual exchange. (author)

  1. Bioinformática como recurso pedagógico para o curso de ciências biológicas na Universidade Estadual do Ceará – UECE – Fortaleza, Estado do Ceará = Bioinformatics as a pedagogical resource for the biology course in the State University of Ceara - UECE - Fortaleza, Ceará State

    Directory of Open Access Journals (Sweden)

    Howard Lopes Ribeiro Junior

    2012-01-01

    Full Text Available O objetivo deste estudo foi aplicar e avaliar conteúdos teórico-práticos de Bioinformática para estudantes do curso de Licenciatura Plena em Ciências Biológicas, matriculados nas disciplinas de Genética geral e Biologia Molecular na Universidade Estadual do Ceará, no ano de 2010. A abordagem teórica consistiu de uma apresentação de conceitos históricos, básicos e específicos dos atuais avanços das pesquisas envolvidas nas áreas da biologia Molecular. A prática de ‘Construção de uma Filogenia Molecular in Silico’ foi elaborada para tornar funcionais os conceitos apresentados na prática anterior (RIBEIRO JUNIOR, 2011, com a utilização do banco de dados do National Center for Biotechnology Information, NCBI, e sua ferramenta de alinhamento de sequências, o BLASTp (Basic Local Alignment Search Tool Protein-Protein. Os resultados positivos obtidos com a aplicação da aula teórica de Introdução à Bioinformática e das atividades práticas foram destacados com as caracterizações das filogenias moleculares das sequências hipotéticas propostas para a execução dos alinhamentos e com as falas dos alunos anteriormente citados. Essas atividades foram consideradas essenciais para que os alunos pudessem vivenciar o passo a passo para uma melhor compreensão da emergente área das ciências da vida: a Bioinformática.The objective of this study was to evaluate and apply the Bioinformatics theoretical contents and practical for the course students in Biological Sciences Degree Fully enrolled in the disciplines of General Genetics and Molecular Biology, State University of Ceara in 2010. The theoretical approach previously tested (RIBEIRO JUNIOR, 2011 consisted of a presentation of historical concepts, basic and specific to current advances in research involved the areas of molecular biology. The practice of "Building a Molecular Phylogeny in Silico" is designed to become functional in practice the concepts presented above

  2. Final Report: Phase II Nevada Water Resources Data, Modeling, and Visualization (DMV) Center

    Energy Technology Data Exchange (ETDEWEB)

    Jackman, Thomas [Desert Research Institute; Minor, Timothy [Desert Research Institute; Pohll, Gregory [Desert Research Institute

    2013-07-22

    Water is unquestionably a critical resource throughout the United States. In the semi-arid west -- an area stressed by increase in human population and sprawl of the built environment -- water is the most important limiting resource. Crucially, science must understand factors that affect availability and distribution of water. To sustain growing consumptive demand, science needs to translate understanding into reliable and robust predictions of availability under weather conditions that could be average but might be extreme. These predictions are needed to support current and long-term planning. Similar to the role of weather forecast and climate prediction, water prediction over short and long temporal scales can contribute to resource strategy, governmental policy and municipal infrastructure decisions, which are arguably tied to the natural variability and unnatural change to climate. Change in seasonal and annual temperature, precipitation, snowmelt, and runoff affect the distribution of water over large temporal and spatial scales, which impact the risk of flooding and the groundwater recharge. Anthropogenic influences and impacts increase the complexity and urgency of the challenge. The goal of this project has been to develop a decision support framework of data acquisition, digital modeling, and 3D visualization. This integrated framework consists of tools for compiling, discovering and projecting our understanding of processes that control the availability and distribution of water. The framework is intended to support the analysis of the complex interactions between processes that affect water supply, from controlled availability to either scarcity or deluge. The developed framework enables DRI to promote excellence in water resource management, particularly within the Lake Tahoe basin. In principle, this framework could be replicated for other watersheds throughout the United States. Phase II of this project builds upon the research conducted during

  3. [Establish and manage a National Resource Center for plutonium, Quarterly report, April 1, 1995--June 30, 1995

    International Nuclear Information System (INIS)

    The initial phase of the Plutonium Information Resource is well under way. Board members developed linkages with Russian scientists and engineers and obtained names of technical team members. Nuclear proposals were reviewed by the Nuclear Review Group, and the proposals were modified to incorporate the review group's comments. Portions of the proposals were approved by the Governing Board. Proposals for education and outreach were reviewed by the Education Proposal Review Group, considered by the Governing Board and approved. The Senior Technical Review Group met to consider the R ampersand D programs associated with fissile materials disposal. A newsletter was published. Progress continued on the high explosives demonstration project, on site-specific environmental work, and the multiattribute utility analysis. Center offices in Amarillo were furnished, equipment was purchased, and the lease was modified

  4. Grant writing for childbirth educators: lessons learned from the resource center for young parents-to-be.

    Science.gov (United States)

    Broussard, Brenda S; Broussard, Anne B

    2010-01-01

    Obtaining funding to support community-based childbirth education programs can be a challenge for childbirth educators who may have little grant-writing experience. This article was written by two nurse educators/nurse-midwives who have been involved for over 10 years with a grant-funded parenting and childbirth education program for pregnant teens. It reviews the background of the Resource Center for Young Parents-To-Be, suggests grant-funding sources, and explains the building of partnerships in the community. The basic steps involved in the grant-writing process are presented as well as the importance of follow-up evaluations and reports. Grant-writing skills and the ability to forge partnerships with other community organizations can be important tools for childbirth educators and health-care professionals. PMID:21197129

  5. Brain metastases from solid tumors: disease outcome according to type of treatment and therapeutic resources of the treating center

    Directory of Open Access Journals (Sweden)

    Pace Andrea

    2011-01-01

    Full Text Available Abstract Background To evaluate the therapeutic strategies commonly employed in the clinic for the management of brain metastases (BMs and to correlate disease outcome with type of treatment and therapeutic resources available at the treating center. Methods Four Cancer centres participated to the survey. Data were collected through a questionnaire filled in by one physician for each centre. Results Clinical data regarding 290 cancer patients with BMs from solid tumors were collected. Median age was 59 and 59% of patients had ≤ 3 brain metastases. A local approach (surgery and stereotactic radiosurgery was adopted in 31% of patients. The local approach demonstrated to be superior in terms of survival compared to the regional/systemic approach (whole brain radiotherapy and chemotherapy, p = Conclusions In clinical practice, local strategies should be integrated in the management of brain metastases. Proper selection of patients who are candidate to local treatments is of crucial importance.

  6. U.S. Department of Energy Regional Resource Centers Report: State of the Wind Industry in the Regions

    Energy Technology Data Exchange (ETDEWEB)

    Baranowski, Ruth [National Renewable Energy Lab. (NREL), Golden, CO (United St; Oteri, Frank [National Renewable Energy Lab. (NREL), Golden, CO (United St; Baring-Gould, Ian [National Renewable Energy Lab. (NREL), Golden, CO (United St; Tegen, Suzanne [National Renewable Energy Lab. (NREL), Golden, CO (United St

    2016-03-01

    The wind industry and the U.S. Department of Energy (DOE) are addressing technical challenges to increasing wind energy's contribution to the national grid (such as reducing turbine costs and increasing energy production and reliability), and they recognize that public acceptance issues can be challenges for wind energy deployment. Wind project development decisions are best made using unbiased information about the benefits and impacts of wind energy. In 2014, DOE established six wind Regional Resource Centers (RRCs) to provide information about wind energy, focusing on regional qualities. This document summarizes the status and drivers for U.S. wind energy development on regional and state levels. It is intended to be a companion to DOE's 2014 Distributed Wind Market Report, 2014 Wind Technologies Market Report, and 2014 Offshore Wind Market and Economic Analysis that provide assessments of the national wind markets for each of these technologies.

  7. A Summary of NASA Summer Faculty Fellowship Work in the E.O. Office and in the Educator Resources Center

    Science.gov (United States)

    Thompson, H. Wendell, Sr.

    2005-01-01

    The Office of Equal Opportunity supports a number of summer programs which are designed to: 1.) Increase the number of elementary and secondary students and teachers who are involved in NASA-related education opportunities; and 2.) Support higher education research capability and opportunities that attract and prepare increasing numbers of students and faculty for NASA-related careers. A part of my work in the E.O. office involved the evaluation of several of the programs in order to determine their level of success and to make recommendations for the improvement of those programs where necessary. As a part of the involvement with one of the programs, the PSTI, I had the great opportunity to interact with the students in a number of their sessions which involved problem-based learning in science, mathematics and technology. A summary of the evaluation of those programs is included in this report. The second part of my work involved assisting the coordinator of the Educator Resource Center at the Space and Rocket Center. I participated in space science workshops for in-service and pre-service teachers. There educational resources were made available to the participants including many hands-on activities that hey could take back to their classes. I participated in the three hour workshops that were offered on Tuesdays and Thursdays of each week, although there were workshops on other days. On Mondays, Wednesdays, and Fridays, I worked in the E.O. office. As a result of my work in the ERC, I developed a Directed Reading PowerPoint Lesson Plan Guide involving remote sensing entitled, Echo the Bat. This was based on a NASA published children's book entitled Echo The Bat, written by Ginger Butcher. I have included a description of the lesson in this report. A summary of the evaluations of several of the summer programs supported by the Equal Opportunity office are included in this report.

  8. Screening Genetic Resources of Capsicum Peppers in Their Primary Center of Diversity in Bolivia and Peru.

    Directory of Open Access Journals (Sweden)

    Maarten van Zonneveld

    Full Text Available For most crops, like Capsicum, their diversity remains under-researched for traits of interest for food, nutrition and other purposes. A small investment in screening this diversity for a wide range of traits is likely to reveal many traditional varieties with distinguished values. One objective of this study was to demonstrate, with Capsicum as model crop, the application of indicators of phenotypic and geographic diversity as effective criteria for selecting promising genebank accessions for multiple uses from crop centers of diversity. A second objective was to evaluate the expression of biochemical and agromorphological properties of the selected Capsicum accessions in different conditions. Four steps were involved: 1 Develop the necessary diversity by expanding genebank collections in Bolivia and Peru; 2 Establish representative subsets of ~100 accessions for biochemical screening of Capsicum fruits; 3 Select promising accessions for different uses after screening; and 4 Examine how these promising accessions express biochemical and agromorphological properties when grown in different environmental conditions. The Peruvian Capsicum collection now contains 712 accessions encompassing all five domesticated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens. The collection in Bolivia now contains 487 accessions, representing all five domesticates plus four wild taxa (C. baccatum var. baccatum, C. caballeroi, C. cardenasii, and C. eximium. Following the biochemical screening, 44 Bolivian and 39 Peruvian accessions were selected as promising, representing wide variation in levels of antioxidant capacity, capsaicinoids, fat, flavonoids, polyphenols, quercetins, tocopherols, and color. In Peru, 23 promising accessions performed well in different environments, while each of the promising Bolivian accessions only performed well in a certain environment. Differences in Capsicum diversity and local contexts led to distinct

  9. Screening Genetic Resources of Capsicum Peppers in Their Primary Center of Diversity in Bolivia and Peru.

    Science.gov (United States)

    van Zonneveld, Maarten; Ramirez, Marleni; Williams, David E; Petz, Michael; Meckelmann, Sven; Avila, Teresa; Bejarano, Carlos; Ríos, Llermé; Peña, Karla; Jäger, Matthias; Libreros, Dimary; Amaya, Karen; Scheldeman, Xavier

    2015-01-01

    For most crops, like Capsicum, their diversity remains under-researched for traits of interest for food, nutrition and other purposes. A small investment in screening this diversity for a wide range of traits is likely to reveal many traditional varieties with distinguished values. One objective of this study was to demonstrate, with Capsicum as model crop, the application of indicators of phenotypic and geographic diversity as effective criteria for selecting promising genebank accessions for multiple uses from crop centers of diversity. A second objective was to evaluate the expression of biochemical and agromorphological properties of the selected Capsicum accessions in different conditions. Four steps were involved: 1) Develop the necessary diversity by expanding genebank collections in Bolivia and Peru; 2) Establish representative subsets of ~100 accessions for biochemical screening of Capsicum fruits; 3) Select promising accessions for different uses after screening; and 4) Examine how these promising accessions express biochemical and agromorphological properties when grown in different environmental conditions. The Peruvian Capsicum collection now contains 712 accessions encompassing all five domesticated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens). The collection in Bolivia now contains 487 accessions, representing all five domesticates plus four wild taxa (C. baccatum var. baccatum, C. caballeroi, C. cardenasii, and C. eximium). Following the biochemical screening, 44 Bolivian and 39 Peruvian accessions were selected as promising, representing wide variation in levels of antioxidant capacity, capsaicinoids, fat, flavonoids, polyphenols, quercetins, tocopherols, and color. In Peru, 23 promising accessions performed well in different environments, while each of the promising Bolivian accessions only performed well in a certain environment. Differences in Capsicum diversity and local contexts led to distinct outcomes in

  10. BioXSD: the common data-exchange format for everyday bioinformatics web services

    DEFF Research Database (Denmark)

    Kalas, M.; Puntervoll, P.; Joseph, A.;

    2010-01-01

    Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use...

  11. Service-aware resources integrated resilience for software defined data center networking based on IP over Flexi-Grid optical networks

    Science.gov (United States)

    Yang, Hui; Zhang, Jie; Zhao, Yongli; Cheng, Lei; Wu, Jialin; Ji, Yuefeng; Han, Jianrui; Lin, Yi; Lee, Young

    2015-01-01

    Due to the performance guarantee of low delay, huge bandwidth and high reliability at a low cost, IP over Flexi-Grid optical network is a very promising networking architecture applied to the interconnection of geographically distributed data centers. It can enable efficient resource utilization and support heterogeneous bandwidth demands in cost-effective, highly-available and energy-effective manner. In case of edge Flexi-Grid optical network node failure, to ensure a high-level quality of service (QoS) for user request after the failure becomes a research focus. In this paper, we propose a novel service-aware resources integrated resilience (SA-RIR) scheme for data center services in software defined data center networking architecture based on IP over Flexi-Grid optical networks. Different from previous works which restore the services just exploiting the optical stratum, the proposed scheme provides the resilience using the multiple stratums resources in case of the edge optical node failure. We quantitatively evaluate the feasibility and performances through the simulation under heavy traffic load scenario in terms of path blocking probability, path resilience latency and resource occupation rate with different failure rates. Simulation results show that, the SA-RIR scheme can enable joint optimization of IP network, Flexi-Grid optical network and data center application stratum resources, and enhance the data center service resilience responsiveness to the dynamic end-to-end demands.

  12. The EGI-Engage EPOS Competence Center - Interoperating heterogeneous AAI mechanisms and Orchestrating distributed computational resources

    Science.gov (United States)

    Bailo, Daniele; Scardaci, Diego; Spinuso, Alessandro; Sterzel, Mariusz; Schwichtenberg, Horst; Gemuend, Andre

    2016-04-01

    manage the use of the subsurface of the Earth. EPOS started its Implementation Phase in October 2015 and is now actively working in order to integrate multidisciplinary data into a single e-infrastructure. Multidisciplinary data are organized and governed by the Thematic Core Services (TCS) - European wide organizations and e-Infrastructure providing community specific data and data products - and are driven by various scientific communities encompassing a wide spectrum of Earth science disciplines. TCS data, data products and services will be integrated into the Integrated Core Services (ICS) system, that will ensure their interoperability and access to these services by the scientific community as well as other users within the society. The EPOS competence center (EPOS CC) goal is to tackle two of the main challenges that the ICS are going to face in the near future, by taking advantage of the technical solutions provided by EGI. In order to do this, we will present the two pilot use cases the EGI-EPOS CC is developing: 1) The AAI pilot, dealing with the provision of transparent and homogeneous access to the ICS infrastructure to users owning different kind of credentials (e.g. eduGain, OpenID Connect, X509 certificates etc.). Here the focus is on the mechanisms which allow the credential delegation. 2) The computational pilot, Improve the back-end services of an existing application in the field of Computational Seismology, developed in the context of the EC funded project VERCE. The application allows the processing and the comparison of data resulting from the simulation of seismic wave propagation following a real earthquake and real measurements recorded by seismographs. While the simulation data is produced directly by the users and stored in a Data Management System, the observations need to be pre-staged from institutional data-services, which are maintained by the community itself. This use case aims at exploiting the EGI FedCloud e-infrastructure for Data

  13. Resources.

    Science.gov (United States)

    Stewart, John; MacDonald, Ian

    1980-01-01

    Presents a guide to resources on television drama available to teachers for classroom use in television curriculum. Lists American and British television drama videorecordings of both series and individual presentations and offers a bibliography of "one-off" single fiction plays produced for British television. (JMF)

  14. 国家啮齿类实验动物种子中心简介%A Brief Introduction to National Resource Center for Rodent Laboratory Animal

    Institute of Scientific and Technical Information of China (English)

    岳秉飞

    2003-01-01

    National Resource Center (NRLARC) for Rodent Laboratory Animal was established in 1998, ratified by State Commission of Science and Technology. Subordinated to laboratory animal center For National Institute for the Control of Pharmaceutical and Biological Products. The major aims are: importing, collecting and conserving the variety of LA and strain of LA, studying new LA protection techniques, developing the new strain and varieties of LA and supplying the standard breeding of LA to several client both at home and abroad.

  15. Animation company "Fast Forwards" production with HP Utility Data Center; film built using Adaptive Enterprise framework enabled by shared, virtual resource

    CERN Multimedia

    2003-01-01

    Hewlett Packard have produced a commercial-quality animated film using an experimental rendering service from HP Labs and running on an HP Utility Data Center (UDC). The project demonstrates how computing resources can be managed virtually and illustrates the value of utility computing, in which an end-user taps into a large pool of virtual resources, but pays only for what is used (1 page).

  16. Bioinformatics for transporter pharmacogenomics and systems biology: data integration and modeling with UML.

    Science.gov (United States)

    Yan, Qing

    2010-01-01

    Bioinformatics is the rational study at an abstract level that can influence the way we understand biomedical facts and the way we apply the biomedical knowledge. Bioinformatics is facing challenges in helping with finding the relationships between genetic structures and functions, analyzing genotype-phenotype associations, and understanding gene-environment interactions at the systems level. One of the most important issues in bioinformatics is data integration. The data integration methods introduced here can be used to organize and integrate both public and in-house data. With the volume of data and the high complexity, computational decision support is essential for integrative transporter studies in pharmacogenomics, nutrigenomics, epigenetics, and systems biology. For the development of such a decision support system, object-oriented (OO) models can be constructed using the Unified Modeling Language (UML). A methodology is developed to build biomedical models at different system levels and construct corresponding UML diagrams, including use case diagrams, class diagrams, and sequence diagrams. By OO modeling using UML, the problems of transporter pharmacogenomics and systems biology can be approached from different angles with a more complete view, which may greatly enhance the efforts in effective drug discovery and development. Bioinformatics resources of membrane transporters and general bioinformatics databases and tools that are frequently used in transporter studies are also collected here. An informatics decision support system based on the models presented here is available at http://www.pharmtao.com/transporter . The methodology developed here can also be used for other biomedical fields. PMID:20419428

  17. Transcatheter Closure of Atrial Septal Defects in a Center With Limited Resources: Outcomes and Short Term Follow-Up

    Directory of Open Access Journals (Sweden)

    Sukman T. Putra

    2015-12-01

    Full Text Available Background: Transcatheter closure of atrial septal defects (ASD has been accepted world-wide as an alternative to surgical closure with excellent results. This interventional, non-surgical technique plays an important role in the treatment of ASD mostly in the developing world where resources are limited. Objectives: To report the outcomes and short term follow-up of transcatheter closure of ASD over a 12-year period at our institution with limited resources. Patients and Methods: This retrospective study included all patients with the diagnosis of secundum ASD and significant shunting (Qp/Qs > 1.5:1 as well as dilated right atrium and right ventricle who had transcatheter closure at Integrated Cardiovascular Center (PJT, Dr. Cipto Mangunkusumo Hospital between October 2002 and October 2014. One hundred fifty-two patients enrolled in this study were candidates for device closure. Right and left heart cardiac catheterization was performed before the procedure. All patients underwent physical examination, ECG, chest X-ray and transthoracal echocardiography (TTE prior to device implantation. Results: A total of 152 patients with significant ASD underwent device implantation. Subjects’ age ranged from 0.63 to 69.6 years, with median 9.36 years and mean 16.30 years. They consisted of 33 (21.7% males and 119 (78.3% females, with mean body weight of 29.9 kg (range 8 to 75; SD 18.2. The device was successfully implanted in 150 patients where the majority of cases received the Amplatzer septal occluder (147/150; 98% and the others received the Heart Lifetech ASD occluder (3/150, 2%, whereas two other cases were not suitable for device closure and we decided for surgical closure. The mean ASD size was 19.75 (range 14 - 25 mm. During the procedure, 5 (4.9% patients had bradycardia and 3 (2.9% patients had supraventricular tachycardia (SVT, all of which resolved. Conclusions: In our center with limited facilities and manpower, transcatheter closure of

  18. KDE Bioscience: platform for bioinformatics analysis workflows.

    Science.gov (United States)

    Lu, Qiang; Hao, Pei; Curcin, Vasa; He, Weizhong; Li, Yuan-Yuan; Luo, Qing-Ming; Guo, Yi-Ke; Li, Yi-Xue

    2006-08-01

    Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research. PMID:16260186

  19. 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 imple

  20. Evolution of web services in bioinformatics

    NARCIS (Netherlands)

    Neerincx, P.B.T.; Leunissen, J.A.M.

    2005-01-01

    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, bioinformatic

  1. 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...

  2. "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). The…

  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. 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…

  5. 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…

  6. Evolutionary Computation Applications in Current Bioinformatics

    OpenAIRE

    Wang, Bing; Zhang, Xiang

    2010-01-01

    This chapter provides an overview of some bioinformatics tasks and the relevance of the evolutionary computation methods, especially GAs. There are two advantages of GA-based approaches. One is that GAs are easier to run in parallel than single trajectory search procedures, and therefore allow groups of processors to be utilized for a search. The other is

  7. Cultural resource survey report for construction of office building, driveway, and parking lot at the Stanford Linear Accelerator Center. Part 1

    International Nuclear Information System (INIS)

    An Environmental Assessment and associated documentation is reported for the construction of an office building and parking lot in support of environmental management personnel activities. As part of the documentation process, the DOE determined that the proposed project constituted an undertaking as defined in Section 106 of the National Historic Preservation Act. In accordance with the regulations implementing Section 106 of the National Historic Preservation Act, a records and literature search and historic resource identification effort were carried out on behalf of the Stanford Linear Accelerator Center (SLAC). This report summarizes cultural resource literature and record searches and a historic resource identification effort

  8. Teaching Sustainable Water Resources and Low Impact Development: A Project Centered Course for First-Year Undergraduates

    Science.gov (United States)

    Cianfrani, C. M.

    2009-12-01

    Teaching Sustainable Water Resources and Low Impact Development: A Project Centered Course for First-Year Undergraduates Christina M. Cianfrani Assistant Professor, School of Natural Science, Hampshire College, 893 West Avenue, Amherst, MA 01002 Sustainable water resources and low impact development principles are taught to first-year undergraduate students using an applied design project sited on campus. All students at Hampshire College are required to take at least one natural science course during their first year as part of their liberal arts education. This requirement is often met with resistance from non-science students. However, ‘sustainability’ has shown to be a popular topic on campus and ‘Sustainable Water Resources’ typically attracts ~25 students (a large class size for Hampshire College). Five second- or third-year students are accepted in the class as advanced students and serve as project leaders. The first-year students often enter the class with only basic high school science background. The class begins with an introduction to global water resources issues to provide a broad perspective. The students then analyze water budgets, both on a watershed basis and a personal daily-use basis. The students form groups of 4 to complete their semester project. Lectures on low impact design principles are combined with group work sessions for the second half of the semester. Students tour the physical site located across the street from campus and begin their project with a site analysis including soils, landcover and topography. They then develop a building plan and identify preventative and mitigative measures for dealing with stormwater. Each group completes TR-55 stormwater calculations for their design (pre- and post-development) to show the state regulations for quantity will be met with their design. Finally, they present their projects to the class and prepare a formal written report. The students have produced a wide variety of creative

  9. Web services at the European Bioinformatics Institute-2009.

    Science.gov (United States)

    McWilliam, Hamish; Valentin, Franck; Goujon, Mickael; Li, Weizhong; Narayanasamy, Menaka; Martin, Jenny; Miyar, Teresa; Lopez, Rodrigo

    2009-07-01

    The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997. In addition to the traditional web form based interfaces, APIs exist for core data resources such as EMBL-Bank, Ensembl, UniProt, InterPro, PDB and ArrayExpress. These APIs are based on Web Services (SOAP/REST) interfaces that allow users to systematically access databases and analytical tools. From the user's point of view, these Web Services provide the same functionality as the browser-based forms. However, using the APIs frees the user from web page constraints and are ideal for the analysis of large batches of data, performing text-mining tasks and the casual or systematic evaluation of mathematical models in regulatory networks. Furthermore, these services are widespread and easy to use; require no prior knowledge of the technology and no more than basic experience in programming. In the following we wish to inform of new and updated services as well as briefly describe planned developments to be made available during the course of 2009-2010. PMID:19435877

  10. Bioinformatics analysis of metastasis-related proteins in hepatocellular carcinoma

    Institute of Scientific and Technical Information of China (English)

    Pei-Ming Song; Yang Zhang; Yu-Fei He; Hui-Min Bao; Jian-Hua Luo; Yin-Kun Liu; Peng-Yuan Yang; Xian Chen

    2008-01-01

    AIM: To analyze the metastasis-related proteins in hepatocellular carcinoma (HCC) and discover the biomark-er candidates for diagnosis and therapeutic intervention of HCC metastasis with bioinformatics tools.METHODS: Metastasis-related proteins were determined by stable isotope labeling and MS analysis and analyzed with bioinformatics resources, including Phobius, Kyoto encyclopedia of genes and genomes (KEGG), online mendelian inheritance in man (OHIH) and human protein reference database (HPRD).RESULTS: All the metastasis-related proteins were linked to 83 pathways in KEGG, including MAPK and p53 signal pathways. Protein-protein interaction network showed that all the metastasis-related proteins were categorized into 19 function groups, including cell cycle, apoptosis and signal transcluction. OMIM analysis linked these proteins to 186 OMIM entries.CONCLUSION: Metastasis-related proteins provide HCC cells with biological advantages in cell proliferation, migration and angiogenesis, and facilitate metastasis of HCC cells. The bird's eye view can reveal a global charac-teristic of metastasis-related proteins and many differen-tially expressed proteins can be identified as candidates for diagnosis and treatment of HCC.

  11. 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.

  12. 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…

  13. A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway

    Directory of Open Access Journals (Sweden)

    Mitali Bhattacharjee

    2012-01-01

    Full Text Available TNF-related weak inducer of apoptosis (TWEAK is a new member of the TNF superfamily. It signals through TNFRSF12A, commonly known as Fn14. The TWEAK-Fn14 interaction regulates cellular activities including proliferation, migration, differentiation, apoptosis, angiogenesis, tissue remodeling and inflammation. Although TWEAK has been reported to be associated with autoimmune diseases, cancers, stroke, and kidney-related disorders, the downstream molecular events of TWEAK-Fn14 signaling are yet not available in any signaling pathway repository. In this paper, we manually compiled from the literature, in particular those reported in human systems, the downstream reactions stimulated by TWEAK-Fn14 interactions. Our manual amassment of the TWEAK-Fn14 pathway has resulted in cataloging of 46 proteins involved in various biochemical reactions and TWEAK-Fn14 induced expression of 28 genes. We have enabled the availability of data in various standard exchange formats from NetPath, a repository for signaling pathways. We believe that this composite molecular interaction pathway will enable identification of new signaling components in TWEAK signaling pathway. This in turn may lead to the identification of potential therapeutic targets in TWEAK-associated disorders.

  14. Technical Perspectives on Knowledge Management in Bioinformatics Workflow Systems

    Directory of Open Access Journals (Sweden)

    Walaa N. Ismail

    2015-01-01

    Full Text Available Workflow systems by it’s nature can help bioin-formaticians to plan for their experiments, store, capture and analysis of the runtime generated data. On the other hand, the life science research usually produces new knowledge at an increasing speed; Knowledge such as papers, databases and other systems knowledge that a researcher needs to deal with is actually a complex task that needs much of efforts and time. Thus the management of knowledge is therefore an important issue for life scientists. Approaches has been developed to organize biological knowledge sources and to record provenance knowledge of an experiment into a readily resource are presently being carried out. This article focuses on the knowledge management of in silico experimentation in bioinformatics workflow systems.

  15. 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.

  16. Integrating Place-based Science and Data into Hydrology and Geoscience Education Using the CUAHSI Water Data Center Resources

    Science.gov (United States)

    Arrigo, J. S.; Dalbotten, D. M.; Hooper, R. P.; Pollak, J.; Geosling, E.

    2014-12-01

    "All water is local." For geoscientist researchers and educators, this simple statement underlies potentially powerful ways to engage students around hydrologic and engineering concepts. Education research has given us strong insight into how students learn. Place-based education gives students a personal and geographical context to connect concepts and processes to their everyday lives. Data-driven exercises build inquiry and critical thinking skills. With the ubiquity of water, the critical roles it plays in earth systems, and its influence on ecosystems, climate, geologic processes, economies, and human health, integrating water data and place-based exercises into the classroom is an excellent opportunity to enhance student learning and stimulate interest in the geosciences. THE CUAHSI Water Data Center (WDC), established in 2013, is the culmination of a decade of work to adapt modern web services technology to work on time-series data (such as a gage record or water-quality series), the most common water data type. It provides unprecedented consolidated access to water quantity and quality data across the US (and increasingly across the world). This allows educators to craft learning exercises around key concepts and locations, from rote problem sets to more exploratory investigations. The web services technology used address key limitations - such as difficulty in discovering data, co-locating data, and download options and access- that have been identified as barriers to integrating real data in classroom exercises. This presentation discusses key aspects of the system, provides example exercises, and discusses how we seek to engage the community to effectively chart a path forward for further development of both the technological and education resources.

  17. Novel bioinformatic developments for exome sequencing.

    Science.gov (United States)

    Lelieveld, Stefan H; Veltman, Joris A; Gilissen, Christian

    2016-06-01

    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 standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing. PMID:27075447

  18. Bioinformatics for saffron (Crocus sativus L. improvement

    Directory of Open Access Journals (Sweden)

    Ghulam A. Parray

    2009-02-01

    Full Text Available Saffron (Crocus sativus L. is a sterile triploid plant and belongs to the Iridaceae (Liliales, Monocots. Its genome is of relatively large size and is poorly characterized. Bioinformatics can play an enormous technical role in the sequence-level structural characterization of saffron genomic DNA. Bioinformatics tools can also help in appreciating the extent of diversity of various geographic or genetic groups of cultivated saffron to infer relationships between groups and accessions. The characterization of the transcriptome of saffron stigmas is the most vital for throwing light on the molecular basis of flavor, color biogenesis, genomic organization and biology of gynoecium of saffron. The information derived can be utilized for constructing biological pathways involved in the biosynthesis of principal components of saffron i.e., crocin, crocetin, safranal, picrocrocin and safchiA

  19. Discovery and Classification of Bioinformatics Web Services

    Energy Technology Data Exchange (ETDEWEB)

    Rocco, D; Critchlow, T

    2002-09-02

    The transition of the World Wide Web from a paradigm of static Web pages to one of dynamic Web services provides new and exciting opportunities for bioinformatics with respect to data dissemination, transformation, and integration. However, the rapid growth of bioinformatics services, coupled with non-standardized interfaces, diminish the potential that these Web services offer. To face this challenge, we examine the notion of a Web service class that defines the functionality provided by a collection of interfaces. These descriptions are an integral part of a larger framework that can be used to discover, classify, and wrapWeb services automatically. We discuss how this framework can be used in the context of the proliferation of sites offering BLAST sequence alignment services for specialized data sets.

  20. A Novel Approach for Bioinformatics Workflow Discovery

    Directory of Open Access Journals (Sweden)

    Walaa Nagy

    2014-11-01

    Full Text Available Workflow systems are typical fit for in the explorative research of bioinformaticians. These systems can help bioinformaticians to design and run their experiments and to automatically capture and store the data generated at runtime. On the other hand, Web services are increasingly used as the preferred method for accessing and processing the information coming from the diverse life science sources. In this work we provide an efficient approach for creating bioinformatic workflow for all-service architecture systems (i.e., all system components are services . This architecture style simplifies the user interaction with workflow systems and facilitates both the change of individual components, and the addition of new components to adopt to other workflow tasks if required. We finally present a case study for the bioinformatics domain to elaborate the applicability of our proposed approach.

  1. Adapting bioinformatics curricula for big data

    OpenAIRE

    Greene, Anna C.; Giffin, Kristine A.; Greene, Casey S; Jason H Moore

    2015-01-01

    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...

  2. Chapter 16: Text Mining for Translational Bioinformatics

    OpenAIRE

    Bretonnel Cohen, K; Hunter, Lawrence E.

    2013-01-01

    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. P...

  3. Genome bioinformatics of tomato and potato

    OpenAIRE

    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 deciphered and are being exploited for fundamental research and applied to improve their breeding programs. The developments in sequencing technologies have also impacted the associated bioinformat...

  4. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    OpenAIRE

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of protein or DNA sequences. An accurate alignment can provide valuable information for experimentation on the newly found sequences. It is indispensable in basic research as well as in practical applic...

  5. Bioinformatics and the discovery of gene function

    OpenAIRE

    Casari, G; Daruvar, Dea; Sander, C.; Schneider, Reinhard

    1996-01-01

    Scientific history was made in completing the yeast genuine sequence, yet its 13 Mb are a mere starting point. Two challenges loom large: to decipher the function of all genes and to describe the workings of the eukaryotic cell in full molecular detail. A combination of experimental and theoretical approaches will be brought to bear on these challenges. What will be next in yeast genome analysis from the point of view of bioinformatics?

  6. A Novel Approach for Bioinformatics Workflow Discovery

    OpenAIRE

    Walaa Nagy; Hoda M.O. Mokhtar

    2014-01-01

    Workflow systems are typical fit for in the explorative research of bioinformaticians. These systems can help bioinformaticians to design and run their experiments and to automatically capture and store the data generated at runtime. On the other hand, Web services are increasingly used as the preferred method for accessing and processing the information coming from the diverse life science sources. In this work we provide an efficient approach for creating bioinformatic workflow for all-serv...

  7. 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).

  8. Management and Marketing of Bioinformatics Tools

    OpenAIRE

    Sudhakar, R.; Gupta, Kuhu; Kumar, Sushant

    2013-01-01

    Bioinformatics can be defined as conceptualization of biology, in specific- Molecular Biology and then application of certain techniques from multiple disciplines such as statistics, computer science and applied mathematics to analyze and understand the vast information related to molecular structures. Hence, its management becomes difficult. The manager must be thorough with the concepts of biology- genetic studies in particular, as well as information technology. Discussed below is the mana...

  9. Bioinformatic pipelines in Python with Leaf

    OpenAIRE

    Napolitano, Francesco; Mariani-Costantini, Renato; Tagliaferri, Roberto

    2013-01-01

    Background An incremental, loosely planned development approach is often used in bioinformatic studies when dealing with custom data analysis in a rapidly changing environment. Unfortunately, the lack of a rigorous software structuring can undermine the maintainability, communicability and replicability of the process. To ameliorate this problem we propose the Leaf system, the aim of which is to seamlessly introduce the pipeline formality on top of a dynamical development process with minimum...

  10. Adapting bioinformatics curricula for big data.

    Science.gov (United States)

    Greene, Anna C; Giffin, Kristine A; Greene, Casey S; Moore, Jason H

    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

  11. Bioinformatics Approach in Plant Genomic Research.

    Science.gov (United States)

    Ong, Quang; Nguyen, Phuc; Thao, Nguyen Phuong; Le, Ly

    2016-08-01

    The advance in genomics technology leads to the dramatic change in plant biology research. Plant biologists now easily access to enormous genomic data to deeply study plant high-density genetic variation at molecular level. Therefore, fully understanding and well manipulating bioinformatics tools to manage and analyze these data are essential in current plant genome research. Many plant genome databases have been established and continued expanding recently. Meanwhile, analytical methods based on bioinformatics are also well developed in many aspects of plant genomic research including comparative genomic analysis, phylogenomics and evolutionary analysis, and genome-wide association study. However, constantly upgrading in computational infrastructures, such as high capacity data storage and high performing analysis software, is the real challenge for plant genome research. This review paper focuses on challenges and opportunities which knowledge and skills in bioinformatics can bring to plant scientists in present plant genomics era as well as future aspects in critical need for effective tools to facilitate the translation of knowledge from new sequencing data to enhancement of plant productivity. PMID:27499685

  12. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows

    OpenAIRE

    Katayama, T.; Arakawa, K.; Nakao, M; Prins, J.C.P.

    2010-01-01

    Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain speci...

  13. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows

    OpenAIRE

    Katayama, Toshiaki; Arakawa, Kazuharu; Nakao, Mitsuteru; Ono, Keiichiro; Aoki-Kinoshita, Kiyoko F; Yamamoto, Yasunori; Yamaguchi, Atsuko; Kawashima, Shuichi; Chun, Hong-Woo; Aerts, Jan; Aranda, Bruno; Barboza, Lord; Bonnal, Raoul JP; Bruskiewich, Richard; Bryne, Jan C

    2010-01-01

    Abstract Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited...

  14. Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions

    OpenAIRE

    Mochida, Keiichi; Shinozaki, Kazuo

    2011-01-01

    Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions. Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications. Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged. Furthermore, in several plant species, the development of omics resources has progre...

  15. The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis.

    Science.gov (United States)

    Alva, Vikram; Nam, Seung-Zin; Söding, Johannes; Lupas, Andrei N

    2016-07-01

    The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAST+, HMMER3, MUSCLE) and internally (e.g. HHpred, HHblits, PCOILS). While a beta version of the Toolkit was released 10 years ago, the current production-level release has been available since 2008 and has serviced more than 1.6 million external user queries. The usage of the Toolkit has continued to increase linearly over the years, reaching more than 400 000 queries in 2015. In fact, through the breadth of its tools and their tight interconnection, the Toolkit has become an excellent platform for experimental scientists as well as a useful resource for teaching bioinformatic inquiry to students in the life sciences. In this article, we report on the evolution of the Toolkit over the last ten years, focusing on the expansion of the tool repertoire (e.g. CS-BLAST, HHblits) and on infrastructural work needed to remain operative in a changing web environment. PMID:27131380

  16. Bioinformatics Tools and Novel Challenges in Long Non-Coding RNAs (lncRNAs Functional Analysis

    Directory of Open Access Journals (Sweden)

    Andrea Masotti

    2011-12-01

    Full Text Available The advent of next generation sequencing revealed that a fraction of transcribed RNAs (short and long RNAs is non-coding. Long non-coding RNAs (lncRNAs have a crucial role in regulating gene expression and in epigenetics (chromatin and histones remodeling. LncRNAs may have different roles: gene activators (signaling, repressors (decoy, cis and trans gene expression regulators (guides and chromatin modificators (scaffolds without the need to be mutually exclusive. LncRNAs are also implicated in a number of diseases. The huge amount of inhomogeneous data produced so far poses several bioinformatics challenges spanning from the simple annotation to the more complex functional annotation. In this review, we report and discuss several bioinformatics resources freely available and dealing with the study of lncRNAs. To our knowledge, this is the first review summarizing all the available bioinformatics resources on lncRNAs appeared in the literature after the completion of the human genome project. Therefore, the aim of this review is to provide a little guide for biologists and bioinformaticians looking for dedicated resources, public repositories and other tools for lncRNAs functional analysis.

  17. Bioinformatics for Diagnostics, Forensics, and Virulence Characterization and Detection

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S; Slezak, T

    2005-04-05

    We summarize four of our group's high-risk/high-payoff research projects funded by the Intelligence Technology Innovation Center (ITIC) in conjunction with our DHS-funded pathogen informatics activities. These are (1) quantitative assessment of genomic sequencing needs to predict high quality DNA and protein signatures for detection, and comparison of draft versus finished sequences for diagnostic signature prediction; (2) development of forensic software to identify SNP and PCR-RFLP variations from a large number of viral pathogen sequences and optimization of the selection of markers for maximum discrimination of those sequences; (3) prediction of signatures for the detection of virulence, antibiotic resistance, and toxin genes and genetic engineering markers in bacteria; (4) bioinformatic characterization of virulence factors to rapidly screen genomic data for potential genes with similar functions and to elucidate potential health threats in novel organisms. The results of (1) are being used by policy makers to set national sequencing priorities. Analyses from (2) are being used in collaborations with the CDC to genotype and characterize many variola strains, and reports from these collaborations have been made to the President. We also determined SNPs for serotype and strain discrimination of 126 foot and mouth disease virus (FMDV) genomes. For (3), currently >1000 probes have been predicted for the specific detection of >4000 virulence, antibiotic resistance, and genetic engineering vector sequences, and we expect to complete the bioinformatic design of a comprehensive ''virulence detection chip'' by August 2005. Results of (4) will be a system to rapidly predict potential virulence pathways and phenotypes in organisms based on their genomic sequences.

  18. 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.

  19. 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.

  20. 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…

  1. BCCTBbp: the Breast Cancer Campaign Tissue Bank bioinformatics portal.

    Science.gov (United States)

    Cutts, Rosalind J; Guerra-Assunção, José Afonso; Gadaleta, Emanuela; Dayem Ullah, Abu Z; Chelala, Claude

    2015-01-01

    BCCTBbp (http://bioinformatics.breastcancertissue bank.org) was initially developed as the data-mining portal of the Breast Cancer Campaign Tissue Bank (BCCTB), a vital resource of breast cancer tissue for researchers to support and promote cutting-edge research. BCCTBbp is dedicated to maximising research on patient tissues by initially storing genomics, methylomics, transcriptomics, proteomics and microRNA data that has been mined from the literature and linking to pathways and mechanisms involved in breast cancer. Currently, the portal holds 146 datasets comprising over 227,795 expression/genomic measurements from various breast tissues (e.g. normal, malignant or benign lesions), cell lines and body fluids. BCCTBbp can be used to build on breast cancer knowledge and maximise the value of existing research. By recording a large number of annotations on samples and studies, and linking to other databases, such as NCBI, Ensembl and Reactome, a wide variety of different investigations can be carried out. Additionally, BCCTBbp has a dedicated analytical layer allowing researchers to further analyse stored datasets. A future important role for BCCTBbp is to make available all data generated on BCCTB tissues thus building a valuable resource of information on the tissues in BCCTB that will save repetition of experiments and expand scientific knowledge. PMID:25332396

  2. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

    Directory of Open Access Journals (Sweden)

    Enis Afgan

    Full Text Available Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.We designed and implemented the Genomics Virtual Laboratory (GVL as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic.This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints

  3. A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines

    Directory of Open Access Journals (Sweden)

    Cieślik Marcin

    2011-02-01

    Full Text Available Abstract Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts. Results To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'. A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption. An add-on module ('NuBio' facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures and functionality (e.g., to parse/write standard file formats. Conclusions PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and

  4. The Revolution in Viral Genomics as Exemplified by the Bioinformatic Analysis of Human Adenoviruses

    Directory of Open Access Journals (Sweden)

    Sarah Torres

    2010-06-01

    Full Text Available Over the past 30 years, genomic and bioinformatic analysis of human adenoviruses has been achieved using a variety of DNA sequencing methods; initially with the use of restriction enzymes and more currently with the use of the GS FLX pyrosequencing technology. Following the conception of DNA sequencing in the 1970s, analysis of adenoviruses has evolved from 100 base pair mRNA fragments to entire genomes. Comparative genomics of adenoviruses made its debut in 1984 when nucleotides and amino acids of coding sequences within the hexon genes of two human adenoviruses (HAdV, HAdV–C2 and HAdV–C5, were compared and analyzed. It was determined that there were three different zones (1-393, 394-1410, 1411-2910 within the hexon gene, of which HAdV–C2 and HAdV–C5 shared zones 1 and 3 with 95% and 89.5% nucleotide identity, respectively. In 1992, HAdV-C5 became the first adenovirus genome to be fully sequenced using the Sanger method. Over the next seven years, whole genome analysis and characterization was completed using bioinformatic tools such as blastn, tblastx, ClustalV and FASTA, in order to determine key proteins in species HAdV-A through HAdV-F. The bioinformatic revolution was initiated with the introduction of a novel species, HAdV-G, that was typed and named by the use of whole genome sequencing and phylogenetics as opposed to traditional serology. HAdV bioinformatics will continue to advance as the latest sequencing technology enables scientists to add to and expand the resource databases. As a result of these advancements, how novel HAdVs are typed has changed. Bioinformatic analysis has become the revolutionary tool that has significantly accelerated the in-depth study of HAdV microevolution through comparative genomics.

  5. Needs assessment of science teachers in secondary schools in Kumasi, Ghana: A basis for in-service education training programs at the Science Resource Centers

    Science.gov (United States)

    Gyamfi, Alexander

    The purpose of this study was twofold. First, it identified the priority needs common to all science teachers in secondary schools in Kumasi, Ghana. Second, it investigated the relationship existing between the identified priority needs and the teacher demographic variables (type of school, teacher qualification, teaching experience, subject discipline, and sex of teacher) to be used as a basis for implementing in-service education training programs at the Science Resource Centers in Kumasi Ghana. An adapted version of the Moore Assessment Profile (MAP) survey instrument and a set of open-ended questions were used to collect data from the science teachers. The researcher handed out one hundred and fifty questionnaire packets, and all one hundred and fifty (100%) were collected within a period of six weeks. The data were analyzed using descriptive statistics, content analysis, and inferential statistics. The descriptive statistics reported the frequency of responses, and it was used to calculate the Need Index (N) of the identified needs of teachers. Sixteen top-priority needs were identified, and the needs were arranged in a hierarchical order according to the magnitude of the Need Index (0.000 ≤ N ≤ 1.000). Content analysis was used to analyze the responses to the open-ended questions. One-way analysis of variance (ANOVA) was used to test the null hypotheses of the study on each of the sixteen identified top-priority needs and the teacher demographic variables. The findings of this study were as follows: (1) The science teachers identified needs related to "more effective use of instructional materials" as a crucial area for in-service training. (2) Host and Satellite schools exhibited significant difference on procuring supplementary science books for students. Subject discipline of teachers exhibited significant differences on utilizing the library and its facilities by students, obtaining information on where to get help on effective science teaching

  6. The Genome Atlas Resource

    OpenAIRE

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik; Hansson, Lena; Ussery, David

    2010-01-01

    Abstract. The Genome Atlas is a resource for addressing the challenges of synchronising prokaryotic genomic sequence data from multiple public repositories. This resource can integrate bioinformatic analyses in various data format and quality. Existing open source tools have been used together with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The r...

  7. 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.

  8. The bioinformatics of next generation sequencing: a meeting report

    Institute of Scientific and Technical Information of China (English)

    Ravi Shankar

    2011-01-01

    @@ The Studio of Computational Biology & Bioinformatics (SCBB), IHBT, CSIR,Palampur, India organized one of the very first national workshop funded by DBT,Govt.of India, on the Bioinformatics issues associated with next generation sequencing approaches.The course structure was designed by SCBB, IHBT.The workshop took place in the IHBT premise on 17 and 18 June 2010.

  9. 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…

  10. 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…

  11. 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…

  12. 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......The mechanisms of immune response to cancer have been studied extensively and great effort has been invested into harnessing the therapeutic potential of the immune system. Immunotherapies have seen significant advances in the past 20 years, but the full potential of protective and therapeutic...... and co-targets for single-epitope and multi-epitope strategies. We provide examples of application to the well-known tumor antigen HER2 and suggest bioinformatics methods to ameliorate therapy resistance and ensure efficient and lasting control of tumors....

  13. 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.

  14. Combining multiple decisions: applications to bioinformatics

    International Nuclear Information System (INIS)

    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

  15. Bioinformatics Analysis of Estrogen-Responsive Genes.

    Science.gov (United States)

    Handel, Adam E

    2016-01-01

    Estrogen is a steroid hormone that plays critical roles in a myriad of intracellular pathways. The expression of many genes is regulated through the steroid hormone receptors ESR1 and ESR2. These bind to DNA and modulate the expression of target genes. Identification of estrogen target genes is greatly facilitated by the use of transcriptomic methods, such as RNA-seq and expression microarrays, and chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq). Combining transcriptomic and ChIP-seq data enables a distinction to be drawn between direct and indirect estrogen target genes. This chapter discusses some methods of identifying estrogen target genes that do not require any expertise in programming languages or complex bioinformatics. PMID:26585125

  16. 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...

  17. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    Next generation sequencing (NGS) has revolutionized the field of genomics and its wide range of applications has resulted in the genome-wide analysis of hundreds of species and the development of thousands of computational tools. This thesis represents my work on NGS analysis of four species, Lotus...... 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...... agricultural and biological importance. Its capacity to form symbiotic relationships with rhizobia and microrrhizal fungi has fascinated researchers for years. Lotus has a small genome of approximately 470 Mb and a short life cycle of 2 to 3 months, which has made Lotus a model legume plant for many molecular...

  18. Plant germplasm centers and microbial culture collections: A users guide to key genetic resources for plant pathology

    Science.gov (United States)

    This feature article discusses the importance and current situations of collections of living microbes and plants. Methods for preservation and resources of collections were presented. Issues, such as correct identification of materials, regulatory and safety aspects of collection management and uti...

  19. Comparison of Online and Onsite Bioinformatics Instruction for a Fully Online Bioinformatics Master’s Program

    Directory of Open Access Journals (Sweden)

    Kristina M. Obom

    2009-12-01

    Full Text Available The completely online Master of Science in Bioinformatics program differs from the onsite program only in the mode of content delivery. Analysis of student satisfaction indicates no statistically significant difference between most online and onsite student responses, however, online and onsite students do differ significantly in their responses to a few questions on the course evaluation queries. Analysis of student exam performance using three assessments indicates that there was no significant difference in grades earned by students in online and onsite courses. These results suggest that our model for online bioinformatics education provides students with a rigorous course of study that is comparable to onsite course instruction and possibly provides a more rigorous course load and more opportunities for participation.

  20. Comparison of Online and Onsite Bioinformatics Instruction for a Fully Online Bioinformatics Master’s Program

    OpenAIRE

    Obom, Kristina. M.; Cummings, Patrick J.

    2009-01-01

    The completely online Master of Science in Bioinformatics program differs from the onsite program only in the mode of content delivery. Analysis of student satisfaction indicates no statistically significant difference between most online and onsite student responses, however, online and onsite students do differ significantly in their responses to a few questions on the course evaluation queries. Analysis of student exam performance using three assessments indicates that there was no signifi...

  1. Can the availability of unrestricted financial support improve the quality of care of thalassemics in a center with limited resources? A single center study from India

    Directory of Open Access Journals (Sweden)

    Prantar Chakrabarti

    2012-12-01

    Full Text Available Comprehensive management of thalassemia demands a multidisciplinary approach, sufficient financial resources, carefully developed expertise of the care givers, as well as significant compliance on the patients’ part. Studies exploring the utility of unrestricted financing within the existing infrastructure, for the management of thalassemia, particularly in the context of a developing country, are scarce. This study aimed to assess the impact of sponsored comprehensive care compared to the routine care of thalassemics provided at Institute of Haematology and Transfusion Medicine, Kolkata, India. Two hundred and twenty patients were selected for the study and distributed in two arms. Regular monthly follow up was done including a Health Related Quality of Life (HRQoL assessment with SF 36 v2 (validated Bengali version. Patients receiving sponsored comprehensive care showed a significant improvement in the mean hemoglobin levels and decrease in mean ferritin. HRQoL assessment revealed a better score in the physical domain though the mental health domain score was not significantly better at nine months. Unrestricted financial support in the form of comprehensive care has a positive impact on the thalassemia patients in a developing country not only in terms of clinical parameters but also in health related quality of life. 地中海贫血症的综合管理需要多学科的研究方法、充足的财政资源,护理人员应具备丰富的专业知识,并且患者应尽可能服从安排。探讨现有基础设施内无限制财政支持的实用性和地中海贫血症管理(尤其是在发展中国家)的研究甚少。 此研究旨在评估与印度加尔各答血液及输血医学会提供的地中海贫血症常规护理相比,综合护理对患者的影响 。 此研究筛选了 220名患者,并分为两组进行研究。每月定期跟进两组患者情况,包括使用第2版SF 36(经验证的孟加拉语版本)进行

  2. High-throughput bioinformatics with the Cyrille2 pipeline system

    Directory of Open Access Journals (Sweden)

    de Groot Joost CW

    2008-02-01

    Full Text Available Abstract Background Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or pipelines. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible. Results We have developed a generic pipeline system called Cyrille2. The system is modular in design and consists of three functionally distinct parts: 1 a web based, graphical user interface (GUI that enables a pipeline operator to manage the system; 2 the Scheduler, which forms the functional core of the system and which tracks what data enters the system and determines what jobs must be scheduled for execution, and; 3 the Executor, which searches for scheduled jobs and executes these on a compute cluster. Conclusion The Cyrille2 system is an extensible, modular system, implementing the stated requirements. Cyrille2 enables easy creation and execution of high throughput, flexible bioinformatics pipelines.

  3. 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.

  4. 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. PMID:27281025

  5. A discrete system simulation study in scheduling and resource allocation for the John A. Burns School of Medicine Clinical Skills Center.

    Science.gov (United States)

    Glaspie, Henry W; Oshiro Wong, Celeste M

    2015-03-01

    The Center for Clinical Skills (CCS) at the University of Hawai'i's John A. Burns School of Medicine (JABSOM) trains medical students in a variety of medical practice education experiences aimed at improving patient care skills of history taking, physical examination, communication, and counseling. Increasing class sizes accentuate the need for efficient scheduling of faculty and students for clinical skills examinations. This research reports an application of a discrete simulation methodology, using a computerized commercial business simulation optimization software package Arena® by Rockwell Automation Inc, to model the flow of students through an objective structure clinical exam (OSCE) using the basic physical examination sequence (BPSE). The goal was to identify the most efficient scheduling of limited volunteer faculty resources to enable all student teams to complete the OSCE within the allocated 4 hours. The simulation models 11 two-person student teams, using resources of 10 examination rooms where physical examination skills are demonstrated on fellow student subjects and assessed by volunteer faculty. Multiple faculty availability models with constrained time parameters and other resources were evaluated. The results of the discrete event simulation suggest that there is no statistical difference in the baseline model and the alternative models with respect to faculty utilization, but statistically significant changes in student wait times. Two models significantly reduced student wait times without compromising faculty utilization. PMID:25821650

  6. 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. PMID:23396756

  7. 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

    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 into interdisci......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 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....

  8. Using Bioinformatics to Develop and Test Hypotheses: E. coli-Specific Virulence Determinants

    Directory of Open Access Journals (Sweden)

    Joanna R. Klein

    2012-09-01

    Full Text Available Bioinformatics, the use of computer resources to understand biological information, is an important tool in research, and can be easily integrated into the curriculum of undergraduate courses. Such an example is provided in this series of four activities that introduces students to the field of bioinformatics as they design PCR based tests for pathogenic E. coli strains. A variety of computer tools are used including BLAST searches at NCBI, bacterial genome searches at the Integrated Microbial Genomes (IMG database, protein analysis at Pfam and literature research at PubMed. In the process, students also learn about virulence factors, enzyme function and horizontal gene transfer. Some or all of the four activities can be incorporated into microbiology or general biology courses taken by students at a variety of levels, ranging from high school through college. The activities build on one another as they teach and reinforce knowledge and skills, promote critical thinking, and provide for student collaboration and presentation. The computer-based activities can be done either in class or outside of class, thus are appropriate for inclusion in online or blended learning formats. Assessment data showed that students learned general microbiology concepts related to pathogenesis and enzyme function, gained skills in using tools of bioinformatics and molecular biology, and successfully developed and tested a scientific hypothesis.

  9. Bioinformatics in cancer therapy and drug design

    International Nuclear Information System (INIS)

    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)

  10. Evaluating the effectiveness of a practical inquiry-based learning bioinformatics module on undergraduate student engagement and applied skills.

    Science.gov (United States)

    Brown, James A L

    2016-05-01

    A pedagogic intervention, in the form of an inquiry-based peer-assisted learning project (as a practical student-led bioinformatics module), was assessed for its ability to increase students' engagement, practical bioinformatic skills and process-specific knowledge. Elements assessed were process-specific knowledge following module completion, qualitative student-based module evaluation and the novelty, scientific validity and quality of written student reports. Bioinformatics is often the starting point for laboratory-based research projects, therefore high importance was placed on allowing students to individually develop and apply processes and methods of scientific research. Students led a bioinformatic inquiry-based project (within a framework of inquiry), discovering, justifying and exploring individually discovered research targets. Detailed assessable reports were produced, displaying data generated and the resources used. Mimicking research settings, undergraduates were divided into small collaborative groups, with distinctive central themes. The module was evaluated by assessing the quality and originality of the students' targets through reports, reflecting students' use and understanding of concepts and tools required to generate their data. Furthermore, evaluation of the bioinformatic module was assessed semi-quantitatively using pre- and post-module quizzes (a non-assessable activity, not contributing to their grade), which incorporated process- and content-specific questions (indicative of their use of the online tools). Qualitative assessment of the teaching intervention was performed using post-module surveys, exploring student satisfaction and other module specific elements. Overall, a positive experience was found, as was a post module increase in correct process-specific answers. In conclusion, an inquiry-based peer-assisted learning module increased students' engagement, practical bioinformatic skills and process-specific knowledge. © 2016 by

  11. Cotton Databases and Web Resources%棉花Databases和Web资源

    Institute of Scientific and Technical Information of China (English)

    Russell J. KOHEL; John Z. YU; Piyush GUPTA; Rajeev AGRAWAL

    2002-01-01

    @@ There are several web sites for which information is available to the cotton research community. Most of these sites relate to resources developed or available to the research community. Few provide bioinformatic tools,which usually relate to the specific data sets and materials presented in the database. Just as the bioinformatics area is evolving, the available resources reflect this evolution.

  12. Survey of Natural Language Processing Techniques in Bioinformatics.

    Science.gov (United States)

    Zeng, Zhiqiang; Shi, Hua; Wu, Yun; Hong, Zhiling

    2015-01-01

    Informatics methods, such as text mining and natural language processing, are always involved in bioinformatics research. In this study, we discuss text mining and natural language processing methods in bioinformatics from two perspectives. First, we aim to search for knowledge on biology, retrieve references using text mining methods, and reconstruct databases. For example, protein-protein interactions and gene-disease relationship can be mined from PubMed. Then, we analyze the applications of text mining and natural language processing techniques in bioinformatics, including predicting protein structure and function, detecting noncoding RNA. Finally, numerous methods and applications, as well as their contributions to bioinformatics, are discussed for future use by text mining and natural language processing researchers. PMID:26525745

  13. Survey of Natural Language Processing Techniques in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Zhiqiang Zeng

    2015-01-01

    Full Text Available Informatics methods, such as text mining and natural language processing, are always involved in bioinformatics research. In this study, we discuss text mining and natural language processing methods in bioinformatics from two perspectives. First, we aim to search for knowledge on biology, retrieve references using text mining methods, and reconstruct databases. For example, protein-protein interactions and gene-disease relationship can be mined from PubMed. Then, we analyze the applications of text mining and natural language processing techniques in bioinformatics, including predicting protein structure and function, detecting noncoding RNA. Finally, numerous methods and applications, as well as their contributions to bioinformatics, are discussed for future use by text mining and natural language processing researchers.

  14. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond

    Science.gov (United States)

    Hiraoka, Satoshi; Yang, Ching-chia; Iwasaki, Wataru

    2016-01-01

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives. PMID:27383682

  15. Creating 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 generally require access to multiple, distributed data sources and analytic tools. The requisite data sources may include large public data repositories, community...

  16. [An overview of feature selection algorithm in bioinformatics].

    Science.gov (United States)

    Li, Xin; Ma, Li; Wang, Jinjia; Zhao, Chun

    2011-04-01

    Feature selection (FS) techniques have become an important tool in bioinformatics field. The core algorithm of it is to select the hidden significant data with low-dimension from high-dimensional data space, and thus to analyse the basic built-in rule of the data. The data of bioinformatics fields are always with high-dimension and small samples, so the research of FS algorithm in the bioinformatics fields has great foreground. In this article, we make the interested reader aware of the possibilities of feature selection, provide basic properties of feature selection techniques, and discuss their uses in the sequence analysis, microarray analysis, mass spectra analysis etc. Finally, the current problems and the prospects of feature selection algorithm in the application of bioinformatics is also discussed. PMID:21604512

  17. Scalable pattern recognition algorithms applications in computational biology and bioinformatics

    CERN Document Server

    Maji, Pradipta

    2014-01-01

    Reviews the development of scalable pattern recognition algorithms for computational biology and bioinformatics Includes numerous examples and experimental results to support the theoretical concepts described Concludes each chapter with directions for future research and a comprehensive bibliography

  18. Characteristics of ambulatory care clinics and pharmacists in Veterans Affairs medical centers. IMPROVE investigators. Impact of Managed Pharmaceutical Care on Resource Utilization and Outcomes in Veterans Affairs Medical Centers.

    Science.gov (United States)

    Alsuwaidan, S; Malone, D C; Billups, S J; Carter, B L

    1998-01-01

    The type and extent of ambulatory care clinical pharmaceutical services in selected Veterans Affairs medical centers (VAMCs) were studied as part of a larger project. Questionnaires were sent to the 174 VAMCs to determine the extent of clinical pharmacy activity in ambulatory care clinics, characteristics of outpatient pharmacies and clinics, and characteristics of ambulatory care pharmacists in VAMCs and to identify sites for the IMPROVE (Impact of Managed Pharmaceutical Care on Resource Utilization and Outcomes in Veterans Affairs Medical Centers) project. Fifty VAMCs responded to the survey. There were 512 ambulatory care clinics within these VAMCs. There was some pharmacist coverage in 75% of the clinics. The highest pharmacist coverage was in walk-in refill, therapeutic drug monitoring, and anticoagulation clinics. Clinical pharmacists at 68% of the VAMCs had prescribing privileges in ambulatory care clinics. Clinical pharmacists managed 29.9% of the clinics. The types of clinics most commonly managed by pharmacists were therapeutic drug monitoring, anticoagulation, walk-in refill, and lipid clinics. Nurse practitioners or physician assistants also were providing primary care in 41% of the clinics. There were 242 ambulatory care clinical pharmacy specialists practicing in the 50 VAMCs. Of these, 41.3% had three years or less of ambulatory care experience. Most pharmacists were in the clinic five days per week. A Pharm.D. degree was the highest degree obtained for 76.9%. Ambulatory care pharmaceutical services are common in VAMCs and are being provided by numerous clinical pharmacists. PMID:9437478

  19. Hands-on, online, and workshop-based K-12 weather and climate education resources from the Center for Multi-scale Modeling of Atmospheric Processes

    Science.gov (United States)

    Foster, S. Q.; Johnson, R. M.; Randall, D. A.; Denning, A.; Burt, M. A.; Gardiner, L.; Genyuk, J.; Hatheway, B.; Jones, B.; La Grave, M. L.; Russell, R. M.

    2009-12-01

    The need for improving the representation of cloud processes in climate models has been one of the most important limitations of the reliability of climate-change simulations. Now in its fourth year, the National Science Foundation-funded Center for Multi-scale Modeling of Atmospheric Processes (CMMAP) at Colorado State University (CSU) is addressing this problem through a revolutionary new approach to representing cloud processes on their native scales, including the cloud-scale interaction processes that are active in cloud systems. CMMAP has set ambitious education and human-resource goals to share basic information about the atmosphere, clouds, weather, climate, and modeling with diverse K-12 and public audiences. This is accomplished through collaborations in resource development and dissemination between CMMAP scientists, CSU’s Little Shop of Physics (LSOP) program, and the Windows to the Universe (W2U) program at University Corporation for Atmospheric Research (UCAR). Little Shop of Physics develops new hands on science activities demonstrating basic science concepts fundamental to understanding atmospheric characteristics, weather, and climate. Videos capture demonstrations of children completing these activities which are broadcast to school districts and public television programs. CMMAP and LSOP educators and scientists partner in teaching a summer professional development workshops for teachers at CSU with a semester's worth of college-level content on the basic physics of the atmosphere, weather, climate, climate modeling, and climate change, as well as dozens of LSOP inquiry-based activities suitable for use in classrooms. The W2U project complements these efforts by developing and broadly disseminating new CMMAP-related online content pages, animations, interactives, image galleries, scientists’ biographies, and LSOP videos to K-12 and public audiences. Reaching nearly 20 million users annually, W2U is highly valued as a curriculum enhancement

  20. Survey of Natural Language Processing Techniques in Bioinformatics

    OpenAIRE

    Zhiqiang Zeng; Hua Shi; Yun Wu; Zhiling Hong

    2015-01-01

    Informatics methods, such as text mining and natural language processing, are always involved in bioinformatics research. In this study, we discuss text mining and natural language processing methods in bioinformatics from two perspectives. First, we aim to search for knowledge on biology, retrieve references using text mining methods, and reconstruct databases. For example, protein-protein interactions and gene-disease relationship can be mined from PubMed. Then, we analyze the applications ...

  1. Big Data Analytics in Bioinformatics: A Machine Learning Perspective

    OpenAIRE

    Kashyap, Hirak; Ahmed, Hasin Afzal; Hoque, Nazrul; Roy, Swarup; Bhattacharyya, Dhruba Kumar

    2015-01-01

    Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big data using the distributed and parallel computing technologies. Usually big data tools perform computation in batch-mode and are not optimized for iterative processing and high data dependency among operations. In the recent years, parallel, incremental, and ...

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    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....

  3. A high-throughput bioinformatics distributed computing platform

    OpenAIRE

    Keane, Thomas M; Page, Andrew J.; McInerney, James O.; Naughton, Thomas J

    2005-01-01

    In the past number of years the demand for high performance computing has greatly increased in the area of bioinformatics. The huge increase in size of many genomic databases has meant that many common tasks in bioinformatics are not possible to complete in a reasonable amount of time on a single processor. Recently distributed computing has emerged as an inexpensive alternative to dedicated parallel computing. We have developed a general-purpose distributed computing platform ...

  4. 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

  5. BioWarehouse: a bioinformatics database warehouse toolkit

    OpenAIRE

    Stringer-Calvert David WJ; Gupta Priyanka; Wagner Valerie; Pouliot Yannick; Lee Thomas J; Tenenbaum Jessica D; Karp Peter D

    2006-01-01

    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) bu...

  6. Can Bioinformatics Be Considered as an Experimental Biological Science?

    OpenAIRE

    Ilzins, Olaf; Isea, Raul; Hoebeke, Johan

    2016-01-01

    The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an experimental science. These examples show how the development of theoretical biological models generates experimentally verifiable computer hypotheses, which necessarily must be validated by experiments in vitro or in vivo.

  7. Presentation an approach for scientific workflow distribution on cloud computing data centers servers to optimization usage of computational resource

    Directory of Open Access Journals (Sweden)

    Ahmad Faraahi

    2012-01-01

    Full Text Available In a distributed system Timing and mapping the priority of tasks among processors is one of the issues attracted most of attention to itself. This issue consists of mapping a DAG with a set of tasks on a number of parallel processors and its purpose is allocating tasks to the available processors in order to satisfy the needs of priority and decency of tasks, and also to minimize the duration time of execution in total graph . Cloud computing system is one of the distributed systems which supplied a suitable condition to execute these kinds of applications, but according to the payment based on the rate of usage in this system, we should also consider reducing computation costs as the other purpose. In this article, well represent an approach to reduce the computation costs and to increase the profitability of computation power in Cloud computing system. To some possible extent, simulations show that the represented approach decreases the costs of using computation resources.

  8. Diabetes - resources

    Science.gov (United States)

    Resources - diabetes ... The following sites provide further information on diabetes : American Diabetes Association -- www.diabetes.org Juvenile Diabetes Research Foundation International -- www.jdrf.org National Center for Chronic Disease Prevention and Health Promotion -- ...

  9. Arthritis - resources

    Science.gov (United States)

    Resources - arthritis ... The following organizations provide more information on arthritis : American Academy of Orthopaedic Surgeons -- orthoinfo.aaos.org/menus/arthritis.cfm Arthritis Foundation -- www.arthritis.org Centers for Disease Control and Prevention -- www. ...

  10. 基于SDN的数据中心网络资源调度机制%Network Resource Scheduling Mechanism Based on SDN in Data Center

    Institute of Scientific and Technical Information of China (English)

    汪正康; 周鹏; 肖俊超; 武延军

    2015-01-01

    With the emergence of Big Data applications in recent years, nowadays data centers are usually deployed with various kinds of Big Data applications and managed by resource manager such as Mesos. Mesos mainly focuses on computing resource and storage resource (CPU and memory), while ignoring network management. But research shows that efficient network resource management is crucial to optimize performance. In this work we present a network management mechanism based on SDN(Software Defined Network). This mechanism can allocate weighted network resource to different jobs based on preconfigured policy. It can allocate more bandwidth to high-priority job to optimize performance while keep the network performance isolation at the same time. We have implemented a prototype system based on SDN controller, floodlight and the experiments show that this prototype has strong usability and high expansibility.%随着大数据应用的不断丰富, 现在的数据中心通常部署着多种集群计算框架, 并由统一的集群资源管理器(如 Mesos)进行管理. 目前的集群资源管理主要关注计算资源和存储资源, 较少的涉及网络资源. 但研究表明高效的网络资源管理对于优化作业性能十分重要.本文提出了一种基于SDN(Software Defined Network)的数据中心网络资源调度机制, 该机制可以根据管理员预设的网络资源分配策略, 加权的进行网络资源调度, 为高优先级的作业分配更多网络资源以优化性能, 并且实现不同作业之间的网络性能隔离. 我们基于开源 SDN 控制器实现了原型系统, 并通过实验验证了该机制的有效性.

  11. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

    OpenAIRE

    Katayama Toshiaki; Arakawa Kazuharu; Nakao Mitsuteru; Ono Keiichiro; Aoki-Kinoshita Kiyoko F; Yamamoto Yasunori; Yamaguchi Atsuko; Kawashima Shuichi; Chun Hong-Woo; Aerts Jan; Aranda Bruno; Barboza Lord; Bonnal Raoul JP; Bruskiewich Richard; Bryne Jan C

    2010-01-01

    Abstract Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited dom...

  12. Automatic Discovery and Inferencing of Complex Bioinformatics Web Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ngu, A; Rocco, D; Critchlow, T; Buttler, D

    2003-12-22

    The World Wide Web provides a vast resource to genomics researchers in the form of web-based access to distributed data sources--e.g. BLAST sequence homology search interfaces. However, the process for seeking the desired scientific information is still very tedious and frustrating. While there are several known servers on genomic data (e.g., GeneBank, EMBL, NCBI), that are shared and accessed frequently, new data sources are created each day in laboratories all over the world. The sharing of these newly discovered genomics results are hindered by the lack of a common interface or data exchange mechanism. Moreover, the number of autonomous genomics sources and their rate of change out-pace the speed at which they can be manually identified, meaning that the available data is not being utilized to its full potential. An automated system that can find, classify, describe and wrap new sources without tedious and low-level coding of source specific wrappers is needed to assist scientists to access to hundreds of dynamically changing bioinformatics web data sources through a single interface. A correct classification of any kind of Web data source must address both the capability of the source and the conversation/interaction semantics which is inherent in the design of the Web data source. In this paper, we propose an automatic approach to classify Web data sources that takes into account both the capability and the conversational semantics of the source. The ability to discover the interaction pattern of a Web source leads to increased accuracy in the classification process. At the same time, it facilitates the extraction of process semantics, which is necessary for the automatic generation of wrappers that can interact correctly with the sources.

  13. 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.

  14. Bioinformatics: Cheap and robust method to explore biomaterial from Indonesia biodiversity

    Science.gov (United States)

    Widodo

    2015-02-01

    Indonesia has a huge amount of biodiversity, which may contain many biomaterials for pharmaceutical application. These resources potency should be explored to discover new drugs for human wealth. However, the bioactive screening using conventional methods is very expensive and time-consuming. Therefore, we developed a methodology for screening the potential of natural resources based on bioinformatics. The method is developed based on the fact that organisms in the same taxon will have similar genes, metabolism and secondary metabolites product. Then we employ bioinformatics to explore the potency of biomaterial from Indonesia biodiversity by comparing species with the well-known taxon containing the active compound through published paper or chemical database. Then we analyze drug-likeness, bioactivity and the target proteins of the active compound based on their molecular structure. The target protein was examined their interaction with other proteins in the cell to determine action mechanism of the active compounds in the cellular level, as well as to predict its side effects and toxicity. By using this method, we succeeded to screen anti-cancer, immunomodulators and anti-inflammation from Indonesia biodiversity. For example, we found anticancer from marine invertebrate by employing the method. The anti-cancer was explore based on the isolated compounds of marine invertebrate from published article and database, and then identified the protein target, followed by molecular pathway analysis. The data suggested that the active compound of the invertebrate able to kill cancer cell. Further, we collect and extract the active compound from the invertebrate, and then examined the activity on cancer cell (MCF7). The MTT result showed that the methanol extract of marine invertebrate was highly potent in killing MCF7 cells. Therefore, we concluded that bioinformatics is cheap and robust way to explore bioactive from Indonesia biodiversity for source of drug and another

  15. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... Safety Education Centers OnSafety Blog Neighborhood Safety Network Community Outreach Resource Center CO Poster Contest Toy Recall ... of the external site as its information collection practices may differ from ours. Linking to this external ...

  16. Hydrologic Engineering Center

    Data.gov (United States)

    Federal Laboratory Consortium — The Hydrologic Engineering Center (HEC), an organization within the Institute for Water Resources, is the designated Center of Expertise for the U.S. Army Corps of...

  17. Implementing Geriatric Resources for Assessment and Care of Elders Team Care in a Veterans Affairs Medical Center: Lessons Learned and Effects Observed.

    Science.gov (United States)

    Schubert, Cathy C; Myers, Laura J; Allen, Katie; Counsell, Steven R

    2016-07-01

    In a randomized clinical trial, Geriatric Resources for Assessment and Care of Elders (GRACE), a model of care that works in collaboration with primary care providers (PCPs) and patient-centered medical homes to provide home-based geriatric care management focusing on geriatric syndromes and psychosocial problems commonly found in older adults, improved care quality and reduced acute care use for high-risk, low-income older adults. To assess the effect of GRACE at a Veterans Affairs (VA) Medical Center (VAMC), veterans aged 65 and older from Marion County, Indiana, with PCPs from four of five VAMC clinics who were not on hospice or dialysis were enrolled in GRACE after discharge home from an acute hospitalization. After an initial home-based transition visit to GRACE enrollees, the GRACE team returned to conduct a geriatric assessment. Guided by 12 protocols and input from an interdisciplinary panel and the PCP, the GRACE team developed and implemented a veteran-centric care plan. Hospitalized veterans from the fifth clinic, who otherwise met enrollment criteria, served as a usual-care comparison group. Demographic, comorbidity, and usage data were drawn from VA databases. The GRACE and comparison groups were similar in age, sex, and burden of comorbidity, although predicted risk of 1-year mortality in GRACE veterans was higher. Even so, GRACE enrollment was associated with 7.1% fewer emergency department visits, 14.8% fewer 30-day readmissions, 37.9% fewer hospital admissions, and 28.5% fewer total bed days of care, saving the VAMC an estimated $200,000 per year after program costs during the study for the 179 veterans enrolled in GRACE. Having engaged, enthusiastic VA leadership and GRACE staff; aligning closely with the medical home; and accommodating patient acuity were among the important lessons learned during implementation. PMID:27305428

  18. Bioinformatic Identification of Conserved Cis-Sequences in Coregulated Genes.

    Science.gov (United States)

    Bülow, Lorenz; Hehl, Reinhard

    2016-01-01

    Bioinformatics tools can be employed to identify conserved cis-sequences in sets of coregulated plant genes because more and more gene expression and genomic sequence data become available. Knowledge on the specific cis-sequences, their enrichment and arrangement within promoters, facilitates the design of functional synthetic plant promoters that are responsive to specific stresses. The present chapter illustrates an example for the bioinformatic identification of conserved Arabidopsis thaliana cis-sequences enriched in drought stress-responsive genes. This workflow can be applied for the identification of cis-sequences in any sets of coregulated genes. The workflow includes detailed protocols to determine sets of coregulated genes, to extract the corresponding promoter sequences, and how to install and run a software package to identify overrepresented motifs. Further bioinformatic analyses that can be performed with the results are discussed. PMID:27557771

  19. Embracing the Future: Bioinformatics for High School Women

    Science.gov (United States)

    Zales, Charlotte Rappe; Cronin, Susan J.

    Sixteen high school women participated in a 5-week residential summer program designed to encourage female and minority students to choose careers in scientific fields. Students gained expertise in bioinformatics through problem-based learning in a complex learning environment of content instruction, speakers, labs, and trips. Innovative hands-on activities filled the program. Students learned biological principles in context and sophisticated bioinformatics tools for processing data. Students additionally mastered a variety of information-searching techniques. Students completed creative individual and group projects, demonstrating the successful integration of biology, information technology, and bioinformatics. Discussions with female scientists allowed students to see themselves in similar roles. Summer residential aspects fostered an atmosphere in which students matured in interacting with others and in their views of diversity.

  20. Application of Bioinformatics and Systems Biology in Medicinal Plant Studies

    Institute of Scientific and Technical Information of China (English)

    DENG You-ping; AI Jun-mei; XIAO Pei-gen

    2010-01-01

    One important purpose to investigate medicinal plants is to understand genes and enzymes that govern the biological metabolic process to produce bioactive compounds.Genome wide high throughput technologies such as genomics,transcriptomics,proteomics and metabolomics can help reach that goal.Such technologies can produce a vast amount of data which desperately need bioinformatics and systems biology to process,manage,distribute and understand these data.By dealing with the"omics"data,bioinformatics and systems biology can also help improve the quality of traditional medicinal materials,develop new approaches for the classification and authentication of medicinal plants,identify new active compounds,and cultivate medicinal plant species that tolerate harsh environmental conditions.In this review,the application of bioinformatics and systems biology in medicinal plants is briefly introduced.

  1. Probabilistic models and machine learning in structural bioinformatics

    DEFF Research Database (Denmark)

    Hamelryck, Thomas

    2009-01-01

    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 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...... 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...

  2. 国家基础研究数据资源中心建设规划研究%CONSTRUCTION PLANNING OF NATIONAL BASIC RESEARCH DATA RESOURCE CENTER

    Institute of Scientific and Technical Information of China (English)

    袁芳; 闫术卓; 邵正隆; 俞春; 宋树仁

    2013-01-01

    Basic research has become the strategic focus of science and technology development all around the world. It is the fundamental guarantee for a country to have great powers among the world. This project research is to build an integrated framework of national basic scientific data resource center. It can also establish a normative and efficient data resource management system and plan an open and shared data resource application service system that could offer an organising support for the basic demand of research innovation and basic scientific development.%基础研究已经成为当今世界各国科学技术发展的战略重点,利用当代科学技术,充分共享和分析基础研究管理数据,是推进基础研究的前沿性、国际化和持续发展的关键支撑.本文提出了拟建立国家基础研究数据资源中心的设想和总体框架,设计集成、整合的国家基础研究数据资源库,实现规范、高效的数据资源管理,规划开放、共享的数据资源应用服务平台,从而构建“布局合理、功能完善、体系健全、共享高效”的基础研究数据资源中心,为实现基础研究“科学技术人才发现与培养、基础学科研究与创新能力的提高以及国家科技整体发展提升”的战略目标提供体系化支撑.

  3. UCSF Center for HIV Information

    Science.gov (United States)

    ... Program For providers and patients VA National Viral Hepatitis Program For providers and patients TARGET Center Technical assistance tools for the Ryan White Community AETC National Resource Center Education and training for clinicians UCSF-Gladstone Center for ...

  4. 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.

  5. Approaches in integrative bioinformatics towards the virtual cell

    CERN Document Server

    Chen, Ming

    2014-01-01

    Approaches in Integrative Bioinformatics provides a basic introduction to biological information systems, as well as guidance for the computational analysis of systems biology. This book also covers a range of issues and methods that reveal the multitude of omics data integration types and the relevance that integrative bioinformatics has today. Topics include biological data integration and manipulation, modeling and simulation of metabolic networks, transcriptomics and phenomics, and virtual cell approaches, as well as a number of applications of network biology. It helps to illustrat

  6. High-performance computational solutions in protein bioinformatics

    CERN Document Server

    Mrozek, Dariusz

    2014-01-01

    Recent developments in computer science enable algorithms previously perceived as too time-consuming to now be efficiently used for applications in bioinformatics and life sciences. This work focuses on proteins and their structures, protein structure similarity searching at main representation levels and various techniques that can be used to accelerate similarity searches. Divided into four parts, the first part provides a formal model of 3D protein structures for functional genomics, comparative bioinformatics and molecular modeling. The second part focuses on the use of multithreading for

  7. From the Editors: Resource Centers for Learning and Research (RCLR, and strategic librarian’s services for an Europe based on knowledge

    Directory of Open Access Journals (Sweden)

    Sílvia Sunyer Lazaro

    2007-07-01

    Full Text Available The development processes of the European Space for Higher Education (ESHE and the European Research Area (ERA are two big challenges that European Union must face, if it has to evolve from an industry-based society to a knowledge-based one. The goals fixed by ESHE and ESR fully affect the main activities of higher education: learning, teaching and research. Being a supporting facility for these activities, university libraries are affected by these processes too. To face that challenge, the Spanish university libraries network (REBIUN advocates a new model of university library, conceived as an active and essential part of a resource center for learning and research (RCLR. In the library service of the RCLR can be found the traditional services of a library, together with others developed recently and of strategic importance for the academic community. The most important of these are: access to quality scientific information, support for the creation of teaching and research materials and the development of repositories to increase the visibility of the knowledge generated in the institution. These services are tailored to the needs of the academic community and usually are designed and developed by a new professional profile: the subject librarian.

  8. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik;

    2010-01-01

    Abstract. The Genome Atlas is a resource for addressing the challenges of synchronising prokaryotic genomic sequence data from multiple public repositories. This resource can integrate bioinformatic analyses in various data format and quality. Existing open source tools have been used together...... with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  9. 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

  10. Squid – a simple bioinformatics grid

    Directory of Open Access Journals (Sweden)

    de Miranda Antonio B

    2005-08-01

    Full Text Available Abstract Background BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. The current version, as an example, is configured for BLAST applications, but adaptation for other computing intensive repetitive tasks can be easily accomplished in the open source version. This enables the allocation of remote resources to perform distributed computing, making large BLAST queries viable without the need of high-end computers. Results Most distributed computing / grid solutions have complex installation procedures requiring a computer specialist, or have limitations regarding operating systems. Squid is a multi-platform, open-source program designed to "keep things simple" while offering high-end computing power for large scale applications. Squid also has an efficient fault tolerance and crash recovery system against data loss, being able to re-route jobs upon node failure and recover even if the master machine fails. Our results show that a Squid application, working with N nodes and proper network resources, can process BLAST queries almost N times faster than if working with only one computer. Conclusion Squid offers high-end computing, even for the non-specialist, and is freely available at the project web site. Its open-source and binary Windows distributions contain detailed instructions and a "plug-n-play" instalation containing a pre-configured example.

  11. 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.

  12. Technical phosphoproteomic and bioinformatic tools useful in cancer research

    Directory of Open Access Journals (Sweden)

    López Elena

    2011-10-01

    Full Text Available Abstract Reversible protein phosphorylation is one of the most important forms of cellular regulation. Thus, phosphoproteomic analysis of protein phosphorylation in cells is a powerful tool to evaluate cell functional status. The importance of protein kinase-regulated signal transduction pathways in human cancer has led to the development of drugs that inhibit protein kinases at the apex or intermediary levels of these pathways. Phosphoproteomic analysis of these signalling pathways will provide important insights for operation and connectivity of these pathways to facilitate identification of the best targets for cancer therapies. Enrichment of phosphorylated proteins or peptides from tissue or bodily fluid samples is required. The application of technologies such as phosphoenrichments, mass spectrometry (MS coupled to bioinformatics tools is crucial for the identification and quantification of protein phosphorylation sites for advancing in such relevant clinical research. A combination of different phosphopeptide enrichments, quantitative techniques and bioinformatic tools is necessary to achieve good phospho-regulation data and good structural analysis of protein studies. The current and most useful proteomics and bioinformatics techniques will be explained with research examples. Our aim in this article is to be helpful for cancer research via detailing proteomics and bioinformatic tools.

  13. Technical phosphoproteomic and bioinformatic tools useful in cancer research.

    Science.gov (United States)

    López, Elena; Wesselink, Jan-Jaap; López, Isabel; Mendieta, Jesús; Gómez-Puertas, Paulino; Muñoz, Sarbelio Rodríguez

    2011-01-01

    Reversible protein phosphorylation is one of the most important forms of cellular regulation. Thus, phosphoproteomic analysis of protein phosphorylation in cells is a powerful tool to evaluate cell functional status. The importance of protein kinase-regulated signal transduction pathways in human cancer has led to the development of drugs that inhibit protein kinases at the apex or intermediary levels of these pathways. Phosphoproteomic analysis of these signalling pathways will provide important insights for operation and connectivity of these pathways to facilitate identification of the best targets for cancer therapies. Enrichment of phosphorylated proteins or peptides from tissue or bodily fluid samples is required. The application of technologies such as phosphoenrichments, mass spectrometry (MS) coupled to bioinformatics tools is crucial for the identification and quantification of protein phosphorylation sites for advancing in such relevant clinical research. A combination of different phosphopeptide enrichments, quantitative techniques and bioinformatic tools is necessary to achieve good phospho-regulation data and good structural analysis of protein studies. The current and most useful proteomics and bioinformatics techniques will be explained with research examples. Our aim in this article is to be helpful for cancer research via detailing proteomics and bioinformatic tools. PMID:21967744

  14. BioRuby: Bioinformatics software for the Ruby programming language

    NARCIS (Netherlands)

    Goto, N.; Prins, J.C.P.; Nakao, M.; Bonnal, R.; Aerts, J.; Katayama, A.

    2010-01-01

    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 suppor

  15. 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...

  16. 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…

  17. 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…

  18. Setubal named deputy director at Virginia Bioinformatics Institute

    OpenAIRE

    Whyte, Barry James

    2005-01-01

    The Virginia Bioinformatics Institute (VBI) at Virginia Tech has announced the appointment of Joao Setubal as the institute's deputy director. As deputy director, Setubal will act on behalf of VBI's executive and scientific director, Bruno Sobral, handling internal administrative functions, as well as scientific decision making.

  19. Bioinformatics Assisted Gene Discovery and Annotation of Human Genome

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinformatics tools and technologies available for large scale gene discovery and annotation from human genome sequences. Some ideas about possible future development are also provided.

  20. Discovery-driven research and bioinformatics in nuclear receptor and coregulator signaling.

    Science.gov (United States)

    McKenna, Neil J

    2011-08-01

    Nuclear receptors (NRs) are a superfamily of ligand-regulated transcription factors that interact with coregulators and other transcription factors to direct tissue-specific programs of gene expression. Recent years have witnessed a rapid acceleration of the output of high-content data platforms in this field, generating discovery-driven datasets that have collectively described: the organization of the NR superfamily (phylogenomics); the expression patterns of NRs, coregulators and their target genes (transcriptomics); ligand- and tissue-specific functional NR and coregulator sites in DNA (cistromics); the organization of nuclear receptors and coregulators into higher order complexes (proteomics); and their downstream effects on homeostasis and metabolism (metabolomics). Significant bioinformatics challenges lie ahead both in the integration of this information into meaningful models of NR and coregulator biology, as well as in the archiving and communication of datasets to the global nuclear receptor signaling community. While holding great promise for the field, the ascendancy of discovery-driven research in this field brings with it a collective responsibility for researchers, publishers and funding agencies alike to ensure the effective archiving and management of these data. This review will discuss factors lying behind the increasing impact of discovery-driven research, examples of high-content datasets and their bioinformatic analysis, as well as a summary of currently curated web resources in this field. This article is part of a Special Issue entitled: Translating nuclear receptors from health to disease. PMID:21029773

  1. GITIRBio: A Semantic and Distributed Service Oriented-Architecture for Bioinformatics Pipeline.

    Science.gov (United States)

    Castillo, Luis F; López-Gartner, Germán; Isaza, Gustavo A; Sánchez, Mariana; Arango, Jeferson; Agudelo-Valencia, Daniel; Castaño, Sergio

    2015-01-01

    The need to process large quantities of data generated from genomic sequencing has resulted in a difficult task for life scientists who are not familiar with the use of command-line operations or developments in high performance computing and parallelization. This knowledge gap, along with unfamiliarity with necessary processes, can hinder the execution of data processing tasks. Furthermore, many of the commonly used bioinformatics tools for the scientific community are presented as isolated, unrelated entities that do not provide an integrated, guided, and assisted interaction with the scheduling facilities of computational resources or distribution, processing and mapping with runtime analysis. This paper presents the first approximation of a Web Services platform-based architecture (GITIRBio) that acts as a distributed front-end system for autonomous and assisted processing of parallel bioinformatics pipelines that has been validated using multiple sequences. Additionally, this platform allows integration with semantic repositories of genes for search annotations. GITIRBio is available at: http://c-head.ucaldas.edu.co:8080/gitirbio. PMID:26527189

  2. An Abstract Description Approach to the Discovery and Classification of Bioinformatics Web Sources

    Energy Technology Data Exchange (ETDEWEB)

    Rocco, D; Critchlow, T J

    2003-05-01

    The World Wide Web provides an incredible resource to genomics researchers in the form of dynamic data sources--e.g. BLAST sequence homology search interfaces. The growth rate of these sources outpaces the speed at which they can be manually classified, meaning that the available data is not being utilized to its full potential. Existing research has not addressed the problems of automatically locating, classifying, and integrating classes of bioinformatics data sources. This paper presents an overview of a system for finding classes of bioinformatics data sources and integrating them behind a unified interface. We examine an approach to classifying these sources automatically that relies on an abstract description format: the service class description. This format allows a domain expert to describe the important features of an entire class of services without tying that description to any particular Web source. We present the features of this description format in the context of BLAST sources to show how the service class description relates to Web sources that are being described. We then show how a service class description can be used to classify an arbitrary Web source to determine if that source is an instance of the described service. To validate the effectiveness of this approach, we have constructed a prototype that can correctly classify approximately two-thirds of the BLAST sources we tested. We then examine these results, consider the factors that affect correct automatic classification, and discuss future work.

  3. 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

  4. 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 …

  5. LEARNING HORMONE ACTION MECHANISMS WITH BIOINFORMATICS

    Directory of Open Access Journals (Sweden)

    João Carlos Sousa

    2007-05-01

    Full Text Available The ability to manage the constantly growing information in genetics availableon the internet is becoming crucial in biochemical education and medicalpractice. Therefore, developing students skills in working with bioinformaticstools is a challenge to undergraduate courses in the molecular life sciences.The regulation of gene transcription by hormones and vitamins is a complextopic that influences all body systems. We describe a student centered activityused in a multidisciplinary “Functional Organ System“ course on the EndocrineSystem. By receiving, as teams, a nucleotide sequence of a hormone orvitamin-response element, students navigate through internet databases to findthe gene to which it belongs. Subsequently, student’s search how thecorresponding hormone/vitamin influences the expression of that particulargene and how a dysfunctional interaction might cause disease. This activity,proposed for 4 consecutive years to cohorts of 50-60 students/year enrolled inthe 2nd year our undergraduate medical degree, revealed that 90% of thestudents developed a better understanding of the usefulness of bioinformaticsand that 98% intend to use them in the future. Since hormones and vitaminsregulate genes of all body organ systems, this web-based activity successfullyintegrates the whole body physiology of the medical curriculum and can be ofrelevance to other courses on molecular life sciences.

  6. 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…

  7. Design and Implementation of an Interdepartmental Bioinformatics Program across Life Science Curricula

    Science.gov (United States)

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

    2007-01-01

    Over the past 10 years, there has been a technical revolution in the life sciences leading to the emergence of a new discipline called bioinformatics. In response, bioinformatics-related topics have been incorporated into various undergraduate courses along with the development of new courses solely focused on bioinformatics. This report describes…

  8. 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'…

  9. Resources and Operations Section

    International Nuclear Information System (INIS)

    Progress is reported on the following: environmental data resources group; EDFB information center; national inventory of biological monitoring; ecological sciences information center; long-range computer planning; educational activities; quality assurance; and industrial and radiation safety

  10. 传统人力资源管理到战略人力资源管理的转型路径--基于人力资源共享服务中心模式%The Transition Path of Traditional Human Resources Management to Strategic Human Resources Management---Based on Human Resources Service Center Mode

    Institute of Scientific and Technical Information of China (English)

    解海美; 陈进

    2014-01-01

    随着经济全球化和信息化的进程加快,越来越多的企业进入大规模、跨区域发展时代,然而传统人力资源管理弊病显现,战略人力资源管理急需推进。文章通过比较传统人力资源管理与人力资源共享服务中心两种模式,表明后者是实现战略管理转型的有效路径,并阐明这一模式的运行机制及其目前的实践进展,以期促进企业战略人力资源管理的实现。%With the economic globalization and information process accelerate, more and more enterprises enter the large-scale, cross regional development era. However, the traditional human resource management problems appeared, strategic human resource management need to promote.By the comparison of the traditional HRM and HR shared service center, this paper shows that HR shared services center is the excellent transition to strategic management, and explains the operation mechanism of this model, and the current practice of progress, in order to promote the implementation of strategic HRM.

  11. Thermodynamic description of Beta amyloid formation using physicochemical scales and fractal bioinformatic scales.

    Science.gov (United States)

    Phillips, J C

    2015-05-20

    Protein function depends on both protein structure and amino acid (aa) sequence. Here we show that modular features of both structure and function can be quantified economically from the aa sequences alone for the small (40,42 aa) plaque-forming (aggregative) amyloid beta fragments. Some edge and center features of the fragments are predicted. Bioinformatic scales based on β strand formation propensities and the thermodynamically second order fractal hydropathicity scale based on evolutionary optimization (self-organized criticality) are contrasted with the standard first order physicochemical scale based on complete protein (water-air) unfolding. The results are consistent with previous studies of these physicochemical factors that show that aggregative properties, even of beta fragments, are driven primarily by near-equilibrium hydropathic forces. PMID:25702750

  12. FY02 CBNP Annual Report Input: Bioinformatics Support for CBNP Research and Deployments

    Energy Technology Data Exchange (ETDEWEB)

    Slezak, T; Wolinsky, M

    2002-10-31

    The events of FY01 dynamically reprogrammed the objectives of the CBNP bioinformatics support team, to meet rapidly-changing Homeland Defense needs and requests from other agencies for assistance: Use computational techniques to determine potential unique DNA signature candidates for microbial and viral pathogens of interest to CBNP researcher and to our collaborating partner agencies such as the Centers for Disease Control and Prevention (CDC), U.S. Department of Agriculture (USDA), Department of Defense (DOD), and Food and Drug Administration (FDA). Develop effective electronic screening measures for DNA signatures to reduce the cost and time of wet-bench screening. Build a comprehensive system for tracking the development and testing of DNA signatures. Build a chain-of-custody sample tracking system for field deployment of the DNA signatures as part of the BASIS project. Provide computational tools for use by CBNP Biological Foundations researchers.

  13. Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology.

    Science.gov (United States)

    Ju, Feng; Zhang, Tong

    2015-11-01

    Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation. PMID:26451629

  14. Federal Agency and Federal Library Reports. Library of Congress; Center for the Book; Federal Library and Information Center Committee; National Commission on Libraries and Information Science; National Agricultural Library; National Library of Medicine;United States Government Printing Office; National Technical Information Service; National Archives and Records Administration; National Center for Education Statistics Library Statistics Program; National Library of Education; Educational Resources Information Center.

    Science.gov (United States)

    Fischer, Audrey; Cole, John Y.; Tarr, Susan M.; Vlach, Rosalie B.; Carey, Len; Mehnert, Robert; Sherman, Andrew M.; Davis, Linda; Vecchiarelli, Marion H.; Chute, Adrienne; Dunn, Christina

    2002-01-01

    Includes reports from Library of Congress, Center for the Book, Federal Library and Information Center Committee, National Commission on Libraries and Information Science, National Agricultural Library, National Library of Medicine, Government Printing Office, National Technical Information Service, National Archives and Records Administration,…

  15. The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

    Science.gov (United States)

    Harb, Omar S; Roos, David S

    2015-01-01

    Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods. PMID:25388105

  16. 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.].

  17. Bioinformatics Data Distribution and Integration via Web Services and XML

    Institute of Scientific and Technical Information of China (English)

    Xiao Li; Yizheng Zhang

    2003-01-01

    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 biological 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.

  18. Bioinformatics Analysis of Zinc Transporter from Baoding Alfalfa

    Institute of Scientific and Technical Information of China (English)

    Haibo WANG; Junyun GUO

    2012-01-01

    [Objective] This study aimed to perform the bioinformatics analysis of Zinc transporter (ZnT) from Baoding Alfalfa. [Method] Based on the amino acid sequence, the physical and chemical properties, hydrophilicity/hydrophobicity, secondary structure of ZnT from Baoding alfalfa were predicted by a series of bioinformatics software. And the transmembrane domains were predicted by using different online tools. [Result] ZnT is a hydrophobic protein containing 408 amino acids with the theoretical pl of 5.94, and it has 7 potential transmembrane hydrophobic regions. In the sec- ondary structure, co-helix (Hh) accounted for 48.04%, extended strand (Ee) for 9.56%, random coil (Cc) for 42.40%, which was accored with the characteristic of transmembrane protein. [Conclusion] mZnT is a member of CDF family, responsible for transporting Zn^2+ out of the cell membrane to reduce the concentration and toxicity of Zn^2+.

  19. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  20. Bioinformatics. Data base and application execution web system

    International Nuclear Information System (INIS)

    Research for the biological systems has reached to the stage that clarifies an organism as a whole from genome, a set of genes. To accomplish the researches, one needs to face a lot of data retrieved from genome sequences. Conventional methods, namely experiments in wet-labs, are, however not designed for dealing with genome scale data. For those data analyses, computer based researches, such as data mining and simulation, are suitable. As a result, bioinformatics, a new discipline combining expertise of biology and information science, is emerging. Here, we report a development of a data base and a web based system for application execution (Execution of Application on web system). Those are one of the efforts to support bioinformatics research by Office of ITBL Promotion. (author)

  1. 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...

  2. 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.

  3. 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.  .

  4. BioJava: an open-source framework for bioinformatics

    OpenAIRE

    Holland, R. C. G.; Down, T. A.; Pocock, M.; Prlić, A.; Huen, D; James, K.; Foisy, S.; Dräger, A.; Yates, A; Heuer, M.; Schreiber, M. J.

    2008-01-01

    Summary: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language. Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website...

  5. Fighting against uncertainty: An essential issue in bioinformatics

    OpenAIRE

    Hamada, Michiaki

    2013-01-01

    Many bioinformatics problems, such as sequence alignment, gene prediction, phylogenetic tree estimation and RNA secondary structure prediction, are often affected by the "uncertainty" of a solution; that is, the probability of the solution is extremely small. This situation arises for estimation problems on high-dimensional discrete spaces in which the number of possible discrete solutions is immense. In the analysis of biological data or the development of prediction algorithms, this uncerta...

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

    OpenAIRE

    Nora Khaldi

    2012-01-01

    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 b...

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

    OpenAIRE

    Knox Barry E; Qin Maochun; McIlvain Vera A; Danko Charles G; Pertsov Arkady M

    2007-01-01

    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 site...

  8. Promoting synergistic research and education in genomics and bioinformatics

    OpenAIRE

    Yang, Jack Y; Yang, Mary Qu; Zhu, Mengxia (Michelle); Arabnia, Hamid R; Deng, Youping

    2008-01-01

    Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology. High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personali...

  9. Drug targets for lymphatic filariasis: A bioinformatics approach

    OpenAIRE

    Om Prakash Sharma; Yellamandaya Vadlamudi; Arun Gupta Kota; Vikrant Kumar Sinha; Muthuvel Suresh Kumar

    2013-01-01

    This review article discusses the current scenario of the national and international burden due to lymphatic filariasis (LF) and describes the active elimination programmes for LF and their achievements to eradicate this most debilitating disease from the earth. Since, bioinformatics is a rapidly growing field of biological study, and it has an increasingly significant role in various fields of biology. We have reviewed its leading involvement in the filarial research using different approach...

  10. 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). PMID:25654371

  11. Promoting synergistic research and education in genomics and bioinformatics

    OpenAIRE

    Arabnia Hamid R; Zhu Mengxia; Yang Mary Qu; Yang Jack Y; Deng Youping

    2008-01-01

    Abstract Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology. High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and ...

  12. Applications of Structural Bioinformatics for the Structural Genomics Era

    OpenAIRE

    Novotny, Marian

    2007-01-01

    Structural bioinformatics deals with the analysis, classification and prediction of three-dimensional structures of biomacromolecules. It is becoming increasingly important as the number of structures is growing rapidly. This thesis describes three studies concerned with protein-function prediction and two studies about protein structure validation. New protein structures are often compared to known structures to find out if they have a known fold, which may provide hints about their function...

  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 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. PMID:22987552

  14. 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.

  15. Bioinformatics: Current practice and future challenges for life science education.

    Science.gov (United States)

    Hack, Catherine; Kendall, Gary

    2005-03-01

    It is widely predicted that the application of high-throughput technologies to the quantification and identification of biological molecules will cause a paradigm shift in the life sciences. However, if the biosciences are to evolve from a predominantly descriptive discipline to an information science, practitioners will require enhanced skills in mathematics, computing, and statistical analysis. Universities have responded to the widely perceived skills gap primarily by developing masters programs in bioinformatics, resulting in a rapid expansion in the provision of postgraduate bioinformatics education. There is, however, a clear need to improve the quantitative and analytical skills of life science undergraduates. This article reviews the response of academia in the United Kingdom and proposes the learning outcomes that graduates should achieve to cope with the new biology. While the analysis discussed here uses the development of bioinformatics education in the United Kingdom as an illustrative example, it is hoped that the issues raised will resonate with all those involved in curriculum development in the life sciences. PMID:21638550

  16. A comparison of common programming languages used in bioinformatics

    Directory of Open Access Journals (Sweden)

    Gillings Michael R

    2008-02-01

    Full Text Available Abstract Background 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. Results 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/ Conclusion 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.

  17. SNPTrack™ : an integrated bioinformatics system for genetic association studies.

    Science.gov (United States)

    Xu, Joshua; Kelly, Reagan; Zhou, Guangxu; Turner, Steven A; Ding, Don; Harris, Stephen C; Hong, Huixiao; Fang, Hong; Tong, Weida

    2012-01-01

    A genetic association study is a complicated process that involves collecting phenotypic data, generating genotypic data, analyzing associations between genotypic and phenotypic data, and interpreting genetic biomarkers identified. SNPTrack is an integrated bioinformatics system developed by the US Food and Drug Administration (FDA) to support the review and analysis of pharmacogenetics data resulting from FDA research or submitted by sponsors. The system integrates data management, analysis, and interpretation in a single platform for genetic association studies. Specifically, it stores genotyping data and single-nucleotide polymorphism (SNP) annotations along with study design data in an Oracle database. It also integrates popular genetic analysis tools, such as PLINK and Haploview. SNPTrack provides genetic analysis capabilities and captures analysis results in its database as SNP lists that can be cross-linked for biological interpretation to gene/protein annotations, Gene Ontology, and pathway analysis data. With SNPTrack, users can do the entire stream of bioinformatics jobs for genetic association studies. SNPTrack is freely available to the public at http://www.fda.gov/ScienceResearch/BioinformaticsTools/SNPTrack/default.htm. PMID:23245293

  18. An Integrative Study on Bioinformatics Computing Concepts, Issues and Problems

    Directory of Open Access Journals (Sweden)

    Muhammad Zakarya

    2011-11-01

    Full Text Available Bioinformatics is the permutation and mishmash of biological science and 4IT. The discipline covers every computational tools and techniques used to administer, examine and manipulate huge sets of biological statistics. The discipline also helps in creation of databases to store up and supervise biological statistics, improvement of computer algorithms to find out relations in these databases and use of computer tools for the study and understanding of biological information, including DNA, RNA, protein sequences, gene expression profiles, protein structures, and biochemical pathways. The study of this paper implements an integrative solution. As we know that solution to a problem in a specific discipline may be a solution to another problem in a different discipline. For example entropy that has been rented from physical sciences is solution to most of the problems and issues in computer science. Another example is bioinformatics, where computing method and applications are implemented over biological information. This paper shows an initiative step towards that and will discuss upon the needs for integration of multiple discipline and sciences. Similarly green chemistry gives birth to a new kind of computing i.e. green computing. In next versions of this paper we will study biological fuel cell and will discuss to develop a mobile battery that will be life time charged using the concepts of biological fuel cell. Another issue that we are going to discuss in our series is brain tumor detection. This paper is a review on BI i.e. bioinformatics to start with.

  19. Synthesis of facilitation, communication, information, and technology to enhance public involvement through the Transportation Resource Exchange Center (T-REX) web site in accordance with the NEPA planning and decision-making process: a best practice

    OpenAIRE

    Espinosa, Judith M; White, Mary E

    2001-01-01

    The Transportation Resource Exchange Center (T-REX) is a first-of-its-kind Virtual Library dedicated to providing information about the transportation of radioactive materials to stakeholders. Guided by the principles of the National Environmental Policy Act (NEPA) planning and decision-making process, the Web site was created to serve as a “one-stop shop,” neutral source for information, to facilitate public involvement, overcome information gaps, and foster clearer communication and underst...

  20. 基于语料库的语言自主学习中心资源建设研究%Corpus-based Resource Constructing in Language Autonomous Learning Center

    Institute of Scientific and Technical Information of China (English)

    邱大平; 贾勤

    2012-01-01

    为解决语言自主学习中心资源匮乏、学生自主学习过程缺乏有效监控和教师缺乏指导学生自主学习的针对性方案的问题,加强语言自主学习中心资源建设,在语料库数据驱动学习理论的基础上,探讨了语料库在自主学习中的优势,介绍了基于语料库的语言自主学习中心资源建设方案。%The serious problems in language autonomous learning center such as a lack of learning resources, effective autonomous learning process monitoring measures and pointed strategies in helping students with autonomous learning call for enhancing resource development in the lan- guage autonomous learning center. Therefore, based on the data driven learning theory, the ad- vantages of applying corpus in autonomous learning were explored in this paper. And the strate- gies in constructing corpus based resources in language autonomous learning center were intro duced.

  1. Carbon Monoxide Information Center

    Medline Plus

    Full Text Available ... Safety Network Community Outreach Resource Center CO Poster Contest Toy Recall Statistics Pool Safely Home / Safety Education / ... VIDEO CPSC announces winners of carbon monoxide poster contest View the blog SAFETY GUIDE Clues You Can ...

  2. Health Center Controlled Network

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Health Center Controlled Network (HCCN) tool is a locator tool designed to make data and information concerning HCCN resources more easily available to our...

  3. Contact Center Manager Administration (CCMA)

    Data.gov (United States)

    Social Security Administration — CCMA is the server that provides a browser-based tool for contact center administrators and supervisors. It is used to manage and configure contact center resources...

  4. Center to Advance Palliative Care

    Science.gov (United States)

    ... Discussion Forum The IPAL Project Palliative Care Leadership Centers (PCLC) Member Resources National Seminar Quick Links Certification ... a Job Manage Job Posts About About The Center to Advance Palliative Care (CAPC) is a national ...

  5. 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

  6. Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis

    Directory of Open Access Journals (Sweden)

    Daniel Lobo

    2012-11-01

    The mechanisms underlying the regenerative abilities of certain model species are of central importance to the basic understanding of pattern formation. Complex organisms such as planaria and salamanders exhibit an exceptional capacity to regenerate complete body regions and organs from amputated pieces. However, despite the outstanding bottom-up efforts of molecular biologists and bioinformatics focused at the level of gene sequence, no comprehensive mechanistic model exists that can account for more than one or two aspects of regeneration. The development of computational approaches that help scientists identify constructive models of pattern regulation is held back by the lack of both flexible morphological representations and a repository for the experimental procedures and their results (altered pattern formation. No formal representation or computational tools exist to efficiently store, search, or mine the available knowledge from regenerative experiments, inhibiting fundamental insights from this huge dataset. To overcome these problems, we present here a new class of ontology to encode formally and unambiguously a very wide range of possible morphologies, manipulations, and experiments. This formalism will pave the way for top-down approaches for the discovery of comprehensive models of regeneration. We chose the planarian regeneration dataset to illustrate a proof-of-principle of this novel bioinformatics of shape; we developed a software tool to facilitate the formalization and mining of the planarian experimental knowledge, and cured a database containing all of the experiments from the principal publications on planarian regeneration. These resources are freely available for the regeneration community and will readily assist researchers in identifying specific functional data in planarian experiments. More importantly, these applications illustrate the presented framework for formalizing knowledge about functional perturbations of morphogenesis, which

  7. Composable languages for bioinformatics: the NYoSh experiment

    Directory of Open Access Journals (Sweden)

    Manuele Simi

    2014-01-01

    Full Text Available Language WorkBenches (LWBs are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell. NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly by end-users with new abstractions and language constructs. We further illustrate language extension and composition with LWBs by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype, which implements a fully featured integrated development environment

  8. Composable languages for bioinformatics: the NYoSh experiment.

    Science.gov (United States)

    Simi, Manuele; Campagne, Fabien

    2014-01-01

    Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly by end-users with new abstractions and language constructs. We further illustrate language extension and composition with LWBs by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype, which implements a fully featured integrated development environment for NYoSh is

  9. Applications of Support Vector Machines In Chemo And Bioinformatics

    Science.gov (United States)

    Jayaraman, V. K.; Sundararajan, V.

    2010-10-01

    Conventional linear & nonlinear tools for classification, regression & data driven modeling are being replaced on a rapid scale by newer techniques & tools based on artificial intelligence and machine learning. While the linear techniques are not applicable for inherently nonlinear problems, newer methods serve as attractive alternatives for solving real life problems. Support Vector Machine (SVM) classifiers are a set of universal feed-forward network based classification algorithms that have been formulated from statistical learning theory and structural risk minimization principle. SVM regression closely follows the classification methodology. In this work recent applications of SVM in Chemo & Bioinformatics will be described with suitable illustrative examples.

  10. SPOT--towards temporal data mining in medicine and bioinformatics.

    Science.gov (United States)

    Tusch, Guenter; Bretl, Chris; O'Connor, Martin; Connor, Martin; Das, Amar

    2008-01-01

    Mining large clinical and bioinformatics databases often includes exploration of temporal data. E.g., in liver transplantation, researchers might look for patients with an unusual time pattern of potential complications of the liver. In Knowledge-based Temporal Abstraction time-stamped data points are transformed into an interval-based representation. We extended this framework by creating an open-source platform, SPOT. It supports the R statistical package and knowledge representation standards (OWL, SWRL) using the open source Semantic Web tool Protégé-OWL. PMID:18999225

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

    International Nuclear Information System (INIS)

    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)

  12. WU-Blast2 server at the European Bioinformatics Institute

    OpenAIRE

    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.

  13. Biophysics and bioinformatics of transcription regulation in bacteria and bacteriophages

    Science.gov (United States)

    Djordjevic, Marko

    2005-11-01

    Due to rapid accumulation of biological data, bioinformatics has become a very important branch of biological research. In this thesis, we develop novel bioinformatic approaches and aid design of biological experiments by using ideas and methods from statistical physics. Identification of transcription factor binding sites within the regulatory segments of genomic DNA is an important step towards understanding of the regulatory circuits that control expression of genes. We propose a novel, biophysics based algorithm, for the supervised detection of transcription factor (TF) binding sites. The method classifies potential binding sites by explicitly estimating the sequence-specific binding energy and the chemical potential of a given TF. In contrast with the widely used information theory based weight matrix method, our approach correctly incorporates saturation in the transcription factor/DNA binding probability. This results in a significant reduction in the number of expected false positives, and in the explicit appearance---and determination---of a binding threshold. The new method was used to identify likely genomic binding sites for the Escherichia coli TFs, and to examine the relationship between TF binding specificity and degree of pleiotropy (number of regulatory targets). We next address how parameters of protein-DNA interactions can be obtained from data on protein binding to random oligos under controlled conditions (SELEX experiment data). We show that 'robust' generation of an appropriate data set is achieved by a suitable modification of the standard SELEX procedure, and propose a novel bioinformatic algorithm for analysis of such data. Finally, we use quantitative data analysis, bioinformatic methods and kinetic modeling to analyze gene expression strategies of bacterial viruses. We study bacteriophage Xp10 that infects rice pathogen Xanthomonas oryzae. Xp10 is an unusual bacteriophage, which has morphology and genome organization that most closely

  14. Bioinformatics pipeline for functional identification and characterization of proteins

    Science.gov (United States)

    Skarzyńska, Agnieszka; Pawełkowicz, Magdalena; Krzywkowski, Tomasz; Świerkula, Katarzyna; PlÄ der, Wojciech; Przybecki, Zbigniew

    2015-09-01

    The new sequencing methods, called Next Generation Sequencing gives an opportunity to possess a vast amount of data in short time. This data requires structural and functional annotation. Functional identification and characterization of predicted proteins could be done by in silico approches, thanks to a numerous computational tools available nowadays. However, there is a need to confirm the results of proteins function prediction using different programs and comparing the results or confirm experimentally. Here we present a bioinformatics pipeline for structural and functional annotation of proteins.

  15. 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...

  16. Provenance of e-Science Experiments - experience from Bioinformatics

    OpenAIRE

    Greenwood, M.; Goble, C.A.; Stevens, R. D.; Zhao, J.(Central China Normal University (HZNU), Wuhan, 430079, China); Addis, M; Marvin, D; Moreau, L; Oinn, T.

    2003-01-01

    Like experiments performed at a laboratory bench, the data associated with an e-Science experiment are of reduced value if other scientists are not able to identify the origin, or provenance, of those data. Provenance information is essential if experiments are to be validated and verified by others, or even by those who originally performed them. In this article, we give an overview of our initial work on the provenance of bioinformatics e-Science experiments within myGrid. We use two kinds ...

  17. The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis.

    OpenAIRE

    Alva, V.; Nam, S.; Söding, J.; Lupas, A.

    2016-01-01

    The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAST+, HMMER3, MUSCLE) and internally (e.g. HHpred, HHblits, PCOILS). While a beta version of the Toolkit was released 10 years ago, the current production-level release has been av...

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

    OpenAIRE

    Park, Hyun-Seok

    2012-01-01

    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...

  19. How to Establish a Bioinformatics Postgraduate Degree Programme: A Case Study from South Africa

    OpenAIRE

    Machanick, Philip; Bishop, Ozlem Tastan

    2014-01-01

    The Research Unit in Bioinformatics at Rhodes University (RUBi), South Africa offers a Masters of Science in Bioinformatics. Growing demand for Bioinformatics qualifications results in applications from across Africa. Courses aim to bridge gaps in the diverse backgrounds of students who range from biologists with no prior computing exposure to computer scientists with no biology background. The programme is evenly split between coursework and research, with diverse modules from a range of dep...

  20. Technosciences in Academia: Rethinking a Conceptual Framework for Bioinformatics Undergraduate Curricula

    Science.gov (United States)

    Symeonidis, Iphigenia Sofia

    This paper aims to elucidate guiding concepts for the design of powerful undergraduate bioinformatics degrees which will lead to a conceptual framework for the curriculum. "Powerful" here should be understood as having truly bioinformatics objectives rather than enrichment of existing computer science or life science degrees on which bioinformatics degrees are often based. As such, the conceptual framework will be one which aims to demonstrate intellectual honesty in regards to the field of bioinformatics. A synthesis/conceptual analysis approach was followed as elaborated by Hurd (1983). The approach takes into account the following: bioinfonnatics educational needs and goals as expressed by different authorities, five undergraduate bioinformatics degrees case-studies, educational implications of bioinformatics as a technoscience and approaches to curriculum design promoting interdisciplinarity and integration. Given these considerations, guiding concepts emerged and a conceptual framework was elaborated. The practice of bioinformatics was given a closer look, which led to defining tool-integration skills and tool-thinking capacity as crucial areas of the bioinformatics activities spectrum. It was argued, finally, that a process-based curriculum as a variation of a concept-based curriculum (where the concepts are processes) might be more conducive to the teaching of bioinformatics given a foundational first year of integrated science education as envisioned by Bialek and Botstein (2004). Furthermore, the curriculum design needs to define new avenues of communication and learning which bypass the traditional disciplinary barriers of academic settings as undertaken by Tador and Tidmor (2005) for graduate studies.

  1. Promoting inter/multidisciplinary education and research in bioinformatics, systems biology and intelligent computing.

    Science.gov (United States)

    Yang, Mary Qu; Niemierko, Andrzej; Yang, Jack Y; Jin, Yufang

    2009-01-01

    Bioinformatics and systems biology are two booming research areas studying live organisms. Though having different focuses, bioinformatics and systems biology often share same or similar engineering and computer science methods to elucidate the mechanisms of multi-level biological systems. Regulatory mechanisms underlying biological processes involve interactions at cellular, sub-cellular, genomic and genetic levels. Accordingly, we need to bridge the gaps of biomedical researches at different levels of studies and foster the interdisciplinary and multidisciplinary research between both bioinformatics and systems biology domains. The synergic research on integrating bioinformatics and systems biology facilitates the advances in biology and medicine. PMID:20090160

  2. Detecting evolution of bioinformatics with a content and co-authorship analysis.

    Science.gov (United States)

    Song, Min; Yang, Christopher C; Tang, Xuning

    2013-12-01

    Bioinformatics is an interdisciplinary research field that applies advanced computational techniques to biological data. Bibliometrics analysis has recently been adopted to understand the knowledge structure of a research field by citation pattern. In this paper, we explore the knowledge structure of Bioinformatics from the perspective of a core open access Bioinformatics journal, BMC Bioinformatics with trend analysis, the content and co-authorship network similarity, and principal component analysis. Publications in four core journals including Bioinformatics - Oxford Journal and four conferences in Bioinformatics were harvested from DBLP. After converting publications into TF-IDF term vectors, we calculate the content similarity, and we also calculate the social network similarity based on the co-authorship network by utilizing the overlap measure between two co-authorship networks. Key terms is extracted and analyzed with PCA, visualization of the co-authorship network is conducted. The experimental results show that Bioinformatics is fast-growing, dynamic and diversified. The content analysis shows that there is an increasing overlap among Bioinformatics journals in terms of topics and more research groups participate in researching Bioinformatics according to the co-authorship network similarity. PMID:23710427

  3. Making sense of genomes of parasitic worms: Tackling bioinformatic challenges.

    Science.gov (United States)

    Korhonen, Pasi K; Young, Neil D; Gasser, Robin B

    2016-01-01

    Billions of people and animals are infected with parasitic worms (helminths). Many of these worms cause diseases that have a major socioeconomic impact worldwide, and are challenging to control because existing treatment methods are often inadequate. There is, therefore, a need to work toward developing new intervention methods, built on a sound understanding of parasitic worms at molecular level, the relationships that they have with their animal hosts and/or the diseases that they cause. Decoding the genomes and transcriptomes of these parasites brings us a step closer to this goal. The key focus of this article is to critically review and discuss bioinformatic tools used for the assembly and annotation of these genomes and transcriptomes, as well as various post-genomic analyses of transcription profiles, biological pathways, synteny, phylogeny, biogeography and the prediction and prioritisation of drug target candidates. Bioinformatic pipelines implemented and established recently provide practical and efficient tools for the assembly and annotation of genomes of parasitic worms, and will be applicable to a wide range of other parasites and eukaryotic organisms. Future research will need to assess the utility of long-read sequence data sets for enhanced genomic assemblies, and develop improved algorithms for gene prediction and post-genomic analyses, to enable comprehensive systems biology explorations of parasitic organisms. PMID:26956711

  4. Swamp Works: A New Approach to Develop Space Mining and Resource Extraction Technologies at the National Aeronautics Space Administration (NASA) Kennedy Space Center (KSC)

    Science.gov (United States)

    Mueller, R. P.; Sibille, L.; Leucht, K.; Smith, J. D.; Townsend, I. I.; Nick, A. J.; Schuler, J. M.

    2015-01-01

    The first steps for In Situ Resource Utilization (ISRU) on target bodies such as the Moon, Mars and Near Earth Asteroids (NEA), and even comets, involve the same sequence of steps as in the terrestrial mining of resources. First exploration including prospecting must occur, and then the resource must be acquired through excavation methods if it is of value. Subsequently a load, haul and dump sequence of events occurs, followed by processing of the resource in an ISRU plant, to produce useful commodities. While these technologies and related supporting operations are mature in terrestrial applications, they will be different in space since the environment and indigenous materials are different than on Earth. In addition, the equipment must be highly automated, since for the majority of the production cycle time, there will be no humans present to assist or intervene. This space mining equipment must withstand a harsh environment which includes vacuum, radical temperature swing cycles, highly abrasive lofted dust, electrostatic effects, van der Waals forces effects, galactic cosmic radiation, solar particle events, high thermal gradients when spanning sunlight terminators, steep slopes into craters / lava tubes and cryogenic temperatures as low as 40 K in permanently shadowed regions. In addition the equipment must be tele-operated from Earth or a local base where the crew is sheltered. If the tele-operation occurs from Earth then significant communications latency effects mandate the use of autonomous control systems in the mining equipment. While this is an extremely challenging engineering design scenario, it is also an opportunity, since the technologies developed in this endeavor could be used in the next generations of terrestrial mining equipment, in order to mine deeper, safer, more economical and with a higher degree of flexibility. New space technologies could precipitate new mining solutions here on Earth. The NASA KSC Swamp Works is an innovation

  5. Research on Learner-Centered of Online Course Resource Construction%以学习者为中心的网络课程资源建设研究

    Institute of Scientific and Technical Information of China (English)

    樊志平

    2014-01-01

    网络课程资源作为信息技术与教育教学深度融合的产物,是教育信息化建设核心内容之一。网络课程资源建设如何体现以学习者为中心,满足每个学习者个性化的需求是当前网络课程资源建设研究的重点。本文以高校网络精品课程建设为例,分析了当前网络课程资源建设存在的一些问题,并提出了解决这些问题的方法,探讨了网络课程资源的建设的途径与建设方案。%As a depth integrated product of information technology and teaching, online course resources is the core content of education, information technology. How to embody learner-centered to meet the needs of individual learners are the focus of online course resources Construction, In this paper, the university elaborate course construction as an example, some of the cur-rent problems existing in online course resources Construction is analyzed, solutions to these problems are proposed, and the idea of building and construction of online course resources are explored.

  6. 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.

  7. JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility

    Directory of Open Access Journals (Sweden)

    Jaschob Daniel

    2012-07-01

    Full Text Available Abstract Background Laboratories engaged in computational biology or bioinformatics frequently need to run lengthy, multistep, and user-driven computational jobs. Each job can tie up a computer for a few minutes to several days, and many laboratories lack the expertise or resources to build and maintain a dedicated computer cluster. Results JobCenter is a client–server application and framework for job management and distributed job execution. The client and server components are both written in Java and are cross-platform and relatively easy to install. All communication with the server is client-driven, which allows worker nodes to run anywhere (even behind external firewalls or “in the cloud” and provides inherent load balancing. Adding a worker node to the worker pool is as simple as dropping the JobCenter client files onto any computer and performing basic configuration, which provides tremendous ease-of-use, flexibility, and limitless horizontal scalability. Each worker installation may be independently configured, including the types of jobs it is able to run. Executed jobs may be written in any language and may include multistep workflows. Conclusions JobCenter is a versatile and scalable distributed job management system that allows laboratories to very efficiently distribute all computational work among available resources. JobCenter is freely available at http://code.google.com/p/jobcenter/.

  8. Teacher Collaboration in a Public School to Set up Language Resource Centers: Portraying Advantages, Benefits, and Challenges Trabajo cooperativo de profesores de un colegio público para crear centros de recursos de lenguas: retrato de sus ventajas, beneficios y desafíos

    OpenAIRE

    Javier Augusto Rojas Serrano

    2008-01-01

    In the present article, the author attempts to describe the benefits, challenges, advantages and disadvantages experienced by teachers in a public school when working collaboratively to implement a language resource center in their institution. Taking as a point of departure the development of a proposal to implement the resource center in their school, some teachers engaged in group work in order to attain the different objectives that were stated at the beginning of the process, thus encoun...

  9. 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

  10. 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

  11. 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…

  12. PayDIBI: Pay-as-you-go data integration for bioinformatics

    NARCIS (Netherlands)

    Wanders, B.

    2012-01-01

    Background: Scientific research in bio-informatics is often data-driven and supported by biolog- ical databases. In a growing number of research projects, researchers like to ask questions that require the combination of information from more than one database. Most bio-informatics papers do not det

  13. 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…

  14. 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…

  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. 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…

  17. 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…

  18. 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...

  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. 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…

  1. 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…

  2. 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 ...

  3. The S-Star Trial Bioinformatics Course: An On-line Learning Success

    Science.gov (United States)

    Lim, Yun Ping; Hoog, Jan-Olov; Gardner, Phyllis; Ranganathan, Shoba; Andersson, Siv; Subbiah, Subramanian; Tan, Tin Wee; Hide, Winston; Weiss, Anthony S.

    2003-01-01

    The S-Star Trial Bioinformatics on-line course (www.s-star.org) is a global experiment in bioinformatics distance education. Six universities from five continents have participated in this project. One hundred and fifty students participated in the first trial course of which 96 followed through the entire course and 70 fulfilled the overall…

  4. Using the Tools and Resources of the RCSB Protein Data Bank.

    Science.gov (United States)

    Costanzo, Luigi Di; Ghosh, Sutapa; Zardecki, Christine; Burley, Stephen K

    2016-01-01

    The Protein Data Bank (PDB) archive is the worldwide repository of experimentally determined three-dimensional structures of large biological molecules found in all three kingdoms of life. Atomic-level structures of these proteins, nucleic acids, and complex assemblies thereof are central to research and education in molecular, cellular, and organismal biology, biochemistry, biophysics, materials science, bioengineering, ecology, and medicine. Several types of information are associated with each PDB archival entry, including atomic coordinates, primary experimental data, polymer sequence(s), and summary metadata. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves as the U.S. data center for the PDB, distributing archival data and supporting both simple and complex queries that return results. These data can be freely downloaded, analyzed, and visualized using RCSB PDB tools and resources to gain a deeper understanding of fundamental biological processes, molecular evolution, human health and disease, and drug discovery. © 2016 by John Wiley & Sons, Inc. PMID:27603019

  5. 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.

  6. 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.

  7. NMR structure improvement: A structural bioinformatics & visualization approach

    Science.gov (United States)

    Block, Jeremy N.

    The overall goal of this project is to enhance the physical accuracy of individual models in macromolecular NMR (Nuclear Magnetic Resonance) structures and the realism of variation within NMR ensembles of models, while improving agreement with the experimental data. A secondary overall goal is to combine synergistically the best aspects of NMR and crystallographic methodologies to better illuminate the underlying joint molecular reality. This is accomplished by using the powerful method of all-atom contact analysis (describing detailed sterics between atoms, including hydrogens); new graphical representations and interactive tools in 3D and virtual reality; and structural bioinformatics approaches to the expanded and enhanced data now available. The resulting better descriptions of macromolecular structure and its dynamic variation enhances the effectiveness of the many biomedical applications that depend on detailed molecular structure, such as mutational analysis, homology modeling, molecular simulations, protein design, and drug design.

  8. Integrative content-driven concepts for bioinformatics ``beyond the cell"

    Indian Academy of Sciences (India)

    Edgar Wingender; Torsten Crass; Jennifer D Hogan; Alexander E Kel; Olga V Kel-Margoulis; Anatolij P Potapov

    2007-01-01

    Bioinformatics has delivered great contributions to genome and genomics research, without which the world-wide success of this and other global (‘omics’) approaches would not have been possible. More recently, it has developed further towards the analysis of different kinds of networks thus laying the foundation for comprehensive description, analysis and manipulation of whole living systems in modern ``systems biology”. The next step which is necessary for developing a systems biology that deals with systemic phenomena is to expand the existing and develop new methodologies that are appropriate to characterize intercellular processes and interactions without omitting the causal underlying molecular mechanisms. Modelling the processes on the different levels of complexity involved requires a comprehensive integration of information on gene regulatory events, signal transduction pathways, protein interaction and metabolic networks as well as cellular functions in the respective tissues/organs.

  9. Bioinformatics in crosslinking chemistry of collagen with selective cross linkers

    Directory of Open Access Journals (Sweden)

    Gopal Ramesh

    2011-10-01

    Full Text Available Abstract Background Identifying the molecular interactions using bioinformatics tools before venturing into wet lab studies saves the energy and time considerably. The present study summarizes, molecular interactions and binding energy calculations made for major structural protein, collagen of Type I and Type III with the chosen cross-linkers, namely, coenzyme Q10, dopaquinone, embelin, embelin complex-1 & 2, idebenone, 5-O-methyl embelin, potassium embelate and vilangin. Results Molecular descriptive analyses suggest, dopaquinone, embelin, idebenone, 5-O-methyl embelin, and potassium embelate display nil violations. And results of docking analyses revealed, best affinity for Type I (- 4.74 kcal/mol and type III (-4.94 kcal/mol collagen was with dopaquinone. Conclusions Among the selected cross-linkers, dopaquinone, embelin, potassium embelate and 5-O-methyl embelin were the suitable cross-linkers for both Type I and Type III collagen and stabilizes the collagen at the expected level.

  10. Study on current situation of nursing human resources in community health service centers of Kunming City%昆明市社区卫生服务中心护理人力资源现状调查

    Institute of Scientific and Technical Information of China (English)

    卢蓉; 姜润生; 黄丽; 徐正英; 沈海文; 张杪

    2013-01-01

    目的 调查昆明市社区卫生服务中心护理人力资源现状.方法 采用自设问卷对昆明市11所社区卫生服务中心的109名社区护士进行调查.结果 社区护理队伍结构不合理,社区护士绩效考核体系不健全,缺乏科学有效的激励措施.结论应重视社区护理,调整队伍结构,建立健全管理体质,加快人才培养步伐.%Objective To investigate the current situation of nursing human resources of community health service centers of Kunming city.Methods A self-designed questionnaire was performed among 109 nurses of 11 community health services centers in Kunming.Results Structure of community nursing team was found unreasonable and the management system of human resources was not well organized.The scientific and effective intentive measures was lack.Conclusion It is suggested to pay more attention to the community nursing services in order to adjust the structure of community nursing team,pefect the management system and speed up the pace of personnel training.

  11. Hydroxysteroid dehydrogenases (HSDs) in bacteria: a bioinformatic perspective.

    Science.gov (United States)

    Kisiela, Michael; Skarka, Adam; Ebert, Bettina; Maser, Edmund

    2012-03-01

    Steroidal compounds including cholesterol, bile acids and steroid hormones play a central role in various physiological processes such as cell signaling, growth, reproduction, and energy homeostasis. Hydroxysteroid dehydrogenases (HSDs), which belong to the superfamily of short-chain dehydrogenases/reductases (SDR) or aldo-keto reductases (AKR), are important enzymes involved in the steroid hormone metabolism. HSDs function as an enzymatic switch that controls the access of receptor-active steroids to nuclear hormone receptors and thereby mediate a fine-tuning of the steroid response. The aim of this study was the identification of classified functional HSDs and the bioinformatic annotation of these proteins in all complete sequenced bacterial genomes followed by a phylogenetic analysis. For the bioinformatic annotation we constructed specific hidden Markov models in an iterative approach to provide a reliable identification for the specific catalytic groups of HSDs. Here, we show a detailed phylogenetic analysis of 3α-, 7α-, 12α-HSDs and two further functional related enzymes (3-ketosteroid-Δ(1)-dehydrogenase, 3-ketosteroid-Δ(4)(5α)-dehydrogenase) from the superfamily of SDRs. For some bacteria that have been previously reported to posses a specific HSD activity, we could annotate the corresponding HSD protein. The dominating phyla that were identified to express HSDs were that of Actinobacteria, Proteobacteria, and Firmicutes. Moreover, some evolutionarily more ancient microorganisms (e.g., Cyanobacteria and Euryachaeota) were found as well. A large number of HSD-expressing bacteria constitute the normal human gastro-intestinal flora. Another group of bacteria were originally isolated from natural habitats like seawater, soil, marine and permafrost sediments. These bacteria include polycyclic aromatic hydrocarbons-degrading species such as Pseudomonas, Burkholderia and Rhodococcus. In conclusion, HSDs are found in a wide variety of microorganisms including

  12. 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. PMID:26358759

  13. 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...

  14. Alaska Science Center: Providing Timely, Relevant, and Impartial Study of the Landscape, Natural Resources, and Natural Hazards for Alaska and Our Nation

    Science.gov (United States)

    USGS Alaska Science Center

    2007-01-01

    The U.S. Geological Survey (USGS), the Nation's largest water, earth, and biological science and civilian mapping agency, has studied the natural features of Alaska since its earliest geologic expeditions in the 1800s. The USGS Alaska Science Center (ASC), with headquarters in Anchorage, Alaska, studies the complex natural science phenomena of Alaska to provide scientific products and results to a wide variety of partners. The complexity of Alaska's unique landscapes and ecosystems requires USGS expertise from many science disciplines to conduct thorough, integrated research.

  15. "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. PMID:26583922

  16. VectorBase

    Data.gov (United States)

    U.S. Department of Health & Human Services — VectorBase is a Bioinformatics Resource Center for invertebrate vectors. It is one of four Bioinformatics Resource Centers funded by NIAID to provide web-based...

  17. Bioinformatic identification of microRNAs and their target genes from Solanum tuberosum expressed sequence tags

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene post-transcriptional expression in plants and animals. Low levels of some miRNAs and time- and tissue-specific expression patterns lead to the difficulty for experimental identification of miRNAs. Here we present a bioinformatic approach for expressed sequence tags (ESTs) prediction of novel miRNAs as well as their targets in Solanum tuberosum. We blasted the databases of S. Tuberosum ESTs to search for potential miRNAs, using previously known miRNA sequences from Arabidopsis, rice and other plant species. By analyzing parameters of plant precursors, including secondary structure, stem length and conservation of miRNAs, and following a variety of filtering criteria, a total of 22 potential miRNAs were detected. Using the newly identified miRNA sequences, we were able to further blast the S. Tuberosum mRNA database and detected 75 potential targets of miRNAs in S. Tuberosum. According to the mRNA annotations provided by the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/), most of the miRNA target genes were predicted to encode transcription factors that regulate cell growth and development, signaling, and metabolism.

  18. Entangled microwaves as a resource for entangling spatially separate solid-state qubits: Superconducting qubits, nitrogen-vacancy centers, and magnetic molecules

    Science.gov (United States)

    Gómez, Angela Viviana; Rodríguez, Ferney Javier; Quiroga, Luis; García-Ripoll, Juan José

    2016-06-01

    Quantum correlations present in a broadband two-line squeezed microwave state can induce entanglement in a spatially separated bipartite system consisting of either two single qubits or two-qubit ensembles. By using an appropriate master equation for a bipartite quantum system in contact with two separate but entangled baths, the generating entanglement process in spatially separated quantum systems is thoroughly characterized. Decoherence thermal effects on the entanglement transfer are also discussed. Our results provide evidence that this entanglement transfer by dissipation is feasible, yielding to a steady-state amount of entanglement in the bipartite quantum system which can be optimized for a wide range of realistic physical systems that include state-of-the-art experiments with nitrogen-vacancy centers in diamond, superconducting qubits, or even magnetic molecules embedded in a crystalline matrix.

  19. Neurogenomics: An opportunity to integrate neuroscience, genomics and bioinformatics research in Africa

    Directory of Open Access Journals (Sweden)

    Thomas K. Karikari

    2015-06-01

    Full Text Available Modern genomic approaches have made enormous contributions to improving our understanding of the function, development and evolution of the nervous system, and the diversity within and between species. However, most of these research advances have been recorded in countries with advanced scientific resources and funding support systems. On the contrary, little is known about, for example, the possible interplay between different genes, non-coding elements and environmental factors in modulating neurological diseases among populations in low-income countries, including many African countries. The unique ancestry of African populations suggests that improved inclusion of these populations in neuroscience-related genomic studies would significantly help to identify novel factors that might shape the future of neuroscience research and neurological healthcare. This perspective is strongly supported by the recent identification that diseased individuals and their kindred from specific sub-Saharan African populations lack common neurological disease-associated genetic mutations. This indicates that there may be population-specific causes of neurological diseases, necessitating further investigations into the contribution of additional, presently-unknown genomic factors. Here, we discuss how the development of neurogenomics research in Africa would help to elucidate disease-related genomic variants, and also provide a good basis to develop more effective therapies. Furthermore, neurogenomics would harness African scientists' expertise in neuroscience, genomics and bioinformatics to extend our understanding of the neural basis of behaviour, development and evolution.

  20. Computing Resource Virtualization in Next Generation Data Center of Shen hua Group%计算资源虚拟化在神华集团新一代数据中心的应用实践

    Institute of Scientific and Technical Information of China (English)

    孟君; 张延生; 狄广义

    2014-01-01

    This article comprehensively combs, analyzes and proves existing outstanding issues of traditional data center in the as-pect of Computing Resource Arrangement, under the background of next generation of enterprise-level data center construction of Shenhua Group. It further inherits and improves the concept of computing resource pool with virtualization technology as the core, based on which it respectively plans, designs and constructs the basic operation platform based on VMware vSphere appli-cation resource pool and Oracle Exadata all-in-one machine database resource pool for more than 50 enterprise-level core busi-ness applications (ERP, CRM, SRM, etc.) of Shenhua Group. Operation practice proves that after the introduction of resource pool, Shenhua data center has achieved good performance in several aspects, such as server integration ratio, resource delivery mode, Five-high KPIs, framework flexibility, even in aspects like IT cost control and energy-saving and emission-reduction, which completely meets the design expectation. It not only provides robust support on reaching Shenhua strategic goal of Scien-tific Development, Re-engineering of Shenhua and Five-Year Economic Output Doubled; but also can be used as an important source of reference for large-scale enterprise information construction and better industry promotional value.%以神华集团新一代企业级数据中心建设为背景,全面梳理、分析和论证了传统数据中心在计算资源部署方面存在的突出问题,进一步继承并完善了以虚拟化技术为内核的计算资源池概念,并依此为基础,分别规划、设计和构建了基于VMware vSphere的应用资源池和基于Oracle Exadata一体机的数据库资源池,作为承载神华集团包括ERP、CRM、SRM等50多个企业级关键业务的基础运行平台。运营实践证明,引入计算资源池之后,集团数据中心在服务器整合比、资源交付模式、“五高”指标、架构

  1. Buying in to bioinformatics: an introduction to commercial sequence analysis software.

    Science.gov (United States)

    Smith, David Roy

    2015-07-01

    Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. PMID:25183247

  2. 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

  3. Human error and crew resource management failures in Naval aviation mishaps: a review of U.S. Naval Safety Center data, 1990-96.

    Science.gov (United States)

    Wiegmann, D A; Shappell, S A

    1999-12-01

    The present study examined the role of human error and crew-resource management (CRM) failures in U.S. Naval aviation mishaps. All tactical jet (TACAIR) and rotary wing Class A flight mishaps between fiscal years 1990-1996 were reviewed. Results indicated that over 75% of both TACAIR and rotary wing mishaps were attributable, at least in part, to some form of human error of which 70% were associated with aircrew human factors. Of these aircrew-related mishaps, approximately 56% involved at least one CRM failure. These percentages are very similar to those observed prior to the implementation of aircrew coordination training (ACT) in the fleet, suggesting that the initial benefits of the program have not persisted and that CRM failures continue to plague Naval aviation. Closer examination of these CRM-related mishaps suggest that the type of flight operations (preflight, routine, emergency) do play a role in the etiology of CRM failures. A larger percentage of CRM failures occurred during non-routine or extremis flight situations when TACAIR mishaps were considered. In contrast, a larger percentage of rotary wing CRM mishaps involved failures that occurred during routine flight operations. These findings illustrate the complex etiology of CRM failures within Naval aviation and support the need for ACT programs tailored to the unique problems faced by specific communities in the fleet. PMID:10596766

  4. Cancer bioinformatics: detection of chromatin states,SNP-containing motifs, and functional enrichment modules

    Institute of Scientific and Technical Information of China (English)

    Xiaobo Zhou

    2013-01-01

    In this editorial preface,I briefly review cancer bioinformatics and introduce the four articles in this special issue highlighting important applications of the field:detection of chromatin states; detection of SNP-containing motifs and association with transcription factor-binding sites; improvements in functional enrichment modules; and gene association studies on aging and cancer.We expect this issue to provide bioinformatics scientists,cancer biologists,and clinical doctors with a better understanding of how cancer bioinformatics can be used to identify candidate biomarkers and targets and to conduct functional analysis.

  5. Bioinformatics, the Clearing-House Mechanism and the Convention on Biological Diversity

    Directory of Open Access Journals (Sweden)

    Marcos R. Silva

    2004-01-01

    Full Text Available This paper will discuss the development and role of the Convention’s Clearing-House Mechanism (CHM, its synergies with the Biosafety Clearing-House (BCH, and its support for bioinformatic initiatives in light of the Convention’s programme areas and cross-cutting issues. Within this context, the paper will also examine the significance of bioinformatics in assisting Parties to implement obligations under the Convention and the role of the CHM in facilitating activities by Parties and Governments to exploit the benefits arising from the evolving bioinformatics global infrastructure.

  6. Cancer bioinformatics: detection of chromatin states, SNP-containing motifs, and functional enrichment modules

    Directory of Open Access Journals (Sweden)

    Xiaobo Zhou

    2013-04-01

    Full Text Available In this editorial preface, I briefly review cancer bioinformatics and introduce the four articles in this special issue highlighting important applications of the field: detection of chromatin states; detection of SNP-containing motifs and association with transcription factor-binding sites; improvements in functional enrichment modules; and gene association studies on aging and cancer. We expect this issue to provide bioinformatics scientists, cancer biologists, and clinical doctors with a better understanding of how cancer bioinformatics can be used to identify candidate biomarkers and targets and to conduct functional analysis.

  7. Tolerance and toxicity of neoadjuvant docetaxel, cisplatin and 5 fluorouracil regimen in technically unresectable oral cancer in resource limited rural based tertiary cancer center

    Directory of Open Access Journals (Sweden)

    V M Patil

    2014-01-01

    Full Text Available Background: Recent studies indicate neoadjuvant chemotherapy (NACT can result in R0 resection in a substantial proportion of patients with technically unresectable oral cavity cancers. However, data regarding the efficacy and safety of docetaxel, cisplatin and 5 fluorouracil (TPF NACT in our setting is lacking. The present audit was proposed to evaluate the toxicities encountered during administration of this regimen. It was hypothesized that TPF NACT would be considered feasible for routine administration if an average relative dose intensity (ARDI of ≥0.90 or more in at least 70% of the patients. Materials and Methods: Technically unresectable oral cancers with Eastern Cooperative Oncology Group PS 0-2, with biopsy proven squamous cell carcinoma underwent two cycles of NACT with TPF regimen. Toxicity and response rates were noted following the CTCAE 4.03 and RECIST criteria. Descriptive analysis of completion rates (completing 2 cycles of planned chemotherapy with ARDI of 0.85 or more, reason for delay, toxicity, and response are presented. Results: The NACT was completed by all patients. The number of subjects who completed all planned cycles of chemotherapy are with the ARDI of the delivered chemotherapy been equal to or >0.85 was 11 (91.67%. All toxicity inclusive Grade 3-5 toxicity was seen in 11 patients (91.67%. The response rate of chemotherapy was 83.33%. There were three complete response, seven partial response, and two stable disease seen post NACT in this study. Conclusion: Docetaxel, cisplatin and 5 fluorouracil regimen can be routinely administered at our center with the supportive care methods and precautionary methods used in our study.

  8. 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.

  9. Competing endogenous RNA and interactome bioinformatic analyses on human telomerase.

    Science.gov (United States)

    Arancio, Walter; Pizzolanti, Giuseppe; Genovese, Swonild Ilenia; Baiamonte, Concetta; Giordano, Carla

    2014-04-01

    We present a classic interactome bioinformatic analysis and a study on competing endogenous (ce) RNAs for hTERT. The hTERT gene codes for the catalytic subunit and limiting component of the human telomerase complex. Human telomerase reverse transcriptase (hTERT) is essential for the integrity of telomeres. Telomere dysfunctions have been widely reported to be involved in aging, cancer, and cellular senescence. The hTERT gene network has been analyzed using the BioGRID interaction database (http://thebiogrid.org/) and related analysis tools such as Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index) and GeneMANIA (http://genemania.org/). The network of interaction of hTERT transcripts has been further analyzed following the competing endogenous (ce) RNA hypotheses (messenger [m] RNAs cross-talk via micro [mi] RNAs) using the miRWalk database and tools (www.ma.uni-heidelberg.de/apps/zmf/mirwalk/). These analyses suggest a role for Akt, nuclear factor-κB (NF-κB), heat shock protein 90 (HSP90), p70/p80 autoantigen, 14-3-3 proteins, and dynein in telomere functions. Roles for histone acetylation/deacetylation and proteoglycan metabolism are also proposed. PMID:24713059

  10. 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. PMID:20658333

  11. Proteomic and Bioinformatics Analyses of Mouse Liver Microsomes

    Directory of Open Access Journals (Sweden)

    Fang Peng

    2012-01-01

    Full Text Available Microsomes are derived mostly from endoplasmic reticulum and are an ideal target to investigate compound metabolism, membrane-bound enzyme functions, lipid-protein interactions, and drug-drug interactions. To better understand the molecular mechanisms of the liver and its diseases, mouse liver microsomes were isolated and enriched with differential centrifugation and sucrose gradient centrifugation, and microsome membrane proteins were further extracted from isolated microsomal fractions by the carbonate method. The enriched microsome proteins were arrayed with two-dimensional gel electrophoresis (2DE and carbonate-extracted microsome membrane proteins with one-dimensional gel electrophoresis (1DE. A total of 183 2DE-arrayed proteins and 99 1DE-separated proteins were identified with tandem mass spectrometry. A total of 259 nonredundant microsomal proteins were obtained and represent the proteomic profile of mouse liver microsomes, including 62 definite microsome membrane proteins. The comprehensive bioinformatics analyses revealed the functional categories of those microsome proteins and provided clues into biological functions of the liver. The systematic analyses of the proteomic profile of mouse liver microsomes not only reveal essential, valuable information about the biological function of the liver, but they also provide important reference data to analyze liver disease-related microsome proteins for biomarker discovery and mechanism clarification of liver disease.

  12. Functional proteomics with new mass spectrometric and bioinformatics tools

    International Nuclear Information System (INIS)

    A comprehensive range of mass spectrometric tools is required to investigate todays life science applications and a strong focus is on addressing the needs of functional proteomics. Application examples are given showing the streamlined process of protein identification from low femtomole amounts of digests. Sample preparation is achieved with a convertible robot for automated 2D gel picking, and MALDI target dispensing. MALDI-TOF or ESI-MS subsequent to enzymatic digestion. A choice of mass spectrometers including Q-q-TOF with multipass capability, MALDI-MS/MS with unsegmented PSD, Ion Trap and FT-MS are discussed for their respective strengths and applications. Bioinformatics software that allows both database work and novel peptide mass spectra interpretation is reviewed. The automated database searching uses either entire digest LC-MSn ESI Ion Trap data or MALDI MS and MS/MS spectra. It is shown how post translational modifications are interactively uncovered and de-novo sequencing of peptides is facilitated

  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. Bioinformatic approaches reveal metagenomic characterization of soil microbial community.

    Science.gov (United States)

    Xu, Zhuofei; Hansen, Martin Asser; Hansen, Lars H; Jacquiod, Samuel; Sørensen, Søren J

    2014-01-01

    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. PMID:24691166

  15. Using Bioinformatic Approaches to Identify Pathways Targeted by Human Leukemogens

    Directory of Open Access Journals (Sweden)

    Luoping Zhang

    2012-07-01

    Full Text Available We have applied bioinformatic approaches to identify pathways common to chemical leukemogens and to determine whether leukemogens could be distinguished from non-leukemogenic carcinogens. From all known and probable carcinogens classified by IARC and NTP, we identified 35 carcinogens that were associated with leukemia risk in human studies and 16 non-leukemogenic carcinogens. Using data on gene/protein targets available in the Comparative Toxicogenomics Database (CTD for 29 of the leukemogens and 11 of the non-leukemogenic carcinogens, we analyzed for enrichment of all 250 human biochemical pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG database. The top pathways targeted by the leukemogens included metabolism of xenobiotics by cytochrome P450, glutathione metabolism, neurotrophin signaling pathway, apoptosis, MAPK signaling, Toll-like receptor signaling and various cancer pathways. The 29 leukemogens formed 18 distinct clusters comprising 1 to 3 chemicals that did not correlate with known mechanism of action or with structural similarity as determined by 2D Tanimoto coefficients in the PubChem database. Unsupervised clustering and one-class support vector machines, based on the pathway data, were unable to distinguish the 29 leukemogens from 11 non-leukemogenic known and probable IARC carcinogens. However, using two-class random forests to estimate leukemogen and non-leukemogen patterns, we estimated a 76% chance of distinguishing a random leukemogen/non-leukemogen pair from each other.

  16. 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.

  17. Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula

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    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.

  18. Whale song analyses using bioinformatics sequence analysis approaches

    Science.gov (United States)

    Chen, Yian A.; Almeida, Jonas S.; Chou, Lien-Siang

    2005-04-01

    Animal songs are frequently analyzed using discrete hierarchical units, such as units, themes and songs. Because animal songs and bio-sequences may be understood as analogous, bioinformatics analysis tools DNA/protein sequence alignment and alignment-free methods are proposed to quantify the theme similarities of the songs of false killer whales recorded off northeast Taiwan. The eighteen themes with discrete units that were identified in an earlier study [Y. A. Chen, masters thesis, University of Charleston, 2001] were compared quantitatively using several distance metrics. These metrics included the scores calculated using the Smith-Waterman algorithm with the repeated procedure; the standardized Euclidian distance and the angle metrics based on word frequencies. The theme classifications based on different metrics were summarized and compared in dendrograms using cluster analyses. The results agree with earlier classifications derived by human observation qualitatively. These methods further quantify the similarities among themes. These methods could be applied to the analyses of other animal songs on a larger scale. For instance, these techniques could be used to investigate song evolution and cultural transmission quantifying the dissimilarities of humpback whale songs across different seasons, years, populations, and geographic regions. [Work supported by SC Sea Grant, and Ilan County Government, Taiwan.

  19. Bioinformatic characterization of glycyl radical enzyme-associated bacterial microcompartments.

    Science.gov (United States)

    Zarzycki, Jan; Erbilgin, Onur; Kerfeld, Cheryl A

    2015-12-01

    Bacterial microcompartments (BMCs) are proteinaceous organelles encapsulating enzymes that catalyze sequential reactions of metabolic pathways. BMCs are phylogenetically widespread; however, only a few BMCs have been experimentally characterized. Among them are the carboxysomes and the propanediol- and ethanolamine-utilizing microcompartments, which play diverse metabolic and ecological roles. The substrate of a BMC is defined by its signature enzyme. In catabolic BMCs, this enzyme typically generates an aldehyde. Recently, it was shown that the most prevalent signature enzymes encoded by BMC loci are glycyl radical enzymes, yet little is known about the function of these BMCs. Here we characterize the glycyl radical enzyme-associated microcompartment (GRM) loci using a combination of bioinformatic analyses and active-site and structural modeling to show that the GRMs comprise five subtypes. We predict distinct functions for the GRMs, including the degradation of choline, propanediol, and fuculose phosphate. This is the first family of BMCs for which identification of the signature enzyme is insufficient for predicting function. The distinct GRM functions are also reflected in differences in shell composition and apparently different assembly pathways. The GRMs are the counterparts of the vitamin B12-dependent propanediol- and ethanolamine-utilizing BMCs, which are frequently associated with virulence. This study provides a comprehensive foundation for experimental investigations of the diverse roles of GRMs. Understanding this plasticity of function within a single BMC family, including characterization of differences in permeability and assembly, can inform approaches to BMC bioengineering and the design of therapeutics. PMID:26407889

  20. 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.