WorldWideScience

Sample records for bioinformatics knowledge environment

  1. A Virtual Bioinformatics Knowledge Environment for Early Cancer Detection

    Science.gov (United States)

    Crichton, Daniel; Srivastava, Sudhir; Johnsey, Donald

    2003-01-01

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

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

    DEFF Research Database (Denmark)

    Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer

    2016-01-01

    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....

  3. 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…

  4. PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.

    Science.gov (United States)

    Kanterakis, Alexandros; Kuiper, Joël; Potamias, George; Swertz, Morris A

    2015-01-01

    Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols. We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page. PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams. PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License.

  5. BioSmalltalk: a pure object system and library for bioinformatics.

    Science.gov (United States)

    Morales, Hernán F; Giovambattista, Guillermo

    2013-09-15

    We have developed BioSmalltalk, a new environment system for pure object-oriented bioinformatics programming. Adaptive end-user programming systems tend to become more important for discovering biological knowledge, as is demonstrated by the emergence of open-source programming toolkits for bioinformatics in the past years. Our software is intended to bridge the gap between bioscientists and rapid software prototyping while preserving the possibility of scaling to whole-system biology applications. BioSmalltalk performs better in terms of execution time and memory usage than Biopython and BioPerl for some classical situations. BioSmalltalk is cross-platform and freely available (MIT license) through the Google Project Hosting at http://code.google.com/p/biosmalltalk hernan.morales@gmail.com Supplementary data are available at Bioinformatics online.

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

    Science.gov (United States)

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

    2016-09-29

    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.

  7. "Broadband" Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP: Educational Model for Upliftment and Sustainable Development.

    Directory of Open Access Journals (Sweden)

    Emile R Chimusa

    2015-11-01

    Full Text Available 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.

  8. "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.

  9. Hermes: Seamless delivery of containerized bioinformatics workflows in hybrid cloud (HTC) environments

    Science.gov (United States)

    Kintsakis, Athanassios M.; Psomopoulos, Fotis E.; Symeonidis, Andreas L.; Mitkas, Pericles A.

    Hermes introduces a new "describe once, run anywhere" paradigm for the execution of bioinformatics workflows in hybrid cloud environments. It combines the traditional features of parallelization-enabled workflow management systems and of distributed computing platforms in a container-based approach. It offers seamless deployment, overcoming the burden of setting up and configuring the software and network requirements. Most importantly, Hermes fosters the reproducibility of scientific workflows by supporting standardization of the software execution environment, thus leading to consistent scientific workflow results and accelerating scientific output.

  10. Hermes: Seamless delivery of containerized bioinformatics workflows in hybrid cloud (HTC environments

    Directory of Open Access Journals (Sweden)

    Athanassios M. Kintsakis

    2017-01-01

    Full Text Available Hermes introduces a new “describe once, run anywhere” paradigm for the execution of bioinformatics workflows in hybrid cloud environments. It combines the traditional features of parallelization-enabled workflow management systems and of distributed computing platforms in a container-based approach. It offers seamless deployment, overcoming the burden of setting up and configuring the software and network requirements. Most importantly, Hermes fosters the reproducibility of scientific workflows by supporting standardization of the software execution environment, thus leading to consistent scientific workflow results and accelerating scientific output.

  11. Planning bioinformatics workflows using an expert system

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T.

    2017-01-01

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

  12. Deep learning in bioinformatics.

    Science.gov (United States)

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2017-09-01

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

  13. Rising Strengths Hong Kong SAR in Bioinformatics.

    Science.gov (United States)

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

    2017-06-01

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

  14. Computational biology and bioinformatics in Nigeria.

    Science.gov (United States)

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

    2014-04-01

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

  15. 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.

  16. 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.

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

    Science.gov (United States)

    Mulder, Nicola; Schwartz, Russell; Brazas, Michelle D; Brooksbank, Cath; Gaeta, Bruno; Morgan, Sarah L; Pauley, Mark A; Rosenwald, Anne; Rustici, Gabriella; Sierk, Michael; Warnow, Tandy; Welch, Lonnie

    2018-02-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

  19. Crowdsourcing for bioinformatics.

    Science.gov (United States)

    Good, Benjamin M; Su, Andrew I

    2013-08-15

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

  20. Comprehensive decision tree models in bioinformatics.

    Directory of Open Access Journals (Sweden)

    Gregor Stiglic

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

  1. Comprehensive decision tree models in bioinformatics.

    Science.gov (United States)

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

    2012-01-01

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

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

    OpenAIRE

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

    2016-01-01

    textabstractMSeqDR 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 ...

  3. 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.

  4. When process mining meets bioinformatics

    NARCIS (Netherlands)

    Jagadeesh Chandra Bose, R.P.; Aalst, van der W.M.P.; Nurcan, S.

    2011-01-01

    Process mining techniques can be used to extract non-trivial process related knowledge and thus generate interesting insights from event logs. Similarly, bioinformatics aims at increasing the understanding of biological processes through the analysis of information associated with biological

  5. 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.

  6. A P2P Framework for Developing Bioinformatics Applications in Dynamic Cloud Environments

    Directory of Open Access Journals (Sweden)

    Chun-Hung Richard Lin

    2013-01-01

    Full Text Available Bioinformatics is advanced from in-house computing infrastructure to cloud computing for tackling the vast quantity of biological data. This advance enables large number of collaborative researches to share their works around the world. In view of that, retrieving biological data over the internet becomes more and more difficult because of the explosive growth and frequent changes. Various efforts have been made to address the problems of data discovery and delivery in the cloud framework, but most of them suffer the hindrance by a MapReduce master server to track all available data. In this paper, we propose an alternative approach, called PRKad, which exploits a Peer-to-Peer (P2P model to achieve efficient data discovery and delivery. PRKad is a Kademlia-based implementation with Round-Trip-Time (RTT as the associated key, and it locates data according to Distributed Hash Table (DHT and XOR metric. The simulation results exhibit that our PRKad has the low link latency to retrieve data. As an interdisciplinary application of P2P computing for bioinformatics, PRKad also provides good scalability for servicing a greater number of users in dynamic cloud environments.

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

    Science.gov (United States)

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

    2015-06-01

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

  8. 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...

  9. 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…

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

    Science.gov (United States)

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

    2016-02-01

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

  11. Combining medical informatics and bioinformatics toward tools for personalized medicine.

    Science.gov (United States)

    Sarachan, B D; Simmons, M K; Subramanian, P; Temkin, J M

    2003-01-01

    Key bioinformatics and medical informatics research areas need to be identified to advance knowledge and understanding of disease risk factors and molecular disease pathology in the 21 st century toward new diagnoses, prognoses, and treatments. Three high-impact informatics areas are identified: predictive medicine (to identify significant correlations within clinical data using statistical and artificial intelligence methods), along with pathway informatics and cellular simulations (that combine biological knowledge with advanced informatics to elucidate molecular disease pathology). Initial predictive models have been developed for a pilot study in Huntington's disease. An initial bioinformatics platform has been developed for the reconstruction and analysis of pathways, and work has begun on pathway simulation. A bioinformatics research program has been established at GE Global Research Center as an important technology toward next generation medical diagnostics. We anticipate that 21 st century medical research will be a combination of informatics tools with traditional biology wet lab research, and that this will translate to increased use of informatics techniques in the clinic.

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

    Science.gov (United States)

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

    2012-07-19

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

  13. Application of Bioinformatics in Chronobiology Research

    Directory of Open Access Journals (Sweden)

    Robson da Silva Lopes

    2013-01-01

    Full Text Available Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through “omics” projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research.

  14. 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...

  15. 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…

  16. Towards a People-Oriented Knowledge Management Environment

    NARCIS (Netherlands)

    Dignum, V.

    2000-01-01

    In this preliminary report we present ongoing research on intelligent knowledge management (KM) environments supporting communication in a virtual environment. An agent community handles the interaction between knowledge sources of different degrees of formality and knowledge users and

  17. Bioinformatics education dissemination with an evolutionary problem solving perspective.

    Science.gov (United States)

    Jungck, John R; Donovan, Samuel S; Weisstein, Anton E; Khiripet, Noppadon; Everse, Stephen J

    2010-11-01

    Bioinformatics is central to biology education in the 21st century. With the generation of terabytes of data per day, the application of computer-based tools to stored and distributed data is fundamentally changing research and its application to problems in medicine, agriculture, conservation and forensics. In light of this 'information revolution,' undergraduate biology curricula must be redesigned to prepare the next generation of informed citizens as well as those who will pursue careers in the life sciences. The BEDROCK initiative (Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting together) has fostered an international community of bioinformatics educators. The initiative's goals are to: (i) Identify and support faculty who can take leadership roles in bioinformatics education; (ii) Highlight and distribute innovative approaches to incorporating evolutionary bioinformatics data and techniques throughout undergraduate education; (iii) Establish mechanisms for the broad dissemination of bioinformatics resource materials and teaching models; (iv) Emphasize phylogenetic thinking and problem solving; and (v) Develop and publish new software tools to help students develop and test evolutionary hypotheses. Since 2002, BEDROCK has offered more than 50 faculty workshops around the world, published many resources and supported an environment for developing and sharing bioinformatics education approaches. The BEDROCK initiative builds on the established pedagogical philosophy and academic community of the BioQUEST Curriculum Consortium to assemble the diverse intellectual and human resources required to sustain an international reform effort in undergraduate bioinformatics education.

  18. GeneDig: a web application for accessing genomic and bioinformatics knowledge.

    Science.gov (United States)

    Suciu, Radu M; Aydin, Emir; Chen, Brian E

    2015-02-28

    With the exponential increase and widespread availability of genomic, transcriptomic, and proteomic data, accessing these '-omics' data is becoming increasingly difficult. The current resources for accessing and analyzing these data have been created to perform highly specific functions intended for specialists, and thus typically emphasize functionality over user experience. We have developed a web-based application, GeneDig.org, that allows any general user access to genomic information with ease and efficiency. GeneDig allows for searching and browsing genes and genomes, while a dynamic navigator displays genomic, RNA, and protein information simultaneously for co-navigation. We demonstrate that our application allows more than five times faster and efficient access to genomic information than any currently available methods. We have developed GeneDig as a platform for bioinformatics integration focused on usability as its central design. This platform will introduce genomic navigation to broader audiences while aiding the bioinformatics analyses performed in everyday biology research.

  19. 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.

    2016-01-01

    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,…

  20. 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.

  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. A bioinformatics potpourri.

    Science.gov (United States)

    Schönbach, Christian; Li, Jinyan; Ma, Lan; Horton, Paul; Sjaugi, Muhammad Farhan; Ranganathan, Shoba

    2018-01-19

    The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.

  3. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

    OpenAIRE

    Bultet, Lisandra Aguilar; Aguilar Rodriguez, Jose; Ahrens, Christian H; Ahrne, Erik Lennart; Ai, Ni; Aimo, Lucila; Akalin, Altuna; Aleksiev, Tyanko; Alocci, Davide; Altenhoff, Adrian; Alves, Isabel; Ambrosini, Giovanna; Pedone, Pascale Anderle; Angelina, Paolo; Anisimova, Maria

    2016-01-01

    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB'...

  4. BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

    Science.gov (United States)

    Moreews, François; Sallou, Olivier; Ménager, Hervé; Le Bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

    2015-01-01

    Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

  5. Patterns of Knowledge Sharing and Knowledge Creation in New Information Environments

    DEFF Research Database (Denmark)

    Nielsen, Jørgen Lerche; Meyer, Kirsten

    2006-01-01

    and creation processes. The aim is to obtain a deeper comprehension of which factors determine whether the use of information technology becomes a success or a failure in relation to knowledge sharing and creation. The paper is based on three previous studies investigating the use of information technology......Do the knowledge sharing and creation processes in collaborating groups benefit from the use of new information environments or are the environments rather inhibitive to the development of these processes? A number of different studies have shown quite varied results when it comes to appraising...... the importance and value of using new information technology in knowledge sharing and creation processes. In this paper we will try to unveil the patterns appearing in the use of new information environment and the users' understanding of the significance of using information technology in knowledge sharing...

  6. Bioinformatics process management: information flow via a computational journal

    Directory of Open Access Journals (Sweden)

    Lushington Gerald

    2007-12-01

    Full Text Available Abstract This paper presents the Bioinformatics Computational Journal (BCJ, a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.

  7. Data mining for bioinformatics applications

    CERN Document Server

    Zengyou, He

    2015-01-01

    Data Mining for Bioinformatics Applications provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems, including problem definition, data collection, data preprocessing, modeling, and validation. The text uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems, containing 45 bioinformatics problems that have been investigated in recent research. For each example, the entire data mining process is described, ranging from data preprocessing to modeling and result validation. Provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems Uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems Contains 45 bioinformatics problems that have been investigated in recent research.

  8. Home Environment Service Knowledge Management System

    DEFF Research Database (Denmark)

    Zhang, Jiang; Rossello Busquet, Ana; Soler, José

    2011-01-01

    This paper makes three contributions to assist households to control their home devices in an easy way and to simplify the software installation and configuration processes across multi-vendor environments. First, a Home Environment Service Knowledge Management System is proposed, which is based...... on the knowledge implemented by ontology and uses the inference function of reasoner to find out available software services according to household requests. Second, this paper provides a concrete methodology to exploit and acquire conflict-free information from ontology knowledge by using a reasoner. At last......, a strategy of calculating the sequence of service dependency hierarchy is proposed by this paper....

  9. Software support environment design knowledge capture

    Science.gov (United States)

    Dollman, Tom

    1990-01-01

    The objective of this task is to assess the potential for using the software support environment (SSE) workstations and associated software for design knowledge capture (DKC) tasks. This assessment will include the identification of required capabilities for DKC and hardware/software modifications needed to support DKC. Several approaches to achieving this objective are discussed and interim results are provided: (1) research into the problem of knowledge engineering in a traditional computer-aided software engineering (CASE) environment, like the SSE; (2) research into the problem of applying SSE CASE tools to develop knowledge based systems; and (3) direct utilization of SSE workstations to support a DKC activity.

  10. Bringing Web 2.0 to bioinformatics.

    Science.gov (United States)

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

    2009-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ting Dong

    2017-09-01

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

  12. New Link in Bioinformatics Services Value Chain: Position, Organization and Business Model

    Directory of Open Access Journals (Sweden)

    Mladen Čudanov

    2012-11-01

    Full Text Available This paper presents development in the bioinformatics services industry value chain, based on cloud computing paradigm. As genome sequencing costs per Megabase exponentially drop, industry needs to adopt. Paper has two parts: theoretical analysis and practical example of Seven Bridges Genomics Company. We are focused on explaining organizational, business and financial aspects of new business model in bioinformatics services, rather than technical side of the problem. In the light of that we present twofold business model fit for core bioinformatics research and Information and Communication Technologie (ICT support in the new environment, with higher level of capital utilization and better resistance to business risks.

  13. Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial

    Directory of Open Access Journals (Sweden)

    Nicolas eServant

    2014-05-01

    Full Text Available Precision medicine (PM requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of i warranting the integration and the traceability of data, ii ensuring the correct processing and analyses of genomic data and iii applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application.

  14. Chapter 16: text mining for translational bioinformatics.

    Science.gov (United States)

    Cohen, K Bretonnel; Hunter, Lawrence E

    2013-04-01

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

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

    Science.gov (United States)

    Vetrivel, Umashankar; Pilla, Kalabharath

    2008-01-01

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

  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. 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/.

  18. Corporate knowledge repository: Adopting academic LMS into corporate environment

    Science.gov (United States)

    Bakar, Muhamad Shahbani Abu; Jalil, Dzulkafli

    2017-10-01

    The growth of Knowledge Economy has transformed human capital to be the vital asset in business organization of the 21st century. Arguably, due to its white-collar nature, knowledge-based industry is more favorable than traditional manufacturing business. However, over dependency on human capital can also be a major challenge as any workers will inevitably leave the company or retire. This situation will possibly create knowledge gap that may impact business continuity of the enterprise. Knowledge retention in the corporate environment has been of many research interests. Learning Management System (LMS) refers to the system that provides the delivery, assessment and management tools for an organization to handle its knowledge repository. By using the aspirations of a proven LMS implemented in an academic environment, this paper proposes LMS model that can be used to enable peer-to-peer knowledge capture and sharing in the knowledge-based organization. Cloud Enterprise Resource Planning (ERP), referred to an ERP solution in the internet cloud environment was chosen as the domain knowledge. The complexity of the Cloud ERP business and its knowledge make it very vulnerable to the knowledge retention problem. This paper discusses how the company's essential knowledge can be retained using the LMS system derived from academic environment into the corporate model.

  19. The Bioinformatics of Integrative Medical Insights: Proposals for an International Psycho-Social and Cultural Bioinformatics Project

    Directory of Open Access Journals (Sweden)

    Ernest Rossi

    2006-01-01

    Full Text Available We propose the formation of an International Psycho-Social and Cultural Bioinformatics Project (IPCBP to explore the research foundations of Integrative Medical Insights (IMI on all levels from the molecular-genomic to the psychological, cultural, social, and spiritual. Just as The Human Genome Project identified the molecular foundations of modern medicine with the new technology of sequencing DNA during the past decade, the IPCBP would extend and integrate this neuroscience knowledge base with the technology of gene expression via DNA/proteomic microarray research and brain imaging in development, stress, healing, rehabilitation, and the psychotherapeutic facilitation of existentional wellness. We anticipate that the IPCBP will require a unique international collaboration of, academic institutions, researchers, and clinical practioners for the creation of a new neuroscience of mind-body communication, brain plasticity, memory, learning, and creative processing during optimal experiential states of art, beauty, and truth. We illustrate this emerging integration of bioinformatics with medicine with a videotape of the classical 4-stage creative process in a neuroscience approach to psychotherapy.

  20. 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.

  1. p3d--Python module for structural bioinformatics.

    Science.gov (United States)

    Fufezan, Christian; Specht, Michael

    2009-08-21

    High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  2. Knowledge exchange between agents in real-time environments

    DEFF Research Database (Denmark)

    Frisvad, Jeppe Revall; Falster, Peter; Møller, Gert Lykke

    2005-01-01

    To obtain unpredictable social interaction between autonomous agents in real-time environments, we present a simple method for logic-based knowledge exchange. A method which is able to form new knowledge rather than do simple exchange of particular rules found in predetermined rule sets. The appl......To obtain unpredictable social interaction between autonomous agents in real-time environments, we present a simple method for logic-based knowledge exchange. A method which is able to form new knowledge rather than do simple exchange of particular rules found in predetermined rule sets...

  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. Accelerating knowledge discovery through community data sharing and integration.

    Science.gov (United States)

    Yip, Y L

    2009-01-01

    To summarize current excellent research in the field of bioinformatics. Synopsis of the articles selected for the IMIA Yearbook 2009. The selection process for this yearbook's section on Bioinformatics results in six excellent articles highlighting several important trends First, it can be noted that Semantic Web technology continues to play an important role in heterogeneous data integration. Novel applications also put more emphasis on its ability to make logical inferences leading to new insights and discoveries. Second, translational research, due to its complex nature, increasingly relies on collective intelligence made available through the adoption of community-defined protocols or software architectures for secure data annotation, sharing and analysis. Advances in systems biology, bio-ontologies and text-ming can also be noted. Current biomedical research gradually evolves towards an environment characterized by intensive collaboration and more sophisticated knowledge processing activities. Enabling technologies, either Semantic Web or other solutions, are expected to play an increasingly important role in generating new knowledge in the foreseeable future.

  5. Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology

    Directory of Open Access Journals (Sweden)

    Fernando González-Nilo

    2011-01-01

    Full Text Available After the progress made during the genomics era, bioinformatics was tasked with supporting the flow of information generated by nanobiotechnology efforts. This challenge requires adapting classical bioinformatic and computational chemistry tools to store, standardize, analyze, and visualize nanobiotechnological information. Thus, old and new bioinformatic and computational chemistry tools have been merged into a new sub-discipline: nanoinformatics. This review takes a second look at the development of this new and exciting area as seen from the perspective of the evolution of nanobiotechnology applied to the life sciences. The knowledge obtained at the nano-scale level implies answers to new questions and the development of new concepts in different fields. The rapid convergence of technologies around nanobiotechnologies has spun off collaborative networks and web platforms created for sharing and discussing the knowledge generated in nanobiotechnology. The implementation of new database schemes suitable for storage, processing and integrating physical, chemical, and biological properties of nanoparticles will be a key element in achieving the promises in this convergent field. In this work, we will review some applications of nanobiotechnology to life sciences in generating new requirements for diverse scientific fields, such as bioinformatics and computational chemistry.

  6. Emerging strengths in Asia Pacific bioinformatics.

    Science.gov (United States)

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

    2008-12-12

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

  7. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.

    Science.gov (United States)

    Connor, Thomas R; Loman, Nicholas J; Thompson, Simon; Smith, Andy; Southgate, Joel; Poplawski, Radoslaw; Bull, Matthew J; Richardson, Emily; Ismail, Matthew; Thompson, Simon Elwood-; Kitchen, Christine; Guest, Martyn; Bakke, Marius; Sheppard, Samuel K; Pallen, Mark J

    2016-09-01

    The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.

  8. Biggest challenges in bioinformatics.

    Science.gov (United States)

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

    2013-04-01

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

  9. Biggest challenges in bioinformatics

    OpenAIRE

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

    2013-01-01

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

  10. 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.

  11. p3d – Python module for structural bioinformatics

    Directory of Open Access Journals (Sweden)

    Fufezan Christian

    2009-08-01

    Full Text Available Abstract Background High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files. p3d's strength arises from the combination of a very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP tree, b set theory and c functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  12. Preface to Introduction to Structural Bioinformatics

    NARCIS (Netherlands)

    Feenstra, K. Anton; Abeln, Sanne

    2018-01-01

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

  13. COMPARISON OF POPULAR BIOINFORMATICS DATABASES

    OpenAIRE

    Abdulganiyu Abdu Yusuf; Zahraddeen Sufyanu; Kabir Yusuf Mamman; Abubakar Umar Suleiman

    2016-01-01

    Bioinformatics is the application of computational tools to capture and interpret biological data. It has wide applications in drug development, crop improvement, agricultural biotechnology and forensic DNA analysis. There are various databases available to researchers in bioinformatics. These databases are customized for a specific need and are ranged in size, scope, and purpose. The main drawbacks of bioinformatics databases include redundant information, constant change, data spread over m...

  14. MACBenAbim: A Multi-platform Mobile Application for searching keyterms in Computational Biology and Bioinformatics.

    Science.gov (United States)

    Oluwagbemi, Olugbenga O; Adewumi, Adewole; Esuruoso, Abimbola

    2012-01-01

    Computational biology and bioinformatics are gradually gaining grounds in Africa and other developing nations of the world. However, in these countries, some of the challenges of computational biology and bioinformatics education are inadequate infrastructures, and lack of readily-available complementary and motivational tools to support learning as well as research. This has lowered the morale of many promising undergraduates, postgraduates and researchers from aspiring to undertake future study in these fields. In this paper, we developed and described MACBenAbim (Multi-platform Mobile Application for Computational Biology and Bioinformatics), a flexible user-friendly tool to search for, define and describe the meanings of keyterms in computational biology and bioinformatics, thus expanding the frontiers of knowledge of the users. This tool also has the capability of achieving visualization of results on a mobile multi-platform context. MACBenAbim is available from the authors for non-commercial purposes.

  15. Establishing bioinformatics research in the Asia Pacific

    OpenAIRE

    Ranganathan, Shoba; Tammi, Martti; 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-...

  16. Generalized Centroid Estimators in Bioinformatics

    Science.gov (United States)

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

    2011-01-01

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

  17. Introduction to bioinformatics.

    Science.gov (United States)

    Can, Tolga

    2014-01-01

    Bioinformatics is an interdisciplinary field mainly involving molecular biology and genetics, computer science, mathematics, and statistics. Data intensive, large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution usually involves the following steps: Collect statistics from biological data. Build a computational model. Solve a computational modeling problem. Test and evaluate a computational algorithm. This chapter gives a brief introduction to bioinformatics by first providing an introduction to biological terminology and then discussing some classical bioinformatics problems organized by the types of data sources. Sequence analysis is the analysis of DNA and protein sequences for clues regarding function and includes subproblems such as identification of homologs, multiple sequence alignment, searching sequence patterns, and evolutionary analyses. Protein structures are three-dimensional data and the associated problems are structure prediction (secondary and tertiary), analysis of protein structures for clues regarding function, and structural alignment. Gene expression data is usually represented as matrices and analysis of microarray data mostly involves statistics analysis, classification, and clustering approaches. Biological networks such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks are usually modeled as graphs and graph theoretic approaches are used to solve associated problems such as construction and analysis of large-scale networks.

  18. BioShaDock: a community driven bioinformatics shared Docker-based tools registry [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    François Moreews

    2015-12-01

    Full Text Available Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

  19. Bioinformatics clouds for big data manipulation.

    Science.gov (United States)

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

    2012-11-28

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

  20. Education for Knowledge Society: Learning and Scientific Innovation Environment

    OpenAIRE

    Alexander O. Karpov

    2017-01-01

    Cognitive-active learning research-type environment is the fundamental component of the education system for the knowledge society. The purpose of the research is the development of conceptual bases and a constructional model of a cognitively active learning environment that stimulates the creation of new knowledge and its socio-economic application. Research methods include epistemic-didactic analysis of empirical material collected as a result of the study of research environments at school...

  1. Modern bioinformatics meets traditional Chinese medicine.

    Science.gov (United States)

    Gu, Peiqin; Chen, Huajun

    2014-11-01

    Traditional Chinese medicine (TCM) is gaining increasing attention with the emergence of integrative medicine and personalized medicine, characterized by pattern differentiation on individual variance and treatments based on natural herbal synergism. Investigating the effectiveness and safety of the potential mechanisms of TCM and the combination principles of drug therapies will bridge the cultural gap with Western medicine and improve the development of integrative medicine. Dealing with rapidly growing amounts of biomedical data and their heterogeneous nature are two important tasks among modern biomedical communities. Bioinformatics, as an emerging interdisciplinary field of computer science and biology, has become a useful tool for easing the data deluge pressure by automating the computation processes with informatics methods. Using these methods to retrieve, store and analyze the biomedical data can effectively reveal the associated knowledge hidden in the data, and thus promote the discovery of integrated information. Recently, these techniques of bioinformatics have been used for facilitating the interactional effects of both Western medicine and TCM. The analysis of TCM data using computational technologies provides biological evidence for the basic understanding of TCM mechanisms, safety and efficacy of TCM treatments. At the same time, the carrier and targets associated with TCM remedies can inspire the rethinking of modern drug development. This review summarizes the significant achievements of applying bioinformatics techniques to many aspects of the research in TCM, such as analysis of TCM-related '-omics' data and techniques for analyzing biological processes and pharmaceutical mechanisms of TCM, which have shown certain potential of bringing new thoughts to both sides. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2016-12-22

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

  3. Designing XML schemas for bioinformatics.

    Science.gov (United States)

    Bruhn, Russel Elton; Burton, Philip John

    2003-06-01

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

  4. Bioinformatics

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren

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

  5. 'Students-as-partners' scheme enhances postgraduate students' employability skills while addressing gaps in bioinformatics education.

    Science.gov (United States)

    Mello, Luciane V; Tregilgas, Luke; Cowley, Gwen; Gupta, Anshul; Makki, Fatima; Jhutty, Anjeet; Shanmugasundram, Achchuthan

    2017-01-01

    Teaching bioinformatics is a longstanding challenge for educators who need to demonstrate to students how skills developed in the classroom may be applied to real world research. This study employed an action research methodology which utilised student-staff partnership and peer-learning. It was centred on the experiences of peer-facilitators, students who had previously taken a postgraduate bioinformatics module, and had applied knowledge and skills gained from it to their own research. It aimed to demonstrate to peer-receivers, current students, how bioinformatics could be used in their own research while developing peer-facilitators' teaching and mentoring skills. This student-centred approach was well received by the peer-receivers, who claimed to have gained improved understanding of bioinformatics and its relevance to research. Equally, peer-facilitators also developed a better understanding of the subject and appreciated that the activity was a rare and invaluable opportunity to develop their teaching and mentoring skills, enhancing their employability.

  6. 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.

  7. 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.

  8. Interdisciplinary Introductory Course in Bioinformatics

    Science.gov (United States)

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

    2010-01-01

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

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

    Science.gov (United States)

    Fristensky, Brian

    2007-01-01

    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. PMID:17291351

  10. 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.

  11. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

    Science.gov (United States)

    Ibrahim, Bashar; Arkhipova, Ksenia; Andeweg, Arno C; Posada-Céspedes, Susana; Enault, François; Gruber, Arthur; Koonin, Eugene V; Kupczok, Anne; Lemey, Philippe; McHardy, Alice C; McMahon, Dino P; Pickett, Brett E; Robertson, David L; Scheuermann, Richard H; Zhernakova, Alexandra; Zwart, Mark P; Schönhuth, Alexander; Dutilh, Bas E; Marz, Manja

    2018-05-14

    The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.

  12. A Critical Analysis of Assessment Quality in Genomics and Bioinformatics Education Research

    Science.gov (United States)

    Campbell, Chad E.; Nehm, Ross H.

    2013-01-01

    The growing importance of genomics and bioinformatics methods and paradigms in biology has been accompanied by an explosion of new curricula and pedagogies. An important question to ask about these educational innovations is whether they are having a meaningful impact on students' knowledge, attitudes, or skills. Although assessments are…

  13. The World-Wide Web: An Interface between Research and Teaching in Bioinformatics

    Directory of Open Access Journals (Sweden)

    James F. Aiton

    1994-01-01

    Full Text Available The rapid expansion occurring in World-Wide Web activity is beginning to make the concepts of ‘global hypermedia’ and ‘universal document readership’ realistic objectives of the new revolution in information technology. One consequence of this increase in usage is that educators and students are becoming more aware of the diversity of the knowledge base which can be accessed via the Internet. Although computerised databases and information services have long played a key role in bioinformatics these same resources can also be used to provide core materials for teaching and learning. The large datasets and arch ives th at have been compiled for biomedical research can be enhanced with the addition of a variety of multimedia elements (images. digital videos. animation etc.. The use of this digitally stored information in structured and self-directed learning environments is likely to increase as activity across World-Wide Web increases.

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

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2013-09-01

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

  15. A Knowledge-based Environment for Software Process Performance Analysis

    Directory of Open Access Journals (Sweden)

    Natália Chaves Lessa Schots

    2015-08-01

    Full Text Available Background: Process performance analysis is a key step for implementing continuous improvement in software organizations. However, the knowledge to execute such analysis is not trivial and the person responsible to executing it must be provided with appropriate support. Aim: This paper presents a knowledge-based environment, named SPEAKER, proposed for supporting software organizations during the execution of process performance analysis. SPEAKER comprises a body of knowledge and a set of activities and tasks for software process performance analysis along with supporting tools to executing these activities and tasks. Method: We conducted an informal literature reviews and a systematic mapping study, which provided basic requirements for the proposed environment. We implemented the SPEAKER environment integrating supporting tools for the execution of activities and tasks of performance analysis and the knowledge necessary to execute them, in order to meet the variability presented by the characteristics of these activities. Results: In this paper, we describe each SPEAKER module and the individual evaluations of these modules, and also present an example of use comprising how the environment can guide the user through a specific performance analysis activity. Conclusion: Although we only conducted individual evaluations of SPEAKER’s modules, the example of use indicates the feasibility of the proposed environment. Therefore, the environment as a whole will be further evaluated to verify if it attains its goal of assisting in the execution of process performance analysis by non-specialist people.

  16. Taking Bioinformatics to Systems Medicine.

    Science.gov (United States)

    van Kampen, Antoine H C; Moerland, Perry D

    2016-01-01

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

  17. ‘Students-as-partners’ scheme enhances postgraduate students’ employability skills while addressing gaps in bioinformatics education

    Science.gov (United States)

    Mello, Luciane V.; Tregilgas, Luke; Cowley, Gwen; Gupta, Anshul; Makki, Fatima; Jhutty, Anjeet; Shanmugasundram, Achchuthan

    2017-01-01

    Abstract Teaching bioinformatics is a longstanding challenge for educators who need to demonstrate to students how skills developed in the classroom may be applied to real world research. This study employed an action research methodology which utilised student–staff partnership and peer-learning. It was centred on the experiences of peer-facilitators, students who had previously taken a postgraduate bioinformatics module, and had applied knowledge and skills gained from it to their own research. It aimed to demonstrate to peer-receivers, current students, how bioinformatics could be used in their own research while developing peer-facilitators’ teaching and mentoring skills. This student-centred approach was well received by the peer-receivers, who claimed to have gained improved understanding of bioinformatics and its relevance to research. Equally, peer-facilitators also developed a better understanding of the subject and appreciated that the activity was a rare and invaluable opportunity to develop their teaching and mentoring skills, enhancing their employability. PMID:29098185

  18. A bioinformatics roadmap for the human vaccines project.

    Science.gov (United States)

    Scheuermann, Richard H; Sinkovits, Robert S; Schenkelberg, Theodore; Koff, Wayne C

    2017-06-01

    Biomedical research has become a data intensive science in which high throughput experimentation is producing comprehensive data about biological systems at an ever-increasing pace. The Human Vaccines Project is a new public-private partnership, with the goal of accelerating development of improved vaccines and immunotherapies for global infectious diseases and cancers by decoding the human immune system. To achieve its mission, the Project is developing a Bioinformatics Hub as an open-source, multidisciplinary effort with the overarching goal of providing an enabling infrastructure to support the data processing, analysis and knowledge extraction procedures required to translate high throughput, high complexity human immunology research data into biomedical knowledge, to determine the core principles driving specific and durable protective immune responses.

  19. Is there room for ethics within bioinformatics education?

    Science.gov (United States)

    Taneri, Bahar

    2011-07-01

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

  20. Knowledge environments representing molecular entities for the virtual physiological human.

    Science.gov (United States)

    Hofmann-Apitius, Martin; Fluck, Juliane; Furlong, Laura; Fornes, Oriol; Kolárik, Corinna; Hanser, Susanne; Boeker, Martin; Schulz, Stefan; Sanz, Ferran; Klinger, Roman; Mevissen, Theo; Gattermayer, Tobias; Oliva, Baldo; Friedrich, Christoph M

    2008-09-13

    In essence, the virtual physiological human (VPH) is a multiscale representation of human physiology spanning from the molecular level via cellular processes and multicellular organization of tissues to complex organ function. The different scales of the VPH deal with different entities, relationships and processes, and in consequence the models used to describe and simulate biological functions vary significantly. Here, we describe methods and strategies to generate knowledge environments representing molecular entities that can be used for modelling the molecular scale of the VPH. Our strategy to generate knowledge environments representing molecular entities is based on the combination of information extraction from scientific text and the integration of information from biomolecular databases. We introduce @neuLink, a first prototype of an automatically generated, disease-specific knowledge environment combining biomolecular, chemical, genetic and medical information. Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH.

  1. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

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

  2. 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…

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

    Science.gov (United States)

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

    2016-01-01

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

  4. Mapping Knowledge and Intellectual Capital in Academic Environments

    OpenAIRE

    Hellström, Tomas; Husted, Kenneth

    2004-01-01

    This paper argues that knowledge mapping may provide a fruitful avenue for intellectual capital management in academic environments such as university departments. However, while some research has been conducted on knowledge mapping and intellectual capital management in the public sector, the university has so far not been directly considered for this type of management. The paper initially reviews the functions and techniques of knowledge mapping and assesses these in the light ...

  5. Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction.

    Science.gov (United States)

    Thiele, Herbert; Glandorf, Jörg; Hufnagel, Peter

    2010-05-27

    With the large variety of Proteomics workflows, as well as the large variety of instruments and data-analysis software available, researchers today face major challenges validating and comparing their Proteomics data. Here we present a new generation of the ProteinScape bioinformatics platform, now enabling researchers to manage Proteomics data from the generation and data warehousing to a central data repository with a strong focus on the improved accuracy, reproducibility and comparability demanded by many researchers in the field. It addresses scientists; current needs in proteomics identification, quantification and validation. But producing large protein lists is not the end point in Proteomics, where one ultimately aims to answer specific questions about the biological condition or disease model of the analyzed sample. In this context, a new tool has been developed at the Spanish Centro Nacional de Biotecnologia Proteomics Facility termed PIKE (Protein information and Knowledge Extractor) that allows researchers to control, filter and access specific information from genomics and proteomic databases, to understand the role and relationships of the proteins identified in the experiments. Additionally, an EU funded project, ProDac, has coordinated systematic data collection in public standards-compliant repositories like PRIDE. This will cover all aspects from generating MS data in the laboratory, assembling the whole annotation information and storing it together with identifications in a standardised format.

  6. Bioinformatics Strategies in Life Sciences: From Data Processing and Data Warehousing to Biological Knowledge Extraction

    Directory of Open Access Journals (Sweden)

    Thiele Herbert

    2010-03-01

    Full Text Available With the large variety of Proteomics workflows, as well as the large variety of instruments and data-analysis software available, researchers today face major challenges validating and comparing their Proteomics data. Here we present a new generation of the ProteinScapeTM bioinformatics platform, now enabling researchers to manage Proteomics data from the generation and data warehousing to a central data repository with a strong focus on the improved accuracy, reproducibility and comparability demanded by many researchers in the field. It addresses scientists` current needs in proteomics identification, quantification and validation. But producing large protein lists is not the end point in Proteomics, where one ultimately aims to answer specific questions about the biological condition or disease model of the analyzed sample. In this context, a new tool has been developed at the Spanish Centro Nacional de Biotecnologia Proteomics Facility termed PIKE (Protein information and Knowledge Extractor that allows researchers to control, filter and access specific information from genomics and proteomic databases, to understand the role and relationships of the proteins identified in the experiments. Additionally, an EU funded project, ProDac, has coordinated systematic data collection in public standards-compliant repositories like PRIDE. This will cover all aspects from generating MS data in the laboratory, assembling the whole annotation information and storing it together with identifications in a standardised format.

  7. Bioinformatics in translational drug discovery.

    Science.gov (United States)

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

    2017-08-31

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

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

    OpenAIRE

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2017-09-01

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

  10. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

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

    2014-01-01

    therapy target discovery in a bioinformatics analysis pipeline. We describe specialized bioinformatics tools and databases for three main bottlenecks in immunotherapy target discovery: the cataloging of potentially antigenic proteins, the identification of potential HLA binders, and the selection epitopes...

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

    NARCIS (Netherlands)

    L. Shen (Lishuang); M.A. Diroma (Maria Angela); M. Gonzalez (Michael); D. Navarro-Gomez (Daniel); J. Leipzig (Jeremy); M.T. Lott (Marie T.); M. van Oven (Mannis); D.C. Wallace; C.C. Muraresku (Colleen Clarke); Z. Zolkipli-Cunningham (Zarazuela); P.F. Chinnery (Patrick); M. Attimonelli (Marcella); S. Zuchner (Stephan); M.J. Falk (Marni J.); X. Gai (Xiaowu)

    2016-01-01

    textabstractMSeqDR 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,

  12. Multi-model-based interactive authoring environment for creating shareable medical knowledge.

    Science.gov (United States)

    Ali, Taqdir; Hussain, Maqbool; Ali Khan, Wajahat; Afzal, Muhammad; Hussain, Jamil; Ali, Rahman; Hassan, Waseem; Jamshed, Arif; Kang, Byeong Ho; Lee, Sungyoung

    2017-10-01

    Technologically integrated healthcare environments can be realized if physicians are encouraged to use smart systems for the creation and sharing of knowledge used in clinical decision support systems (CDSS). While CDSSs are heading toward smart environments, they lack support for abstraction of technology-oriented knowledge from physicians. Therefore, abstraction in the form of a user-friendly and flexible authoring environment is required in order for physicians to create shareable and interoperable knowledge for CDSS workflows. Our proposed system provides a user-friendly authoring environment to create Arden Syntax MLM (Medical Logic Module) as shareable knowledge rules for intelligent decision-making by CDSS. Existing systems are not physician friendly and lack interoperability and shareability of knowledge. In this paper, we proposed Intelligent-Knowledge Authoring Tool (I-KAT), a knowledge authoring environment that overcomes the above mentioned limitations. Shareability is achieved by creating a knowledge base from MLMs using Arden Syntax. Interoperability is enhanced using standard data models and terminologies. However, creation of shareable and interoperable knowledge using Arden Syntax without abstraction increases complexity, which ultimately makes it difficult for physicians to use the authoring environment. Therefore, physician friendliness is provided by abstraction at the application layer to reduce complexity. This abstraction is regulated by mappings created between legacy system concepts, which are modeled as domain clinical model (DCM) and decision support standards such as virtual medical record (vMR) and Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT). We represent these mappings with a semantic reconciliation model (SRM). The objective of the study is the creation of shareable and interoperable knowledge using a user-friendly and flexible I-KAT. Therefore we evaluated our system using completeness and user satisfaction

  13. Mapping Knowledge and Intellectual Capital in Academic Environments

    DEFF Research Database (Denmark)

    Hellström, Tomas; Husted, Kenneth

    2003-01-01

    This paper argues that knowledge mapping may provide a fruitful avenue for intellectual capitalmanagement in academic environments such as university departments. However, while some researchhas been conducted on knowledge mapping and intellectual capital management in the public sector...... reflect of the uses of knowledge mapping at their departments and institutes. Finally a number ofsuggestions are made as to the rationale and conduct of knowledge mapping in academe.Keywords: Knowledge mapping, academic, intellectual capital management, focus group, researchmanagement......,the university has so far not been directly considered for this type of management. The paper initiallyreviews the functions and techniques of knowledge mapping and assesses these in the light of academicdemands. Secondly, the result of a focus group study is presented, where academic leaders were askedto...

  14. Semantic Data Integration and Knowledge Management to Represent Biological Network Associations.

    Science.gov (United States)

    Losko, Sascha; Heumann, Klaus

    2017-01-01

    The vast quantities of information generated by academic and industrial research groups are reflected in a rapidly growing body of scientific literature and exponentially expanding resources of formalized data, including experimental data, originating from a multitude of "-omics" platforms, phenotype information, and clinical data. For bioinformatics, the challenge remains to structure this information so that scientists can identify relevant information, to integrate this information as specific "knowledge bases," and to formalize this knowledge across multiple scientific domains to facilitate hypothesis generation and validation. Here we report on progress made in building a generic knowledge management environment capable of representing and mining both explicit and implicit knowledge and, thus, generating new knowledge. Risk management in drug discovery and clinical research is used as a typical example to illustrate this approach. In this chapter we introduce techniques and concepts (such as ontologies, semantic objects, typed relationships, contexts, graphs, and information layers) that are used to represent complex biomedical networks. The BioXM™ Knowledge Management Environment is used as an example to demonstrate how a domain such as oncology is represented and how this representation is utilized for research.

  15. The GMOD Drupal bioinformatic server framework.

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G

    2010-12-15

    Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com.

  16. Education for Knowledge Society: Learning and Scientific Innovation Environment

    Directory of Open Access Journals (Sweden)

    Alexander O. Karpov

    2017-11-01

    Full Text Available Cognitive-active learning research-type environment is the fundamental component of the education system for the knowledge society. The purpose of the research is the development of conceptual bases and a constructional model of a cognitively active learning environment that stimulates the creation of new knowledge and its socio-economic application. Research methods include epistemic-didactic analysis of empirical material collected as a result of the study of research environments at schools and universities; conceptualization and theoretical modeling of the cognitively active surrounding, which provides an infrastructure of the research-type cognitive process. The empirical material summarized in this work was collected in the research-cognitive space of the “Step into the Future” program, which is one of the most powerful systems of research education in present-day Russia. The article presents key points of the author's concept of generative learning environments and a model of learning and scientific innovation environment implemented at Russian schools and universities.

  17. Knowledge Building in an Online Environment: A Design-Based Research Study

    Science.gov (United States)

    Li, Qing

    2009-01-01

    This article explores knowledge-building in an online distance-learning environment. The research examines how knowledge-building principles can be translated into online classroom practice for graduate students. Specifically, how do the course components and the online learning environments created in two online graduate courses contribute to…

  18. Nuclear Regulator Knowledge Management in a Dynamic Nuclear Industry Environment

    International Nuclear Information System (INIS)

    Turner, J.

    2016-01-01

    Full text: The paper outlines the experiences to date in developing mature knowledge management within the UK’s nuclear regulatory body The Office for Nuclear Regulation (ONR). In 2010 concerns over the loss of knowledge due to the age profile within the organization instigated a review of knowledge management and the development of a knowledge management initiative. Initially activities focused on knowledge capture but in order to move to through life knowledge transfer, knowledge management was then aligned with organizational resilience initiatives. A review of progress highlighted the need to better engage the whole organization to achieve the desired level of maturity for knowledge management. Knowledge management activities now cover organizational culture and environment and all aspects of organizational resilience. Benefits to date include clear understanding of core knowledge requirements, better specifications for recruitment and training and the ability to deploy new regulatory approaches. During the period of implementing the knowledge management programme ONR undertook several organizational changes in moving to become a separate statutory body. The UK nuclear industry was in a period of increased activity including the planning of new nuclear reactors. This dynamic environment caused challenges for embedding knowledge management within ONR which are discussed in the paper. (author

  19. Tacit knowledge in action: basic notions of knowledge sharing in computer supported work environments

    OpenAIRE

    Mackenzie Owen, John

    2001-01-01

    An important characteristic of most computer supported work environments is the distribution of work over individuals or teams in different locations. This leads to what we nowadays call `virtual' environments. In these environments communication between actors is to a large degree mediated, i.e. established through communications media (telephone, fax, computer networks) rather in a face-to-face way. Unfortunately, mediated communication limits the effectiveness of knowledge exchange in virt...

  20. 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…

  1. 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.

  2. The GMOD Drupal Bioinformatic Server Framework

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G.

    2010-01-01

    Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). Results: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Conclusion: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Availability and implementation: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com Contact: alexie@butterflybase.org PMID:20971988

  3. 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…

  4. Databases and Associated Bioinformatic Tools in Studies of Food Allergens, Epitopes and Haptens – a Review

    Directory of Open Access Journals (Sweden)

    Bucholska Justyna

    2018-06-01

    Full Text Available Allergies and/or food intolerances are a growing problem of the modern world. Diffi culties associated with the correct diagnosis of food allergies result in the need to classify the factors causing allergies and allergens themselves. Therefore, internet databases and other bioinformatic tools play a special role in deepening knowledge of biologically-important compounds. Internet repositories, as a source of information on different chemical compounds, including those related to allergy and intolerance, are increasingly being used by scientists. Bioinformatic methods play a signifi cant role in biological and medical sciences, and their importance in food science is increasing. This study aimed at presenting selected databases and tools of bioinformatic analysis useful in research on food allergies, allergens (11 databases, epitopes (7 databases, and haptens (2 databases. It also presents examples of the application of computer methods in studies related to allergies.

  5. Bioinformatics and Cancer

    Science.gov (United States)

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

  6. Data mining in bioinformatics using Weka.

    Science.gov (United States)

    Frank, Eibe; Hall, Mark; Trigg, Len; Holmes, Geoffrey; Witten, Ian H

    2004-10-12

    The Weka machine learning workbench provides a general-purpose environment for automatic classification, regression, clustering and feature selection-common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data pre-processing methods complemented by graphical user interfaces for data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it. http://www.cs.waikato.ac.nz/ml/weka.

  7. Nutrition Knowledge and Training Needs in the School Environment

    Science.gov (United States)

    Jones, Anna Marie

    The nutrition environment in schools can influence the risk for childhood overweight and obesity, which in turn can have life-long implications for risk of chronic disease. This dissertation aimed to examine the nutrition environment in primary public schools in California with regards to the amount of nutrition education provided in the classroom, the nutrition knowledge of teachers, and the training needs of school nutrition personnel. In order to determine nutrition knowledge of teachers, a valid and reliable questionnaire was developed to assess knowledge. The systematic process involved cognitive interviews, a mail-based pretest that utilized a random sample of addresses in California, and validity and reliability testing in a sample of university students. Results indicated that the questionnaire had adequate construct validity, internal consistency reliability, and test-retest reliability. Following the validation of the knowledge questionnaire, it was used in a study of public school teachers in California to determine the relationship between demographic and classroom characteristics and nutrition knowledge, in addition to barriers to nutrition education and resources used to plan nutrition lessons. Nutrition knowledge was not found to be associated with teaching nutrition in the classroom, however it was associated with gender, identifying as Hispanic or Latino, and grade level grouping taught. The most common barriers to nutrition education were time, and unrelated subject matter. The most commonly used resources to plan nutrition lessons were Dairy Council of California educational materials. The school nutrition program was the second area of the school nutrition environment to be examined, and the primary focus was to determine the perceived training needs of California school nutrition personnel. Respondents indicated a need for training in topics related to: program management; the Healthy, Hunger-Free Kids Act of 2010; nutrition, health and

  8. 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…

  9. Bioinformatics research in the Asia Pacific: a 2007 update.

    Science.gov (United States)

    Ranganathan, Shoba; Gribskov, Michael; Tan, Tin Wee

    2008-01-01

    We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2007 Conference was organized as the 6th annual conference of the Asia-Pacific Bioinformatics Network, on Aug. 27-30, 2007 at Hong Kong, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea) and New Delhi (India). Besides a scientific meeting at Hong Kong, satellite events organized are a pre-conference training workshop at Hanoi, Vietnam and a post-conference workshop at Nansha, China. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. We have organized the papers into thematic areas, highlighting the growing contribution of research excellence from this region, to global bioinformatics endeavours.

  10. Biogem: an effective tool based approach for scaling up open source software development in bioinformatics

    NARCIS (Netherlands)

    Bonnal, R.J.P.; Smant, G.; Prins, J.C.P.

    2012-01-01

    Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software

  11. What kind of knowledge do small companies need to improve their working environment?

    DEFF Research Database (Denmark)

    Antonsson, Ann-Beth; Hasle, Peter

    2015-01-01

    towards knowledge-based behaviour. Additionally the time required increases when moving from skill- to knowledge-based behaviour. On the other hand, skill-based behaviour lacks the ability to solve problems and adapt to new situations. In the working environment risk assessment as well as the development...... of management routines are typically knowledge-based activities, whereas the application of good practice is more of skill or rule-based. For small companies, time as well as knowledge is an important constraint for the work environment management. Therefore the conclusion could be to focus on and provide skill......Background One of the main obstacles identified for small companies´ improvement of the working environment is lack of knowledge. Aim To discuss what kind of knowledge is required by small companies if they are to be able to improve their working environment and the pros and cons of different kinds...

  12. PROMOTING THE MANAGEMENT BASED ON KNOWLEDGE IN THE ROMANIAN ORGANIZATIONAL ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    Alin NIOAȚĂ

    2012-05-01

    Full Text Available The organizations based on knowledge are intelligent collective actors of the informational society and they are determinant for affirming it as a knowledge society; belonging to the contemporary reality both as an environment of professional and managerial environment and as an object of scientific research and strategic project, they mark the convergence between two phenomena defining the human nature – the knowledge one and the organization one – in a symbolic social construction for the ideas of collective competence, intelligent action and sustainable performance.

  13. When cloud computing meets bioinformatics: a review.

    Science.gov (United States)

    Zhou, Shuigeng; Liao, Ruiqi; Guan, Jihong

    2013-10-01

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

  14. Application of machine learning methods in bioinformatics

    Science.gov (United States)

    Yang, Haoyu; An, Zheng; Zhou, Haotian; Hou, Yawen

    2018-05-01

    Faced with the development of bioinformatics, high-throughput genomic technology have enabled biology to enter the era of big data. [1] Bioinformatics is an interdisciplinary, including the acquisition, management, analysis, interpretation and application of biological information, etc. It derives from the Human Genome Project. The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets.[2]. This paper analyzes and compares various algorithms of machine learning and their applications in bioinformatics.

  15. Man - Environment - Knowledge. 2. ed.

    International Nuclear Information System (INIS)

    Fritsch, B.

    1991-01-01

    The book brings together certain facts which were collated and processed on the subject of ''Man-Environment-Knowledge'' within the scope of a tutorial function of the same name organised and held by the ''ETH'' (the Swiss Federal Institute of Technology in Zurich). Starting off from certain important fundamental facts which reproduce the current state of our planet in the form of data, it goes on to illustrate those interconnections and processes that are important for the understanding of the world in which we live. figs., tabs., [800 refs.

  16. Innovation and Virtual Environments: Towards Virtual Knowledge Brokers

    OpenAIRE

    VERONA G; PRANDELLI E.; SAWHNEY M.

    2006-01-01

    The authors examine the implications of virtual customer environments for supporting the innovation process. By building on the literature of knowledge brokers, they introduce the concept of virtual knowledge brokers — actors who leverage the internet to support third parties’ innovation activities. These actors enable firms to extend their reach in engaging with customers and they also allow firms to have a richer dialogue with customers because of their perceived neutrality. Consequently...

  17. Knowledge Acquisition and Job Training for Advanced Technical Skills Using Immersive Virtual Environment

    Science.gov (United States)

    Watanuki, Keiichi; Kojima, Kazuyuki

    The environment in which Japanese industry has achieved great respect is changing tremendously due to the globalization of world economies, while Asian countries are undergoing economic and technical development as well as benefiting from the advances in information technology. For example, in the design of custom-made casting products, a designer who lacks knowledge of casting may not be able to produce a good design. In order to obtain a good design and manufacturing result, it is necessary to equip the designer and manufacturer with a support system related to casting design, or a so-called knowledge transfer and creation system. This paper proposes a new virtual reality based knowledge acquisition and job training system for casting design, which is composed of the explicit and tacit knowledge transfer systems using synchronized multimedia and the knowledge internalization system using portable virtual environment. In our proposed system, the education content is displayed in the immersive virtual environment, whereby a trainee may experience work in the virtual site operation. Provided that the trainee has gained explicit and tacit knowledge of casting through the multimedia-based knowledge transfer system, the immersive virtual environment catalyzes the internalization of knowledge and also enables the trainee to gain tacit knowledge before undergoing on-the-job training at a real-time operation site.

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  19. Ubiquitous mobile knowledge construction in collaborative learning environments.

    Science.gov (United States)

    Baloian, Nelson; Zurita, Gustavo

    2012-01-01

    Knowledge management is a critical activity for any organization. It has been said to be a differentiating factor and an important source of competitiveness if this knowledge is constructed and shared among its members, thus creating a learning organization. Knowledge construction is critical for any collaborative organizational learning environment. Nowadays workers must perform knowledge creation tasks while in motion, not just in static physical locations; therefore it is also required that knowledge construction activities be performed in ubiquitous scenarios, and supported by mobile and pervasive computational systems. These knowledge creation systems should help people in or outside organizations convert their tacit knowledge into explicit knowledge, thus supporting the knowledge construction process. Therefore in our understanding, we consider highly relevant that undergraduate university students learn about the knowledge construction process supported by mobile and ubiquitous computing. This has been a little explored issue in this field. This paper presents the design, implementation, and an evaluation of a system called MCKC for Mobile Collaborative Knowledge Construction, supporting collaborative face-to-face tacit knowledge construction and sharing in ubiquitous scenarios. The MCKC system can be used by undergraduate students to learn how to construct knowledge, allowing them anytime and anywhere to create, make explicit and share their knowledge with their co-learners, using visual metaphors, gestures and sketches to implement the human-computer interface of mobile devices (PDAs).

  20. A Critical Analysis of Assessment Quality in Genomics and Bioinformatics Education Research

    Science.gov (United States)

    Campbell, Chad E.; Nehm, Ross H.

    2013-01-01

    The growing importance of genomics and bioinformatics methods and paradigms in biology has been accompanied by an explosion of new curricula and pedagogies. An important question to ask about these educational innovations is whether they are having a meaningful impact on students’ knowledge, attitudes, or skills. Although assessments are necessary tools for answering this question, their outputs are dependent on their quality. Our study 1) reviews the central importance of reliability and construct validity evidence in the development and evaluation of science assessments and 2) examines the extent to which published assessments in genomics and bioinformatics education (GBE) have been developed using such evidence. We identified 95 GBE articles (out of 226) that contained claims of knowledge increases, affective changes, or skill acquisition. We found that 1) the purpose of most of these studies was to assess summative learning gains associated with curricular change at the undergraduate level, and 2) a minority (<10%) of studies provided any reliability or validity evidence, and only one study out of the 95 sampled mentioned both validity and reliability. Our findings raise concerns about the quality of evidence derived from these instruments. We end with recommendations for improving assessment quality in GBE. PMID:24006400

  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

    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. 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.

  3. 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…

  4. Maintenance of nuclear knowledge in an antinuclear environment

    International Nuclear Information System (INIS)

    Boeck, H.; Villa, M.

    2008-01-01

    In this work authors present the maintenance of nuclear knowledge in an antinuclear environment in Austria. Participation of the TRIGA Mark II research reactor in the Atominstitut in different courses, in research projects and education is presented.

  5. Development of Bioinformatics Infrastructure for Genomics Research.

    Science.gov (United States)

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

    2017-06-01

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

  6. Fuzzy Logic in Medicine and Bioinformatics

    Directory of Open Access Journals (Sweden)

    Angela Torres

    2006-01-01

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

  7. 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.

  8. Parallel evolutionary computation in bioinformatics applications.

    Science.gov (United States)

    Pinho, Jorge; Sobral, João Luis; Rocha, Miguel

    2013-05-01

    A large number of optimization problems within the field of Bioinformatics require methods able to handle its inherent complexity (e.g. NP-hard problems) and also demand increased computational efforts. In this context, the use of parallel architectures is a necessity. In this work, we propose ParJECoLi, a Java based library that offers a large set of metaheuristic methods (such as Evolutionary Algorithms) and also addresses the issue of its efficient execution on a wide range of parallel architectures. The proposed approach focuses on the easiness of use, making the adaptation to distinct parallel environments (multicore, cluster, grid) transparent to the user. Indeed, this work shows how the development of the optimization library can proceed independently of its adaptation for several architectures, making use of Aspect-Oriented Programming. The pluggable nature of parallelism related modules allows the user to easily configure its environment, adding parallelism modules to the base source code when needed. The performance of the platform is validated with two case studies within biological model optimization. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  9. 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. © 2016 WILEY PERIODICALS, INC.

  10. The home environment: A mediator of nutrition knowledge and diet quality in adolescents.

    Science.gov (United States)

    Tabbakh, Tamara; Freeland-Graves, Jean H

    2016-10-01

    The objective of this research was to assess adherence to the Healthy Eating Index-2010 of mothers and their adolescents (11-14 years old) and to examine the role of the home environment as a mediator of maternal nutrition knowledge and adolescent diet quality. It is hypothesized that mothers with greater knowledge impact the diet quality of their adolescents by creation of healthier home environments. A sample of 206 mother-adolescent dyads separately completed the Multidimensional Home Environment Scale, a Food Frequency Questionnaire, and a Nutrition Knowledge Scale. Body mass index-for-age percentiles were derived from weight and height measurements obtained by researcher; diet quality was estimated via the Healthy Eating Index (HEI)-2010. Percent of maximum score on nutrition knowledge for both mothers and adolescents were poor, with lowest scores on recommendations of healthy eating and physical activity (48% and 19%, respectively). A model of maternal nutrition knowledge (independent variable) and adolescent diet quality (dependent variable) indicated that greater knowledge was associated with higher scores on total fruit (p = 0.02), whole grains (p = 0.05), seafood and plant proteins (p = 0.01), and overall diet quality (p empty calories (p = 0.01). Inclusion of the home environment as a mediator yielded significant estimates of the indirect effect (β = 0.61, 95% CI: 0.3-1.0). Within the home environment, psychological (β = 0.46), social (β = 0.23), and environmental (β = 0.65) variables were all significant mediators of nutrition knowledge on diet quality. These results emphasize the importance of maternal nutrition knowledge and the mediating effect of the home environment on the diet quality of adolescents. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine.

    Science.gov (United States)

    Vamathevan, J; Birney, E

    2017-08-01

    Objectives: To highlight and provide insights into key developments in translational bioinformatics between 2014 and 2016. Methods: This review describes some of the most influential bioinformatics papers and resources that have been published between 2014 and 2016 as well as the national genome sequencing initiatives that utilize these resources to routinely embed genomic medicine into healthcare. Also discussed are some applications of the secondary use of patient data followed by a comprehensive view of the open challenges and emergent technologies. Results: Although data generation can be performed routinely, analyses and data integration methods still require active research and standardization to improve streamlining of clinical interpretation. The secondary use of patient data has resulted in the development of novel algorithms and has enabled a refined understanding of cellular and phenotypic mechanisms. New data storage and data sharing approaches are required to enable diverse biomedical communities to contribute to genomic discovery. Conclusion: The translation of genomics data into actionable knowledge for use in healthcare is transforming the clinical landscape in an unprecedented way. Exciting and innovative models that bridge the gap between clinical and academic research are set to open up the field of translational bioinformatics for rapid growth in a digital era. Georg Thieme Verlag KG Stuttgart.

  12. 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.

  13. 4273π: bioinformatics education on low cost ARM hardware.

    Science.gov (United States)

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

    2013-08-12

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

  14. OpenHelix: bioinformatics education outside of a different box.

    Science.gov (United States)

    Williams, Jennifer M; Mangan, Mary E; Perreault-Micale, Cynthia; Lathe, Scott; Sirohi, Neeraj; Lathe, Warren C

    2010-11-01

    The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review.

  15. Development of a cloud-based Bioinformatics Training Platform.

    Science.gov (United States)

    Revote, Jerico; Watson-Haigh, Nathan S; Quenette, Steve; Bethwaite, Blair; McGrath, Annette; Shang, Catherine A

    2017-05-01

    The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. © The Author 2016. Published by Oxford University Press.

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

    Science.gov (United States)

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

    2009-12-03

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

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

    Science.gov (United States)

    Diaz Acosta, B.

    2011-01-01

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

  18. Programming Not Required: Skills and Knowledge for the Digital Library Environment

    Science.gov (United States)

    Howard, Katherine

    2010-01-01

    Education for Library and Information professionals in managing the digital environment has been a key topic for discussion within the LIS environment for some time. However, before designing and implementing a program for digital library education, it is prudent to ensure that the skills and knowledge required to work in this environment are…

  19. 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...... for interactions between RNA and proteins.Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology....

  20. Adapting bioinformatics curricula for big data

    Science.gov (United States)

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

    2016-01-01

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

  1. Examining Collaborative Knowledge Construction in Microblogging-Based Learning Environments

    Directory of Open Access Journals (Sweden)

    Tian Luo

    2017-09-01

    Full Text Available Aim/Purpose: The purpose of the study is to provide foundational research to exemplify how knowledge construction takes place in microblogging-based learning environments, to understand learner interaction representing the knowledge construction process, and to analyze learner perception, thereby suggesting a model of delivery for microblogging. Background: Up-and-coming digital native learners crave the real-time, multimedia, global-interconnectedness of microblogging, yet there has been limited research that specifically proposes a working model of Twitter’s classroom integration for designers and practitioners without bundling it in with other social media tools. Methodology: This semester-long study utilized a case-study research design via a multi-dimensional approach in a hybrid classroom with both face-to-face and online environments. Tweets were collected from four types of activities and coded based on content within their contextual setting. Twenty-four college students participated in the study. Contribution: The findings shed light on the process of knowledge construction in mi-croblogging and reveal key types of knowledge manifested during learning activities. The study also proposes a model for delivering microblogging to formal learning environments applicable to various contexts for designers and practitioners. Findings: There are distinct learner interaction patterns representing the process of knowledge construction in microblogging activities ranging from low-order to high-order cognitive tasks. Students generally were in favor of the Twitter integration in this study. Recommendations for Practitioners: The three central activities (exploring hashtags, discussion topics, and participating in live chats along with the backchannel activity formulate a working model that represents the sequential process of Twitter integration into classrooms. Impact on Society: Microblogging allows learners omnichannel access while hashtags

  2. Conceptual Diagnosis Model Based on Distinct Knowledge Dyads for Interdisciplinary Environments

    Directory of Open Access Journals (Sweden)

    Cristian VIZITIU

    2014-06-01

    Full Text Available The present paper has a synergic dual purpose of bringing a psychological and neuroscience related perspective oriented towards decision making and knowledge creation diagnosis in the frame of Knowledge Management. !e conceptual model is built by means ofCognitive-Emotional and Explicit-Tacit knowledge dyads and structured on Analytic Hierarchy Process (AHP according to the hypothesis which designates the first dyad as an accessing mechanism of knowledge stored in the second dyad. Due to the well acknowledged needsconcerning new advanced decision making instruments and enhanced knowledge creation processes in the field of technical space projects emphasized by a high level of complexity, the herein study tries also to prove the relevance of the proposed conceptual diagnosis modelin Systems Engineering (SE methodology which foresees at its turn concurrent engineering within interdisciplinary working environments. !e theoretical model, entitled DiagnoSE, has the potential to provide practical implications to space/space related business sector butnot merely, and on the other hand, to trigger and inspire other knowledge management related researches for refining and testing the proposed instrument in SE or other similar decision making based working environment.

  3. Developing library bioinformatics services in context: the Purdue University Libraries bioinformationist program.

    Science.gov (United States)

    Rein, Diane C

    2006-07-01

    Purdue University is a major agricultural, engineering, biomedical, and applied life science research institution with an increasing focus on bioinformatics research that spans multiple disciplines and campus academic units. The Purdue University Libraries (PUL) hired a molecular biosciences specialist to discover, engage, and support bioinformatics needs across the campus. After an extended period of information needs assessment and environmental scanning, the specialist developed a week of focused bioinformatics instruction (Bioinformatics Week) to launch system-wide, library-based bioinformatics services. The specialist employed a two-tiered approach to assess user information requirements and expectations. The first phase involved careful observation and collection of information needs in-context throughout the campus, attending laboratory meetings, interviewing department chairs and individual researchers, and engaging in strategic planning efforts. Based on the information gathered during the integration phase, several survey instruments were developed to facilitate more critical user assessment and the recovery of quantifiable data prior to planning. Given information gathered while working with clients and through formal needs assessments, as well as the success of instructional approaches used in Bioinformatics Week, the specialist is developing bioinformatics support services for the Purdue community. The specialist is also engaged in training PUL faculty librarians in bioinformatics to provide a sustaining culture of library-based bioinformatics support and understanding of Purdue's bioinformatics-related decision and policy making.

  4. Knowledge Flow Rules of Modern Design under Distributed Resource Environment

    Directory of Open Access Journals (Sweden)

    Junning Li

    2013-01-01

    Full Text Available The process of modern design under the distributed resource environment is interpreted as the process of knowledge flow and integration. As the acquisition of new knowledge strongly depends on resources, knowledge flow can be influenced by technical, economic, and social relation factors, and so forth. In order to achieve greater efficiency of knowledge flow and make the product more competitive, the root causes of the above factors should be acquired first. In this paper, the authors attempt to reveal the nature of design knowledge flow from the perspectives of fluid dynamics and energy. The knowledge field effect and knowledge agglomeration effect are analyzed, respectively, in which the knowledge field effect model considering single task node and the single knowledge energy model in the knowledge flow are established, then the general expression of knowledge energy conservation with consideration of the kinetic energy and potential energy of knowledge is built. Then, the knowledge flow rules and their influential factors including complete transfer and incomplete transfer of design knowledge are studied. Finally, the coupling knowledge flows in the knowledge service platform for modern design are analyzed to certify the feasibility of the research work.

  5. Host-parasite interactions and ecology of the malaria parasite-a bioinformatics approach.

    Science.gov (United States)

    Izak, Dariusz; Klim, Joanna; Kaczanowski, Szymon

    2018-04-25

    Malaria remains one of the highest mortality infectious diseases. Malaria is caused by parasites from the genus Plasmodium. Most deaths are caused by infections involving Plasmodium falciparum, which has a complex life cycle. Malaria parasites are extremely well adapted for interactions with their host and their host's immune system and are able to suppress the human immune system, erase immunological memory and rapidly alter exposed antigens. Owing to this rapid evolution, parasites develop drug resistance and express novel forms of antigenic proteins that are not recognized by the host immune system. There is an emerging need for novel interventions, including novel drugs and vaccines. Designing novel therapies requires knowledge about host-parasite interactions, which is still limited. However, significant progress has recently been achieved in this field through the application of bioinformatics analysis of parasite genome sequences. In this review, we describe the main achievements in 'malarial' bioinformatics and provide examples of successful applications of protein sequence analysis. These examples include the prediction of protein functions based on homology and the prediction of protein surface localization via domain and motif analysis. Additionally, we describe PlasmoDB, a database that stores accumulated experimental data. This tool allows data mining of the stored information and will play an important role in the development of malaria science. Finally, we illustrate the application of bioinformatics in the development of population genetics research on malaria parasites, an approach referred to as reverse ecology.

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

    African Journals Online (AJOL)

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

  7. Promoting synergistic research and education in genomics and bioinformatics.

    Science.gov (United States)

    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 personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to handle the massive bioinformatics and personalized healthcare data, which will obviously have a profound effect on how biomedical research will be conducted toward the improvement of human health and prolonging of human life in the future. The International Society of Intelligent Biological Medicine (http://www.isibm.org) and its official journals, the International Journal of Functional Informatics and Personalized Medicine (http://www.inderscience.com/ijfipm) and the International Journal of Computational Biology and Drug Design (http://www.inderscience.com/ijcbdd) in collaboration with International Conference on Bioinformatics and Computational Biology (Biocomp), touch tomorrow's bioinformatics and personalized medicine throughout today's efforts in promoting the research, education and awareness of the upcoming integrated inter/multidisciplinary field. The 2007 international conference on Bioinformatics and Computational Biology (BIOCOMP07) was held in Las Vegas, the United States of American on June 25-28, 2007. The conference attracted over 400 papers, covering broad research areas in the genomics, biomedicine and bioinformatics. The Biocomp 2007 provides a common platform for the cross fertilization of ideas, and to help shape knowledge and

  8. BioWarehouse: a bioinformatics database warehouse toolkit.

    Science.gov (United States)

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

    2006-03-23

    This article addresses the problem of interoperation of heterogeneous bioinformatics databases. 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. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

  9. 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.

  10. 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.…

  11. 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. © The Author 2015. Published by Oxford University Press.

  12. Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

    Science.gov (United States)

    Vincent, J.

    2011-01-01

    The Skate Genome Project, a pilot project of the North East Cyber infrastructure Consortium, aims to produce a draft genome sequence of Leucoraja erinacea, the Little Skate. The pilot project was designed to also develop expertise in large scale collaborations across the NECC region. An overview of the bioinformatics and infrastructure challenges faced during the first year of the project will be presented. Results to date and lessons learned from the perspective of a bioinformatics core will be highlighted.

  13. 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

  14. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

    Science.gov (United States)

    Stephan, Christian; Hamacher, Michael; Blüggel, Martin; Körting, Gerhard; Chamrad, Daniel; Scheer, Christian; Marcus, Katrin; Reidegeld, Kai A; Lohaus, Christiane; Schäfer, Heike; Martens, Lennart; Jones, Philip; Müller, Michael; Auyeung, Kevin; Taylor, Chris; Binz, Pierre-Alain; Thiele, Herbert; Parkinson, David; Meyer, Helmut E; Apweiler, Rolf

    2005-09-01

    The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

  15. 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…

  16. 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…

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

    Science.gov (United States)

    Fu, Zhiyan; Lin, Jing

    2017-01-01

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

  18. Knowledge-inducing Global Path Planning for Robots in Environment with Hybrid Terrain

    Directory of Open Access Journals (Sweden)

    Yi-nan Guo

    2010-09-01

    Full Text Available In complex environment with hybrid terrain, different regions may have different terrain. Path planning for robots in such environment is an open NP-complete problem, which lacks effective methods. The paper develops a novel global path planning method based on common sense and evolution knowledge by adopting dual evolution structure in culture algorithms. Common sense describes terrain information and feasibility of environment, which is used to evaluate and select the paths. Evolution knowledge describes the angle relationship between the path and the obstacles, or the common segments of paths, which is used to judge and repair infeasible individuals. Taken two types of environments with different obstacles and terrain as examples, simulation results indicate that the algorithm can effectively solve path planning problem in complex environment and decrease the computation complexity for judgment and repair of infeasible individuals. It also can improve the convergence speed and have better computation stability.

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

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

  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. © The Author 2014. Published by Oxford University Press.

  2. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

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

  3. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

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

  4. Bioinformatics of cardiovascular miRNA biology.

    Science.gov (United States)

    Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

    2015-12-01

    MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. 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

  6. 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…

  7. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-08-01

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

  8. Bioinformatics-Aided Venomics

    Directory of Open Access Journals (Sweden)

    Quentin Kaas

    2015-06-01

    Full Text Available Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future.

  9. Documenting the emergence of bio-ontologies: or, why researching bioinformatics requires HPSSB.

    Science.gov (United States)

    Leonelli, Sabina

    2010-01-01

    This paper reflects on the analytic challenges emerging from the study of bioinformatic tools recently created to store and disseminate biological data, such as databases, repositories, and bio-ontologies. I focus my discussion on the Gene Ontology, a term that defines three entities at once: a classification system facilitating the distribution and use of genomic data as evidence towards new insights; an expert community specialised in the curation of those data; and a scientific institution promoting the use of this tool among experimental biologists. These three dimensions of the Gene Ontology can be clearly distinguished analytically, but are tightly intertwined in practice. I suggest that this is true of all bioinformatic tools: they need to be understood simultaneously as epistemic, social, and institutional entities, since they shape the knowledge extracted from data and at the same time regulate the organisation, development, and communication of research. This viewpoint has one important implication for the methodologies used to study these tools; that is, the need to integrate historical, philosophical, and sociological approaches. I illustrate this claim through examples of misunderstandings that may result from a narrowly disciplinary study of the Gene Ontology, as I experienced them in my own research.

  10. Knowledge sharing in a multicultural environment: challenges and opportunities

    Directory of Open Access Journals (Sweden)

    Luyanda Dube

    2012-12-01

    Full Text Available The article underscores the process of knowledge sharing in a multicultural organisational environment. Generally,multiculturalism emanates from being influenced by different contexts that provide the potential for human diversity. Itresults in disparate behavioural patterns and bodies of knowledge which lead to variance in terms of racial, sexual, ageand cultural orientations. The process of sharing knowledge is complex and is susceptible to multicultural variances.Considering that knowledge sharing processes and probable multicultural influences are contextual, the purpose of thearticle is to establish the extent of knowledge flows in the Department of Information Science at the University of SouthAfrica. In particular the article seeks to give an overall view on how knowledge is shared across intergenerational, culturaland interracial lines in the Department. The qualitative approach was considered appropriate for this study because itfocuses on observing events from the perspectives of those who are involved and is aimed at understanding the attitude,behaviour and opinions of those individuals (Powell & Connaway 2004. A basic interpretive qualitative research designwas used for this study. Data was collected through interviews and document analysis. The data were inductively analysedand the findings are presented and discussed using references to the literature that informed the study.

  11. Individual Differences in Spatial Knowledge Acquisition from a Virtual Environment: An Eye-Tracking Study

    Directory of Open Access Journals (Sweden)

    Ryosuke Uenaka

    2011-05-01

    Full Text Available Previous studies have shown that spatial knowledge acquisition differs across individuals in both real and virtual environments. For example, in a real environment, Ishikawa & Montello (2006 showed that some participants had almost perfect configural knowledge of the environment after one or two learning trials, whereas others performed at chance even after repeated learning trials. Using a virtual version of Ishikawa & Montello's layouts, we measured eye movements while participants were learning a layout of a route, as eye movements are shown to be closely linked to performance in spatial navigation tasks. We prepared three different layouts of a route depicted in a desktop virtual environment, along with the locations of four landmarks on that route. After learning each of the routes, we administered three different measures of spatial knowledge: numbering the landmark order, estimation of direction, and map sketching. Self-reported sense-of-direction (SDQ-S was also measured. Behavioral analyses showed positive correlations across the routes in the estimation of direction. However, consistent correlations were not observed between eye movements and performance of the estimation of direction in each route. Those results suggest that eye movements do not predict individual differences in spatial knowledge acquisition.

  12. 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....

  13. Peer Mentoring for Bioinformatics presentation

    OpenAIRE

    Budd, Aidan

    2014-01-01

    A handout used in a HUB (Heidelberg Unseminars in Bioinformatics) meeting focused on career development for bioinformaticians. It describes an activity for use to help introduce the idea of peer mentoring, potnetially acting as an opportunity to create peer-mentoring groups.

  14. [Factors affecting the adoption of ICT tools in experiments with bioinformatics in biopharmaceutical organizations: a case study in the Brazilian Cancer Institute].

    Science.gov (United States)

    Pitassi, Claudio; Gonçalves, Antonio Augusto; Moreno Júnior, Valter de Assis

    2014-01-01

    The scope of this article is to identify and analyze the factors that influence the adoption of ICT tools in experiments with bioinformatics at the Brazilian Cancer Institute (INCA). It involves a descriptive and exploratory qualitative field study. Evidence was collected mainly based on in-depth interviews with the management team at the Research Center and the IT Division. The answers were analyzed using the categorical content method. The categories were selected from the scientific literature and consolidated in the Technology-Organization-Environment (TOE) framework created for this study. The model proposed made it possible to demonstrate how the factors selected impacted INCA´s adoption of bioinformatics systems and tools, contributing to the investigation of two critical areas for the development of the health industry in Brazil, namely technological innovation and bioinformatics. Based on the evidence collected, a research question was posed: to what extent can the alignment of the factors related to the adoption of ICT tools in experiments with bioinformatics increase the innovation capacity of a Brazilian biopharmaceutical organization?

  15. PubData: search engine for bioinformatics databases worldwide

    OpenAIRE

    Vand, Kasra; Wahlestedt, Thor; Khomtchouk, Kelly; Sayed, Mohammed; Wahlestedt, Claes; Khomtchouk, Bohdan

    2016-01-01

    We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the use...

  16. Enhancing students’ vocabulary knowledge using the Facebook environment

    Directory of Open Access Journals (Sweden)

    Muhammad Kamarul Kabilan

    2016-01-01

    Full Text Available This study investigates the effectiveness of using Facebook in enhancing vocabulary knowledge among Community College students. Thirty-three (33 Community College students are exposed to the use of Facebook as an environment of learning and enhancing their English vocabulary. They are given a pre-test and a post-test and the findings indicate that students perform significantly better in the post-test compared to the pre-test. It appears that Facebook could be considered as a supplementary learning environment or learning platform or a learning tool; with meaningful and engaging activities that require students to collaborate, network and functions as a community of practice, particularly for introverted students with low proficiency levels and have low self-esteem.

  17. DynaLearn-An Intelligent Learning Environment for Learning Conceptual Knowledge

    NARCIS (Netherlands)

    Bredeweg, Bert; Liem, Jochem; Beek, Wouter; Linnebank, Floris; Gracia, Jorge; Lozano, Esther; Wißner, Michael; Bühling, René; Salles, Paulo; Noble, Richard; Zitek, Andreas; Borisova, Petya; Mioduser, David

    2013-01-01

    Articulating thought in computerbased media is a powerful means for humans to develop their understanding of phenomena. We have created DynaLearn, an intelligent learning environment that allows learners to acquire conceptual knowledge by constructing and simulating qualitative models of how systems

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

    African Journals Online (AJOL)

    Bioinformatics is an interdisciplinary subject, which uses computer application, statistics, mathematics and engineering for the analysis and management of biological information. It has become an important tool for basic and applied research in veterinary sciences. Bioinformatics has brought about advancements into ...

  19. BioGPS descriptors for rational engineering of enzyme promiscuity and structure based bioinformatic analysis.

    Directory of Open Access Journals (Sweden)

    Valerio Ferrario

    Full Text Available A new bioinformatic methodology was developed founded on the Unsupervised Pattern Cognition Analysis of GRID-based BioGPS descriptors (Global Positioning System in Biological Space. The procedure relies entirely on three-dimensional structure analysis of enzymes and does not stem from sequence or structure alignment. The BioGPS descriptors account for chemical, geometrical and physical-chemical features of enzymes and are able to describe comprehensively the active site of enzymes in terms of "pre-organized environment" able to stabilize the transition state of a given reaction. The efficiency of this new bioinformatic strategy was demonstrated by the consistent clustering of four different Ser hydrolases classes, which are characterized by the same active site organization but able to catalyze different reactions. The method was validated by considering, as a case study, the engineering of amidase activity into the scaffold of a lipase. The BioGPS tool predicted correctly the properties of lipase variants, as demonstrated by the projection of mutants inside the BioGPS "roadmap".

  20. 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...

  1. Bioinformatics of genomic association mapping

    NARCIS (Netherlands)

    Vaez Barzani, Ahmad

    2015-01-01

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

  2. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    Bioinformatics is an emerging scientific discipline that uses information ... complex biological questions. ... and computer programs for various purposes of primer ..... polymerase chain reaction: Human Immunodeficiency Virus 1 model studies.

  3. 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

  4. The Effects of a Systematically Designed Online Learning Environment on Preservice Teachers' Professional Knowledge

    Science.gov (United States)

    Evens, Marie; Larmuseau, Charlotte; Dewaele, Katrien; Van Craesbeek, Leen; Elen, Jan; Depaepe, Fien

    2017-01-01

    This study examines the effects of an online learning environment on preservice teachers' pedagogical content knowledge (PCK), content knowledge (CK) (related to French in primary teacher education), and pedagogical knowledge (PK) in a quasi-experimental design. More specifically, the following research question is addressed: Is a systematically…

  5. Enhancing students’ vocabulary knowledge using the Facebook environment

    OpenAIRE

    Muhammad Kamarul Kabilan; Tuti Zalina Mohamed Ernes Zahar

    2016-01-01

    This study investigates the effectiveness of using Facebook in enhancing vocabulary knowledge among Community College students. Thirty-three (33) Community College students are exposed to the use of Facebook as an environment of learning and enhancing their English vocabulary. They are given a pre-test and a post-test and the findings indicate that students perform significantly better in the post-test compared to the pre-test. It appears that Facebook could be considered as a supplementary l...

  6. 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…

  7. Taking Bioinformatics to Systems Medicine

    NARCIS (Netherlands)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Michael R Clay

    2017-04-01

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

  9. Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

    Science.gov (United States)

    Menegidio, Fabiano B; Jabes, Daniela L; Costa de Oliveira, Regina; Nunes, Luiz R

    2018-02-01

    This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects. Source code and instructions for local installation are available at https://github.com/DugongBioinformatics, under the MIT open source license. Luiz.nunes@ufabc.edu.br. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  10. Best practices in bioinformatics training for life scientists

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...... 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...

  11. 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…

  12. 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…

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

    Directory of Open Access Journals (Sweden)

    Katrina Pavelin

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

  14. Application of bioinformatics tools and databases in microbial dehalogenation research (a review).

    Science.gov (United States)

    Satpathy, R; Konkimalla, V B; Ratha, J

    2015-01-01

    Microbial dehalogenation is a biochemical process in which the halogenated substances are catalyzed enzymatically in to their non-halogenated form. The microorganisms have a wide range of organohalogen degradation ability both explicit and non-specific in nature. Most of these halogenated organic compounds being pollutants need to be remediated; therefore, the current approaches are to explore the potential of microbes at a molecular level for effective biodegradation of these substances. Several microorganisms with dehalogenation activity have been identified and characterized. In this aspect, the bioinformatics plays a key role to gain deeper knowledge in this field of dehalogenation. To facilitate the data mining, many tools have been developed to annotate these data from databases. Therefore, with the discovery of a microorganism one can predict a gene/protein, sequence analysis, can perform structural modelling, metabolic pathway analysis, biodegradation study and so on. This review highlights various methods of bioinformatics approach that describes the application of various databases and specific tools in the microbial dehalogenation fields with special focus on dehalogenase enzymes. Attempts have also been made to decipher some recent applications of in silico modeling methods that comprise of gene finding, protein modelling, Quantitative Structure Biodegradibility Relationship (QSBR) study and reconstruction of metabolic pathways employed in dehalogenation research area.

  15. An overview of bioinformatics methods for modeling biological pathways in yeast.

    Science.gov (United States)

    Hou, Jie; Acharya, Lipi; Zhu, Dongxiao; Cheng, Jianlin

    2016-03-01

    The advent of high-throughput genomics techniques, along with the completion of genome sequencing projects, identification of protein-protein interactions and reconstruction of genome-scale pathways, has accelerated the development of systems biology research in the yeast organism Saccharomyces cerevisiae In particular, discovery of biological pathways in yeast has become an important forefront in systems biology, which aims to understand the interactions among molecules within a cell leading to certain cellular processes in response to a specific environment. While the existing theoretical and experimental approaches enable the investigation of well-known pathways involved in metabolism, gene regulation and signal transduction, bioinformatics methods offer new insights into computational modeling of biological pathways. A wide range of computational approaches has been proposed in the past for reconstructing biological pathways from high-throughput datasets. Here we review selected bioinformatics approaches for modeling biological pathways inS. cerevisiae, including metabolic pathways, gene-regulatory pathways and signaling pathways. We start with reviewing the research on biological pathways followed by discussing key biological databases. In addition, several representative computational approaches for modeling biological pathways in yeast are discussed. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  16. Fundamentals of bioinformatics and computational biology methods and exercises in matlab

    CERN Document Server

    Singh, Gautam B

    2015-01-01

    This book offers comprehensive coverage of all the core topics of bioinformatics, and includes practical examples completed using the MATLAB bioinformatics toolbox™. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics. This chapter will enable physical science students to fully understand and appreciate the ultimate goals of applying the principles of information technology to challenges in biological data management, sequence analysis, and systems biology. The first part of the book also includes a survey of existing biological databases, tools that have become essential in today’s biotechnology research. The second part of the book covers methodologies for retrieving biological information, including fundamental algorithms for sequence compar...

  17. An Adaptive Approach to Managing Knowledge Development in a Project-Based Learning Environment

    Science.gov (United States)

    Tilchin, Oleg; Kittany, Mohamed

    2016-01-01

    In this paper we propose an adaptive approach to managing the development of students' knowledge in the comprehensive project-based learning (PBL) environment. Subject study is realized by two-stage PBL. It shapes adaptive knowledge management (KM) process and promotes the correct balance between personalized and collaborative learning. The…

  18. Bioinformatics Methods for Interpreting Toxicogenomics Data: The Role of Text-Mining

    NARCIS (Netherlands)

    Hettne, K.M.; Kleinjans, J.; Stierum, R.H.; Boorsma, A.; Kors, J.A.

    2014-01-01

    This chapter concerns the application of bioinformatics methods to the analysis of toxicogenomics data. The chapter starts with an introduction covering how bioinformatics has been applied in toxicogenomics data analysis, and continues with a description of the foundations of a specific

  19. Influenza research database: an integrated bioinformatics resource for influenza virus research

    Science.gov (United States)

    The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics, an...

  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. Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches.

    Science.gov (United States)

    Oulas, Anastasis; Minadakis, George; Zachariou, Margarita; Sokratous, Kleitos; Bourdakou, Marilena M; Spyrou, George M

    2017-11-27

    Systems Bioinformatics is a relatively new approach, which lies in the intersection of systems biology and classical bioinformatics. It focuses on integrating information across different levels using a bottom-up approach as in systems biology with a data-driven top-down approach as in bioinformatics. The advent of omics technologies has provided the stepping-stone for the emergence of Systems Bioinformatics. These technologies provide a spectrum of information ranging from genomics, transcriptomics and proteomics to epigenomics, pharmacogenomics, metagenomics and metabolomics. Systems Bioinformatics is the framework in which systems approaches are applied to such data, setting the level of resolution as well as the boundary of the system of interest and studying the emerging properties of the system as a whole rather than the sum of the properties derived from the system's individual components. A key approach in Systems Bioinformatics is the construction of multiple networks representing each level of the omics spectrum and their integration in a layered network that exchanges information within and between layers. Here, we provide evidence on how Systems Bioinformatics enhances computational therapeutics and diagnostics, hence paving the way to precision medicine. The aim of this review is to familiarize the reader with the emerging field of Systems Bioinformatics and to provide a comprehensive overview of its current state-of-the-art methods and technologies. Moreover, we provide examples of success stories and case studies that utilize such methods and tools to significantly advance research in the fields of systems biology and systems medicine. © The Author 2017. Published by Oxford University Press.

  2. Effects of environment and education on knowledge and attitude of nursing students towards leprosy.

    Science.gov (United States)

    Rajkumar, E; Julious, S; Salome, A; Jennifer, G; John, A S; Kannan, L; Richard, J

    2011-01-01

    The objective of this cross-sectional comparative study was to find the effects of environment and education on knowledge and attitude of nursing students towards leprosy. Data were collected, using a pretested questionnaire, from the first year and third year students of a School of Nursing attached to a leprosy specialty hospital and also from a comparable School of Nursing attached to a general hospital. The results showed that trainees acquired more knowledge on leprosy during training in both schools of nursing. However, those trained in leprosy hospital environment had higher knowledge and attitude scores than those trained in general hospital environment. The attitude of the trainees attached to leprosy hospital was favourable even before they had formal training in leprosy. Those trained in the general hospital showed more favourable attitude after training compared to before training. School of Nursing attached to leprosy hospital provided an atmosphere conducive to learning and understanding more about leprosy. The trainees retained what was learnt because of regular association with patients affected by leprosy. For employment in hospital or community based services or research related to leprosy, nurses trained in a leprosy hospital would have added value of knowledge and attitude.

  3. The growing need for microservices in bioinformatics

    Directory of Open Access Journals (Sweden)

    Christopher L Williams

    2016-01-01

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

  4. The growing need for microservices in bioinformatics.

    Science.gov (United States)

    Williams, Christopher L; Sica, Jeffrey C; Killen, Robert T; Balis, Ulysses G J

    2016-01-01

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

  5. The growing need for microservices in bioinformatics

    Science.gov (United States)

    Williams, Christopher L.; Sica, Jeffrey C.; Killen, Robert T.; Balis, Ulysses G. J.

    2016-01-01

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

  6. Illuminate Knowledge Elements in Geoscience Literature

    Science.gov (United States)

    Ma, X.; Zheng, J. G.; Wang, H.; Fox, P. A.

    2015-12-01

    There are numerous dark data hidden in geoscience literature. Efficient retrieval and reuse of those data will greatly benefit geoscience researches of nowadays. Among the works of data rescue, a topic of interest is illuminating the knowledge framework, i.e. entities and relationships, embedded in documents. Entity recognition and linking have received extensive attention in news and social media analysis, as well as in bioinformatics. In the domain of geoscience, however, such works are limited. We will present our work on how to use knowledge bases on the Web, such as ontologies and vocabularies, to facilitate entity recognition and linking in geoscience literature. The work deploys an un-supervised collective inference approach [1] to link entity mentions in unstructured texts to a knowledge base, which leverages the meaningful information and structures in ontologies and vocabularies for similarity computation and entity ranking. Our work is still in the initial stage towards the detection of knowledge frameworks in literature, and we have been collecting geoscience ontologies and vocabularies in order to build a comprehensive geoscience knowledge base [2]. We hope the work will initiate new ideas and collaborations on dark data rescue, as well as on the synthesis of data and knowledge from geoscience literature. References: 1. Zheng, J., Howsmon, D., Zhang, B., Hahn, J., McGuinness, D.L., Hendler, J., and Ji, H. 2014. Entity linking for biomedical literature. In Proceedings of ACM 8th International Workshop on Data and Text Mining in Bioinformatics, Shanghai, China. 2. Ma, X. Zheng, J., 2015. Linking geoscience entity mentions to the Web of Data. ESIP 2015 Summer Meeting, Pacific Grove, CA.

  7. 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…

  8. Capture and Reuse of Knowledge in ICT-based Decisional Environments

    Directory of Open Access Journals (Sweden)

    Florin Gheorghe FILIP

    2009-01-01

    Full Text Available Health care practitioners continually confront with a wide range of challenges, seeking to making difficult diagnoses, avoiding errors, ensuring highest quality, maximizing efficacy and reducing costs. Information technology has the potential to reduce clinical errors and to im-prove the decision making in the clinical milieu. This paper presents a pilot development of a clinical decision support systems (CDSS entitled MEDIS that was designed to incorporate knowledge from heterogeneous environments with the purpose of increasing the efficiency and the quality of the decision making process, and reducing costs based on advances of in-formation technologies, especially under the impact of the transition towards the mobile space. The system aims to capture and reuse knowledge in order to provide real-time access to clinical knowledge for a variety of users, including medical personnel, patients, teachers and students.

  9. A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

    Science.gov (United States)

    Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

    2012-07-01

    The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

  10. 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…

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

    Science.gov (United States)

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

    2015-06-02

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

  12. SPECIES DATABASES AND THE BIOINFORMATICS REVOLUTION.

    Science.gov (United States)

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

  13. PERFECT KNOWLEDGE MANAGEMENT SYSTEM AS REQUIREMENT FOR AN ENTERPRISE TO SURVIVE IN MARKET COMPETITION ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    A. E. Zhukov

    2012-01-01

    Full Text Available Knowledge, along with skills and abilities forms the concept of professional qualification. Knowledge management as function and type of enterprise management activities includes making the knowledge more practically valuable and creating an active learning environment. Acquisition and assimilation of new knowledge includes six steps discussed in the article: definition, acquisition, selection, storage, distribution, use, development and implementation.

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

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

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

  15. Bioinformatics in New Generation Flavivirus Vaccines

    Directory of Open Access Journals (Sweden)

    Penelope Koraka

    2010-01-01

    Full Text Available Flavivirus infections are the most prevalent arthropod-borne infections world wide, often causing severe disease especially among children, the elderly, and the immunocompromised. In the absence of effective antiviral treatment, prevention through vaccination would greatly reduce morbidity and mortality associated with flavivirus infections. Despite the success of the empirically developed vaccines against yellow fever virus, Japanese encephalitis virus and tick-borne encephalitis virus, there is an increasing need for a more rational design and development of safe and effective vaccines. Several bioinformatic tools are available to support such rational vaccine design. In doing so, several parameters have to be taken into account, such as safety for the target population, overall immunogenicity of the candidate vaccine, and efficacy and longevity of the immune responses triggered. Examples of how bio-informatics is applied to assist in the rational design and improvements of vaccines, particularly flavivirus vaccines, are presented and discussed.

  16. Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades.

    Science.gov (United States)

    Wren, Jonathan D

    2016-09-01

    To analyze the relative proportion of bioinformatics papers and their non-bioinformatics counterparts in the top 20 most cited papers annually for the past two decades. When defining bioinformatics papers as encompassing both those that provide software for data analysis or methods underlying data analysis software, we find that over the past two decades, more than a third (34%) of the most cited papers in science were bioinformatics papers, which is approximately a 31-fold enrichment relative to the total number of bioinformatics papers published. More than half of the most cited papers during this span were bioinformatics papers. Yet, the average 5-year JIF of top 20 bioinformatics papers was 7.7, whereas the average JIF for top 20 non-bioinformatics papers was 25.8, significantly higher (P papers, bioinformatics journals tended to have higher Gini coefficients, suggesting that development of novel bioinformatics resources may be somewhat 'hit or miss'. That is, relative to other fields, bioinformatics produces some programs that are extremely widely adopted and cited, yet there are fewer of intermediate success. jdwren@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  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. Cross-Analysis of Data Collected on Knowledge Management Practices in Canadian Forces Environments

    National Research Council Canada - National Science Library

    Lecocq, R; Gauvin, M

    2004-01-01

    ...) practices, namely on Knowledge Creation, Learning and Collaboration, the present work performs a detailed comparison of the states of these practices between the different military environments...

  19. Open source tools and toolkits for bioinformatics: significance, and where are we?

    Science.gov (United States)

    Stajich, Jason E; Lapp, Hilmar

    2006-09-01

    This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

  20. mORCA: sailing bioinformatics world with mobile devices.

    Science.gov (United States)

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

    2018-03-01

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

  1. 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.

  2. Nuclear Knowledge Creation and Transfer in Enriched Learning Environments: A Practical Approach

    International Nuclear Information System (INIS)

    Ruiz, F.; Gonzalez, J.; Delgado, J.L.

    2016-01-01

    Full text: Technology, the social nature of learning and the generational learning style are conforming new models of training that are changing the roles of the instructors, the channels of communication and the proper learning content of the knowledge to be transferred. New training methodologies are being using in the primary and secondary education and “Vintage” classroom learning does not meet the educational requirements of these methodologies; therefore, it’s necessary to incorporate them in the Knowledge Management processes used in the nuclear industry. This paper describes a practical approach of an enriched learning environment with the purpose of creating and transferring nuclear knowledge. (author

  3. Knowledge management a competitive edge for law firms in Botswana in the changing business environment

    Directory of Open Access Journals (Sweden)

    Madeleine Fombad

    2015-08-01

    Full Text Available Background: Law firms in Botswana offer a particularly interesting context to explore the effects of transition in the knowledge economy. Acquiring and leveraging knowledge effectively in law firms through knowledge management can result in competitive advantage; yet the adoption of this approach remains in its infancy. Objectives: This article investigates the factors that will motivate the adoption of knowledge management in law firms in Botswana, and creates an awareness of the potential benefits of knowledge management in these firms. Method: The article uses both quantitative and qualitative research methods and the survey research design. A survey was performed on all 115 registered law firms and 217 lawyers in Botswana. Interviews were conducted with selected lawyers for more insight. Results: Several changes in the legal environment have motivated law firms to adopt knowledge management. Furthermore, lawyers appreciate the potential benefits of knowledge management. Conclusion: With the rise of the knowledge-based economy, coupled with the pressures faced by the legal industry in recent years, law firms in Botswana can no longer afford to rely on the traditional methods of managing knowledge. Knowledge management will, therefore, enhance the cost effectiveness of these firms. Strategic knowledge management certainly helps to prepare law firms in Botswana to be alive to the fact that the systematic harnessing of legal knowledge is no longer a luxury, but an absolute necessity in the knowledge economy. It will also provide an enabling business environment for private sector development and growth and, therefore, facilitate Botswana’s drive towards the knowledge-based economy.

  4. A global perspective on evolving bioinformatics and data science training needs.

    Science.gov (United States)

    Attwood, Teresa K; Blackford, Sarah; Brazas, Michelle D; Davies, Angela; Schneider, Maria Victoria

    2017-08-29

    Bioinformatics is now intrinsic to life science research, but the past decade has witnessed a continuing deficiency in this essential expertise. Basic data stewardship is still taught relatively rarely in life science education programmes, creating a chasm between theory and practice, and fuelling demand for bioinformatics training across all educational levels and career roles. Concerned by this, surveys have been conducted in recent years to monitor bioinformatics and computational training needs worldwide. This article briefly reviews the principal findings of a number of these studies. We see that there is still a strong appetite for short courses to improve expertise and confidence in data analysis and interpretation; strikingly, however, the most urgent appeal is for bioinformatics to be woven into the fabric of life science degree programmes. Satisfying the relentless training needs of current and future generations of life scientists will require a concerted response from stakeholders across the globe, who need to deliver sustainable solutions capable of both transforming education curricula and cultivating a new cadre of trainer scientists. © The Author 2017. Published by Oxford University Press.

  5. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

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

  6. 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'…

  7. A Knowledge Comparison Environment for Supporting Meaningful Learning of E-Book Users

    Directory of Open Access Journals (Sweden)

    Jingyun Wang

    2016-05-01

    Full Text Available In this paper, we present an ontology-based visualization support system which can provide a meaningful learning environment to help e-book learners to effectively construct their knowledge frameworks. In this personalized visualization support system, learners are encouraged to actively locate new knowledge in their own knowledge framework and check the logical consistency of their ideas for clearing up misunderstandings; on the other hand, instructors will be able to decide the group distribution for collaborative learning activities based on the knowledge structure of learners. For facilitating those visualization supports, a method to semi-automatically construct a course-centered ontology to describe the required information in a map structure is presented. To automatically manipulate this course-centered ontology to provide visualization learning supports, a prototype system is designed and developed.

  8. Advance in structural bioinformatics

    CERN Document Server

    Wei, Dongqing; Zhao, Tangzhen; Dai, Hao

    2014-01-01

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

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

    Science.gov (United States)

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

    2017-09-15

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

  10. What is bioinformatics? A proposed definition and overview of the field.

    Science.gov (United States)

    Luscombe, N M; Greenbaum, D; Gerstein, M

    2001-01-01

    The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems. Our definition is as follows: Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomics experiments (e.g. expression data). Additional information includes the text of scientific papers and "relationship data" from metabolic pathways, taxonomy trees, and protein-protein interaction networks. Bioinformatics employs a wide range of computational techniques including sequence and structural alignment, database design and data mining, macromolecular geometry, phylogenetic tree construction, prediction of protein structure and function, gene finding, and expression data clustering. The emphasis is on approaches integrating a variety of computational methods and heterogeneous data sources. Finally, bioinformatics is a practical discipline. We survey some representative applications, such as finding homologues, designing drugs, and performing large-scale censuses. Additional information pertinent to the review is available over the web at http://bioinfo.mbb.yale.edu/what-is-it.

  11. An overview of topic modeling and its current applications in bioinformatics.

    Science.gov (United States)

    Liu, Lin; Tang, Lin; Dong, Wen; Yao, Shaowen; Zhou, Wei

    2016-01-01

    With the rapid accumulation of biological datasets, machine learning methods designed to automate data analysis are urgently needed. In recent years, so-called topic models that originated from the field of natural language processing have been receiving much attention in bioinformatics because of their interpretability. Our aim was to review the application and development of topic models for bioinformatics. This paper starts with the description of a topic model, with a focus on the understanding of topic modeling. A general outline is provided on how to build an application in a topic model and how to develop a topic model. Meanwhile, the literature on application of topic models to biological data was searched and analyzed in depth. According to the types of models and the analogy between the concept of document-topic-word and a biological object (as well as the tasks of a topic model), we categorized the related studies and provided an outlook on the use of topic models for the development of bioinformatics applications. Topic modeling is a useful method (in contrast to the traditional means of data reduction in bioinformatics) and enhances researchers' ability to interpret biological information. Nevertheless, due to the lack of topic models optimized for specific biological data, the studies on topic modeling in biological data still have a long and challenging road ahead. We believe that topic models are a promising method for various applications in bioinformatics research.

  12. "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).…

  13. 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…

  14. 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…

  15. 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…

  16. Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

    Science.gov (United States)

    Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

    2012-01-01

    With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

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

    Science.gov (United States)

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

    2016-06-13

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

  18. A Quick Guide for Building a Successful Bioinformatics Community

    Science.gov (United States)

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

    2015-01-01

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

  19. 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…

  20. XML schemas for common bioinformatic data types and their application in workflow systems.

    Science.gov (United States)

    Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

    2006-11-06

    Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

  1. XML schemas for common bioinformatic data types and their application in workflow systems

    Science.gov (United States)

    Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

    2006-01-01

    Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

  2. BioRuby: bioinformatics software for the Ruby programming language.

    Science.gov (United States)

    Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

    2010-10-15

    The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

  3. Genomics and bioinformatics resources for translational science in Rosaceae.

    Science.gov (United States)

    Jung, Sook; Main, Dorrie

    2014-01-01

    Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.

  4. A Collaborative Extensible User Environment for Simulation and Knowledge Management

    Energy Technology Data Exchange (ETDEWEB)

    Freedman, Vicky L.; Lansing, Carina S.; Porter, Ellen A.; Schuchardt, Karen L.; Guillen, Zoe C.; Sivaramakrishnan, Chandrika; Gorton, Ian

    2015-06-01

    In scientific simulation, scientists use measured data to create numerical models, execute simulations and analyze results from advanced simulators executing on high performance computing platforms. This process usually requires a team of scientists collaborating on data collection, model creation and analysis, and on authorship of publications and data. This paper shows that scientific teams can benefit from a user environment called Akuna that permits subsurface scientists in disparate locations to collaborate on numerical modeling and analysis projects. The Akuna user environment is built on the Velo framework that provides both a rich client environment for conducting and analyzing simulations and a Web environment for data sharing and annotation. Akuna is an extensible toolset that integrates with Velo, and is designed to support any type of simulator. This is achieved through data-driven user interface generation, use of a customizable knowledge management platform, and an extensible framework for simulation execution, monitoring and analysis. This paper describes how the customized Velo content management system and the Akuna toolset are used to integrate and enhance an effective collaborative research and application environment. The extensible architecture of Akuna is also described and demonstrates its usage for creation and execution of a 3D subsurface simulation.

  5. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

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

  6. 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…

  7. DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function.

    Science.gov (United States)

    Cheng, Liang; Hu, Yang; Sun, Jie; Zhou, Meng; Jiang, Qinghua

    2018-06-01

    DincRNA aims to provide a comprehensive web-based bioinformatics toolkit to elucidate the entangled relationships among diseases and non-coding RNAs (ncRNAs) from the perspective of disease similarity. The quantitative way to illustrate relationships of pair-wise diseases always depends on their molecular mechanisms, and structures of the directed acyclic graph of Disease Ontology (DO). Corresponding methods for calculating similarity of pair-wise diseases involve Resnik's, Lin's, Wang's, PSB and SemFunSim methods. Recently, disease similarity was validated suitable for calculating functional similarities of ncRNAs and prioritizing ncRNA-disease pairs, and it has been widely applied for predicting the ncRNA function due to the limited biological knowledge from wet lab experiments of these RNAs. For this purpose, a large number of algorithms and priori knowledge need to be integrated. e.g. 'pair-wise best, pairs-average' (PBPA) and 'pair-wise all, pairs-maximum' (PAPM) methods for calculating functional similarities of ncRNAs, and random walk with restart (RWR) method for prioritizing ncRNA-disease pairs. To facilitate the exploration of disease associations and ncRNA function, DincRNA implemented all of the above eight algorithms based on DO and disease-related genes. Currently, it provides the function to query disease similarity scores, miRNA and lncRNA functional similarity scores, and the prioritization scores of lncRNA-disease and miRNA-disease pairs. http://bio-annotation.cn:18080/DincRNAClient/. biofomeng@hotmail.com or qhjiang@hit.edu.cn. Supplementary data are available at Bioinformatics online.

  8. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  10. Accessible Knowledge - Knowledge on Accessibility

    DEFF Research Database (Denmark)

    Kirkeby, Inge Mette

    2015-01-01

    Although serious efforts are made internationally and nationally, it is a slow process to make our physical environment accessible. In the actual design process, architects play a major role. But what kinds of knowledge, including research-based knowledge, do practicing architects make use of when...... designing accessible environments? The answer to the question is crucially important since it affects how knowledge is distributed and how accessibility can be ensured. In order to get first-hand knowledge about the design process and the sources from which they gain knowledge, 11 qualitative interviews...... were conducted with architects with experience of designing for accessibility. The analysis draws on two theoretical distinctions. The first is research-based knowledge versus knowledge used by architects. The second is context-independent knowledge versus context-dependent knowledge. The practitioners...

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

    Directory of Open Access Journals (Sweden)

    Geraint Duck

    Full Text Available 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.

  12. Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

    Science.gov (United States)

    Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

    2012-07-01

    With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders

    Directory of Open Access Journals (Sweden)

    Martin Hofmann-Apitius

    2015-12-01

    Full Text Available Since the decoding of the Human Genome, techniques from bioinformatics, statistics, and machine learning have been instrumental in uncovering patterns in increasing amounts and types of different data produced by technical profiling technologies applied to clinical samples, animal models, and cellular systems. Yet, progress on unravelling biological mechanisms, causally driving diseases, has been limited, in part due to the inherent complexity of biological systems. Whereas we have witnessed progress in the areas of cancer, cardiovascular and metabolic diseases, the area of neurodegenerative diseases has proved to be very challenging. This is in part because the aetiology of neurodegenerative diseases such as Alzheimer´s disease or Parkinson´s disease is unknown, rendering it very difficult to discern early causal events. Here we describe a panel of bioinformatics and modeling approaches that have recently been developed to identify candidate mechanisms of neurodegenerative diseases based on publicly available data and knowledge. We identify two complementary strategies—data mining techniques using genetic data as a starting point to be further enriched using other data-types, or alternatively to encode prior knowledge about disease mechanisms in a model based framework supporting reasoning and enrichment analysis. Our review illustrates the challenges entailed in integrating heterogeneous, multiscale and multimodal information in the area of neurology in general and neurodegeneration in particular. We conclude, that progress would be accelerated by increasing efforts on performing systematic collection of multiple data-types over time from each individual suffering from neurodegenerative disease. The work presented here has been driven by project AETIONOMY; a project funded in the course of the Innovative Medicines Initiative (IMI; which is a public-private partnership of the European Federation of Pharmaceutical Industry Associations

  14. Computational biology of genome expression and regulation--a review of microarray bioinformatics.

    Science.gov (United States)

    Wang, Junbai

    2008-01-01

    Microarray technology is being used widely in various biomedical research areas; the corresponding microarray data analysis is an essential step toward the best utilizing of array technologies. Here we review two components of the microarray data analysis: a low level of microarray data analysis that emphasizes the designing, the quality control, and the preprocessing of microarray experiments, then a high level of microarray data analysis that focuses on the domain-specific microarray applications such as tumor classification, biomarker prediction, analyzing array CGH experiments, and reverse engineering of gene expression networks. Additionally, we will review the recent development of building a predictive model in genome expression and regulation studies. This review may help biologists grasp a basic knowledge of microarray bioinformatics as well as its potential impact on the future evolvement of biomedical research fields.

  15. clubber: removing the bioinformatics bottleneck in big data analyses

    Science.gov (United States)

    Miller, Maximilian; Zhu, Chengsheng; Bromberg, Yana

    2018-01-01

    With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these “big data” analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber’s goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment. PMID:28609295

  16. clubber: removing the bioinformatics bottleneck in big data analyses.

    Science.gov (United States)

    Miller, Maximilian; Zhu, Chengsheng; Bromberg, Yana

    2017-06-13

    With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these "big data" analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber's goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment.

  17. clubber: removing the bioinformatics bottleneck in big data analyses

    Directory of Open Access Journals (Sweden)

    Miller Maximilian

    2017-06-01

    Full Text Available With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these “big data” analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber’s goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min clearly illustrate the importance of clubber in the everyday computational biology environment.

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

    Science.gov (United States)

    Fourment, Mathieu; Gillings, Michael R

    2008-02-05

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

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

    Science.gov (United States)

    Cazals, Frédéric; Dreyfus, Tom

    2017-04-01

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

  20. Green Fluorescent Protein-Focused Bioinformatics Laboratory Experiment Suitable for Undergraduates in Biochemistry Courses

    Science.gov (United States)

    Rowe, Laura

    2017-01-01

    An introductory bioinformatics laboratory experiment focused on protein analysis has been developed that is suitable for undergraduate students in introductory biochemistry courses. The laboratory experiment is designed to be potentially used as a "stand-alone" activity in which students are introduced to basic bioinformatics tools and…

  1. Rough-fuzzy pattern recognition applications in bioinformatics and medical imaging

    CERN Document Server

    Maji, Pradipta

    2012-01-01

    Learn how to apply rough-fuzzy computing techniques to solve problems in bioinformatics and medical image processing Emphasizing applications in bioinformatics and medical image processing, this text offers a clear framework that enables readers to take advantage of the latest rough-fuzzy computing techniques to build working pattern recognition models. The authors explain step by step how to integrate rough sets with fuzzy sets in order to best manage the uncertainties in mining large data sets. Chapters are logically organized according to the major phases of pattern recognition systems dev

  2. Bioinformatics and moonlighting proteins

    Directory of Open Access Journals (Sweden)

    Sergio eHernández

    2015-06-01

    Full Text Available Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyse and describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are: a remote homology searches using Psi-Blast, b detection of functional motifs and domains, c analysis of data from protein-protein interaction databases (PPIs, d match the query protein sequence to 3D databases (i.e., algorithms as PISITE, e mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs have the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations –it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/, previously published by our group, has been used as a benchmark for the all of the analyses.

  3. VET Students' Integration of Knowledge Engaged with in School-Based and Workplace-Based Learning Environments in the Netherlands

    Science.gov (United States)

    Baartman, L. K. J.; Kilbrink, N.; de Bruijn, E.

    2018-01-01

    In vocational education, students learn in different school-based and workplace-based learning environments and engage with different types of knowledge in these environments. Students are expected to integrate these experiences and make meaning of them in relation to their own professional knowledge base. This study focuses both on…

  4. Knowledge exchange and learning from failures in distributed environments: The role of contractor relationship management and work characteristics

    International Nuclear Information System (INIS)

    Gressgård, Leif Jarle; Hansen, Kåre

    2015-01-01

    Learning from failures is vital for improvement of safety performance, reliability, and resilience in organizations. In order for such learning to take place in distributed environments, knowledge has to be shared among organizational members at different locations and units. This paper reports on a study conducted in the context of drilling and well operations on the Norwegian Continental Shelf, which represents a high-risk distributed organizational environment. The study investigates the relationships between organizations' abilities to learn from failures, knowledge exchange within and between organizational units, quality of contractor relationship management, and work characteristics. The results show that knowledge exchange between units is the most important predictor of perceived ability to learn from failures. Contractor relationship management, leadership involvement, role clarity, and empowerment are also important factors for failure-based learning, both directly and through increased knowledge exchange. The results of the study enhance our understanding of how abilities to learn from failures can be improved in distributed environments where similar work processes take place at different locations and involve employees from several companies. Theoretical contributions and practical implications are discussed. - Highlights: • We investigate factors affecting failure-based learning in distributed environments. • Knowledge exchange between units is the most important predictor. • Contractor relationship management is positively related to knowledge exchange. • Leadership involvement, role clarity, and empowerment are significant variables. • Respondents from an operator firm and eight contractors are included in the study

  5. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    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; Nyrö nen, Tommi; Rother, Kristian; Schneider, Maria Victoria; Attwood, Teresa K

    2013-01-01

    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

  6. Engaging Students in a Bioinformatics Activity to Introduce Gene Structure and Function

    Directory of Open Access Journals (Sweden)

    Barbara J. May

    2013-02-01

    Full Text Available Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools.  This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools.  Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the putative function of this gene with the use of additional online databases.

  7. Rise and demise of bioinformatics? Promise and progress.

    Directory of Open Access Journals (Sweden)

    Christos A Ouzounis

    Full Text Available The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself.

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

    Science.gov (United States)

    Counsell, Damian

    2002-01-01

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

  9. Effects of prior knowledge on learning from different compositions of representations in a mobile learning environment

    NARCIS (Netherlands)

    T.-C. Liu (Tzu-Chien); Y.-C. Lin (Yi-Chun); G.W.C. Paas (Fred)

    2014-01-01

    textabstractTwo experiments examined the effects of prior knowledge on learning from different compositions of multiple representations in a mobile learning environment on plant leaf morphology for primary school students. Experiment 1 compared the learning effects of a mobile learning environment

  10. ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser

    Directory of Open Access Journals (Sweden)

    Jonas S Almeida

    2012-01-01

    Full Text Available Background: Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. Materials and Methods: ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Results : Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH′s popular ImageJ application. Conclusions : The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without

  11. ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

    Science.gov (United States)

    Almeida, Jonas S; Iriabho, Egiebade E; Gorrepati, Vijaya L; Wilkinson, Sean R; Grüneberg, Alexander; Robbins, David E; Hackney, James R

    2012-01-01

    Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local "download and installation".

  12. 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

  13. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics

    CERN Document Server

    Mohamad, Mohd; Rocha, Miguel; Paz, Juan; Pinto, Tiago

    2017-01-01

    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 constantly evolving, distinct types of omics data technologies, have created an increasingly complex set of challenges for the growing fields of Bioinformatics and Computational Biology. The analysis of the datasets produced and their integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Clearly, Biology is more and more a science of information and requires tools from the computational sciences. In the last few years, we have seen the rise of a new generation of interdisciplinary scientists with a strong background in the biological and computational sciences. In this context, the interaction of r...

  14. 8th International Conference on Practical Applications of Computational Biology & Bioinformatics

    CERN Document Server

    Rocha, Miguel; Fdez-Riverola, Florentino; Santana, Juan

    2014-01-01

    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 of the datasets produced and their integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Clearly, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researche...

  15. 10th International Conference on Practical Applications of Computational Biology & Bioinformatics

    CERN Document Server

    Rocha, Miguel; Fdez-Riverola, Florentino; Mayo, Francisco; Paz, Juan

    2016-01-01

    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 of the datasets produced and their integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Clearly, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researche...

  16. RISE OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY IN INDIA: A LOOK THROUGH PUBLICATIONS

    Directory of Open Access Journals (Sweden)

    Anjali Srivastava

    2017-09-01

    Full Text Available Computational biology and bioinformatics have been part and parcel of biomedical research for few decades now. However, the institutionalization of bioinformatics research took place with the establishment of Distributed Information Centres (DISCs in the research institutions of repute in various disciplines by the Department of Biotechnology, Government of India. Though, at initial stages, this endeavor was mainly focused on providing infrastructure for using information technology and internet based communication and tools for carrying out computational biology and in-silico assisted research in varied arena of research starting from disease biology to agricultural crops, spices, veterinary science and many more, the natural outcome of establishment of such facilities resulted into new experiments with bioinformatics tools. Thus, Biotechnology Information Systems (BTIS grew into a solid movement and a large number of publications started coming out of these centres. In the end of last century, bioinformatics started developing like a full-fledged research subject. In the last decade, a need was felt to actually make a factual estimation of the result of this endeavor of DBT which had, by then, established about two hundred centres in almost all disciplines of biomedical research. In a bid to evaluate the efforts and outcome of these centres, BTIS Centre at CSIR-CDRI, Lucknow was entrusted with collecting and collating the publications of these centres. However, when the full data was compiled, the DBT task force felt that the study must include Non-BTIS centres also so as to expand the report to have a glimpse of bioinformatics publications from the country.

  17. Assessing Perceived Knowledge Creation: The Role of Organizational Knowledge and Market Environment

    Directory of Open Access Journals (Sweden)

    Khalid Abdul Wahid

    2016-06-01

    Full Text Available The purpose of this research is to investigate the impact of organizational knowledge factors and market knowledge factors on knowledge creation among Thai innovative companies. 464 questionnaires were distributed to Thai innovative companies registered under the National Innovation Agency (NIA and 217 were returned. Structural Equation Modelling (SEM is used to determine the effect of two sets of knowledge creation sources: organizational knowledge (social interaction, organizational routines and information system and market knowledge (customer orientation, competitor orientation and supplier orientation on knowledge creation (product and service outcome, process outcome and market outcome. The results indicated that the integration of organizational knowledge and market knowledge is the main driver of knowledge creation. Furthermore, the findings suggest that social interaction and customer orientation are the most significant predictors of knowledge creation. This study provides an empirical analysis on the importance of different sources of knowledge in the knowledge creation process in SMEs and its impact on companies’ innovative knowledge outcomes.

  18. Romanian Business Environment in the Context of Economic Competitiveness Based on Knowledge

    Directory of Open Access Journals (Sweden)

    Ion STEGAROIU

    2012-11-01

    Full Text Available The changes of production factors priorities affect more and more the evolution of global economy, requiring reorientation of development policies both at company level and at national economies level to adapt to the phenomenon called: “the new economy” or “knowledge economy”. If for classical economy the ability to compete - competitiveness- depends largely on the quantity or the amount of production factors, at the present, has gained importance the efficiency of their use. The idea of making this article appeared both from the necessity of a systematic research to approach the Romanian competitive environment and the desire to stoop to this important conference theme. We can certainly say that the actual business environment is characterized by a particularly dynamic due to changes that occur within it, especially under the impact of technical and scientific revolution which brought to the fore the knowledge as an essential element of achieving a high competitiveness. It is intended that the proposed theme of this article to have an economic importance for the actual information and adequacy of the current economy in Romania.

  19. Secure Encapsulation and Publication of Biological Services in the Cloud Computing Environment

    Science.gov (United States)

    Zhang, Weizhe; Wang, Xuehui; Lu, Bo; Kim, Tai-hoon

    2013-01-01

    Secure encapsulation and publication for bioinformatics software products based on web service are presented, and the basic function of biological information is realized in the cloud computing environment. In the encapsulation phase, the workflow and function of bioinformatics software are conducted, the encapsulation interfaces are designed, and the runtime interaction between users and computers is simulated. In the publication phase, the execution and management mechanisms and principles of the GRAM components are analyzed. The functions such as remote user job submission and job status query are implemented by using the GRAM components. The services of bioinformatics software are published to remote users. Finally the basic prototype system of the biological cloud is achieved. PMID:24078906

  20. Secure Encapsulation and Publication of Biological Services in the Cloud Computing Environment

    Directory of Open Access Journals (Sweden)

    Weizhe Zhang

    2013-01-01

    Full Text Available Secure encapsulation and publication for bioinformatics software products based on web service are presented, and the basic function of biological information is realized in the cloud computing environment. In the encapsulation phase, the workflow and function of bioinformatics software are conducted, the encapsulation interfaces are designed, and the runtime interaction between users and computers is simulated. In the publication phase, the execution and management mechanisms and principles of the GRAM components are analyzed. The functions such as remote user job submission and job status query are implemented by using the GRAM components. The services of bioinformatics software are published to remote users. Finally the basic prototype system of the biological cloud is achieved.

  1. Secure encapsulation and publication of biological services in the cloud computing environment.

    Science.gov (United States)

    Zhang, Weizhe; Wang, Xuehui; Lu, Bo; Kim, Tai-hoon

    2013-01-01

    Secure encapsulation and publication for bioinformatics software products based on web service are presented, and the basic function of biological information is realized in the cloud computing environment. In the encapsulation phase, the workflow and function of bioinformatics software are conducted, the encapsulation interfaces are designed, and the runtime interaction between users and computers is simulated. In the publication phase, the execution and management mechanisms and principles of the GRAM components are analyzed. The functions such as remote user job submission and job status query are implemented by using the GRAM components. The services of bioinformatics software are published to remote users. Finally the basic prototype system of the biological cloud is achieved.

  2. Knowledge, attitudes, and environment: what primary care providers say about pre-school vision screening.

    Science.gov (United States)

    Marsh-Tootle, Wendy L; Funkhouser, Ellen; Frazier, Marcela G; Crenshaw, Katie; Wall, Terry C

    2010-02-01

    To evaluate knowledge, attitudes, and environment of primary care providers, and to develop a conceptual framework showing their impact on self-reported pre-school vision screening (PVS) behaviors. Eligible primary care providers were individuals who filed claims with Medicaid agencies in Alabama, South Carolina, or Illinois, for at least eight well child checks for children aged 3 or 4 years during 1 year. Responses were obtained on-line from providers who enrolled in the intervention arm of a randomized trial to improve PVS. We calculated a summary score per provider per facet: (1) for behavior and knowledge, each correct answer was assigned a value of +1; and (2) for attitudes and environment, responses indicating support for PVS were assigned a value of +1, and other responses were assigned -1. Responses were available from 53 participants (43 of 49 enrolled pediatricians, 8 of 14 enrolled family physicians, one general physician, and one nurse practitioner). Recognizing that amblyopia often presents without outward signs was positively related to good PVS: [odds ratio (OR) = 3.9; p = 0.06]. Reporting that "preschool VS interrupts patient flow" posed a significant barrier (OR = 0.2; p = 0.05). Providers with high summed scores on attitudes (OR = 6.0; p = 0.03), or knowledge and attitudes (OR = 11.4; p attitudes or environment, and "good" PVS behavior (p = 0.04). PVS is influenced by positive attitudes, especially when combined with knowledge about amblyopia. Interventions to improve PVS should target multiple facets, emphasizing (1) asymptomatic children are at risk for amblyopia, (2) specific evidence-based tests have high testability and sensitivity for amblyopia in pre-school children, and (3) new tests minimize interruptions to patient flow.

  3. A review of bioinformatics training applied to research in molecular medicine, agriculture and biodiversity in Costa Rica and Central America.

    Science.gov (United States)

    Orozco, Allan; Morera, Jessica; Jiménez, Sergio; Boza, Ricardo

    2013-09-01

    Today, Bioinformatics has become a scientific discipline with great relevance for the Molecular Biosciences and for the Omics sciences in general. Although developed countries have progressed with large strides in Bioinformatics education and research, in other regions, such as Central America, the advances have occurred in a gradual way and with little support from the Academia, either at the undergraduate or graduate level. To address this problem, the University of Costa Rica's Medical School, a regional leader in Bioinformatics in Central America, has been conducting a series of Bioinformatics workshops, seminars and courses, leading to the creation of the region's first Bioinformatics Master's Degree. The recent creation of the Central American Bioinformatics Network (BioCANET), associated to the deployment of a supporting computational infrastructure (HPC Cluster) devoted to provide computing support for Molecular Biology in the region, is providing a foundational stone for the development of Bioinformatics in the area. Central American bioinformaticians have participated in the creation of as well as co-founded the Iberoamerican Bioinformatics Society (SOIBIO). In this article, we review the most recent activities in education and research in Bioinformatics from several regional institutions. These activities have resulted in further advances for Molecular Medicine, Agriculture and Biodiversity research in Costa Rica and the rest of the Central American countries. Finally, we provide summary information on the first Central America Bioinformatics International Congress, as well as the creation of the first Bioinformatics company (Indromics Bioinformatics), spin-off the Academy in Central America and the Caribbean.

  4. 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:…

  5. Protein raftophilicity. How bioinformatics can help membranologists

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Sperotto, Maria Maddalena

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

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

    African Journals Online (AJOL)

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

  7. An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids.

    Science.gov (United States)

    Barrero, Roberto A; Napier, Kathryn R; Cunnington, James; Liefting, Lia; Keenan, Sandi; Frampton, Rebekah A; Szabo, Tamas; Bulman, Simon; Hunter, Adam; Ward, Lisa; Whattam, Mark; Bellgard, Matthew I

    2017-01-11

    Detection and preventing entry of exotic viruses and viroids at the border is critical for protecting plant industries trade worldwide. Existing post entry quarantine screening protocols rely on time-consuming biological indicators and/or molecular assays that require knowledge of infecting viral pathogens. Plants have developed the ability to recognise and respond to viral infections through Dicer-like enzymes that cleave viral sequences into specific small RNA products. Many studies reported the use of a broad range of small RNAs encompassing the product sizes of several Dicer enzymes involved in distinct biological pathways. Here we optimise the assembly of viral sequences by using specific small RNA subsets. We sequenced the small RNA fractions of 21 plants held at quarantine glasshouse facilities in Australia and New Zealand. Benchmarking of several de novo assembler tools yielded SPAdes using a kmer of 19 to produce the best assembly outcomes. We also found that de novo assembly using 21-25 nt small RNAs can result in chimeric assemblies of viral sequences and plant host sequences. Such non-specific assemblies can be resolved by using 21-22 nt or 24 nt small RNAs subsets. Among the 21 selected samples, we identified contigs with sequence similarity to 18 viruses and 3 viroids in 13 samples. Most of the viruses were assembled using only 21-22 nt long virus-derived siRNAs (viRNAs), except for one Citrus endogenous pararetrovirus that was more efficiently assembled using 24 nt long viRNAs. All three viroids found in this study were fully assembled using either 21-22 nt or 24 nt viRNAs. Optimised analysis workflows were customised within the Yabi web-based analytical environment. We present a fully automated viral surveillance and diagnosis web-based bioinformatics toolkit that provides a flexible, user-friendly, robust and scalable interface for the discovery and diagnosis of viral pathogens. We have implemented an automated viral surveillance and

  8. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

    Science.gov (United States)

    Mulder, Nicola J.; Adebiyi, Ezekiel; Alami, Raouf; Benkahla, Alia; Brandful, James; Doumbia, Seydou; Everett, Dean; Fadlelmola, Faisal M.; Gaboun, Fatima; Gaseitsiwe, Simani; Ghazal, Hassan; Hazelhurst, Scott; Hide, Winston; Ibrahimi, Azeddine; Jaufeerally Fakim, Yasmina; Jongeneel, C. Victor; Joubert, Fourie; Kassim, Samar; Kayondo, Jonathan; Kumuthini, Judit; Lyantagaye, Sylvester; Makani, Julie; Mansour Alzohairy, Ahmed; Masiga, Daniel; Moussa, Ahmed; Nash, Oyekanmi; Ouwe Missi Oukem-Boyer, Odile; Owusu-Dabo, Ellis; Panji, Sumir; Patterton, Hugh; Radouani, Fouzia; Sadki, Khalid; Seghrouchni, Fouad; Tastan Bishop, Özlem; Tiffin, Nicki; Ulenga, Nzovu

    2016-01-01

    The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet. PMID:26627985

  9. An Approach for Externalization of Expert Tacit Knowledge Using a Query Management System in an E-Learning Environment

    Science.gov (United States)

    Khan, Abdul Azeez; Khader, Sheik Abdul

    2014-01-01

    E-learning or electronic learning platforms facilitate delivery of the knowledge spectrum to the learning community through information and communication technologies. The transfer of knowledge takes place from experts to learners, and externalization of the knowledge transfer is significant. In the e-learning environment, the learners seek…

  10. Bioinformatics education in high school: implications for promoting science, technology, engineering, and mathematics careers.

    Science.gov (United States)

    Kovarik, Dina N; Patterson, Davis G; Cohen, Carolyn; Sanders, Elizabeth A; Peterson, Karen A; Porter, Sandra G; Chowning, Jeanne Ting

    2013-01-01

    We investigated the effects of our Bio-ITEST teacher professional development model and bioinformatics curricula on cognitive traits (awareness, engagement, self-efficacy, and relevance) in high school teachers and students that are known to accompany a developing interest in science, technology, engineering, and mathematics (STEM) careers. The program included best practices in adult education and diverse resources to empower teachers to integrate STEM career information into their classrooms. The introductory unit, Using Bioinformatics: Genetic Testing, uses bioinformatics to teach basic concepts in genetics and molecular biology, and the advanced unit, Using Bioinformatics: Genetic Research, utilizes bioinformatics to study evolution and support student research with DNA barcoding. Pre-post surveys demonstrated significant growth (n = 24) among teachers in their preparation to teach the curricula and infuse career awareness into their classes, and these gains were sustained through the end of the academic year. Introductory unit students (n = 289) showed significant gains in awareness, relevance, and self-efficacy. While these students did not show significant gains in engagement, advanced unit students (n = 41) showed gains in all four cognitive areas. Lessons learned during Bio-ITEST are explored in the context of recommendations for other programs that wish to increase student interest in STEM careers.

  11. Analysis of requirements for teaching materials based on the course bioinformatics for plant metabolism

    Science.gov (United States)

    Balqis, Widodo, Lukiati, Betty; Amin, Mohamad

    2017-05-01

    A way to improve the quality of learning in the course of Plant Metabolism in the Department of Biology, State University of Malang, is to develop teaching materials. This research evaluates the needs of bioinformatics-based teaching material in the course Plant Metabolism by the Analyze, Design, Develop, Implement, and Evaluate (ADDIE) development model. Data were collected through questionnaires distributed to the students in the Plant Metabolism course of the Department of Biology, University of Malang, and analysis of the plan of lectures semester (RPS). Learning gains of this course show that it is not yet integrated into the field of bioinformatics. All respondents stated that plant metabolism books do not include bioinformatics and fail to explain the metabolism of a chemical compound of a local plant in Indonesia. Respondents thought that bioinformatics can explain examples and metabolism of a secondary metabolite analysis techniques and discuss potential medicinal compounds from local plants. As many as 65% of the respondents said that the existing metabolism book could not be used to understand secondary metabolism in lectures of plant metabolism. Therefore, the development of teaching materials including plant metabolism-based bioinformatics is important to improve the understanding of the lecture material in plant metabolism.

  12. Graduate Students' Knowledge Construction and Attitudes toward Online Synchronous Videoconferencing Collaborative Learning Environments

    Science.gov (United States)

    Akarasriworn, Chatchada; Ku, Heng-Yu

    2013-01-01

    This study investigated 28 graduate students' knowledge construction and attitudes toward online synchronous videoconferencing collaborative learning environments. These students took an online course, self-selected 3 or 4 group members to form groups, and worked on projects across 16 weeks. Each group utilized Elluminate "Live!" for the…

  13. Integrating knowledge and control into hypermedia-based training environments: Experiments with HyperCLIPS

    Science.gov (United States)

    Hill, Randall W., Jr.

    1990-01-01

    The issues of knowledge representation and control in hypermedia-based training environments are discussed. The main objective is to integrate the flexible presentation capability of hypermedia with a knowledge-based approach to lesson discourse management. The instructional goals and their associated concepts are represented in a knowledge representation structure called a 'concept network'. Its functional usages are many: it is used to control the navigation through a presentation space, generate tests for student evaluation, and model the student. This architecture was implemented in HyperCLIPS, a hybrid system that creates a bridge between HyperCard, a popular hypertext-like system used for building user interfaces to data bases and other applications, and CLIPS, a highly portable government-owned expert system shell.

  14. A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

    Science.gov (United States)

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

  15. BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.

    Science.gov (United States)

    Fosso, Bruno; Santamaria, Monica; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente, Gabriel; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano

    2015-07-01

    Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent

  16. How to Develop the Knowledge Management Environment

    International Nuclear Information System (INIS)

    Pleslic, S.

    2016-01-01

    Full text: Knowledge as the most valuable asset in organization should be managed properly and carefully. When we are trying to manage knowledge, we should not intent to create big knowledge repositories that will capture everything that anybody ever knew. It is better to follow people who have knowledge and to develop culture and technology that will help them to share knowledge and experience. The key elements for successful knowledge management are: people, processes and technology. Technology should be standard and reliable to facilitate knowledge sharing. KM processes should be defined to simplify creation, sharing and use of knowledge. People are the most valuable resource of organizational knowledge because they can create new knowledge, share knowledge around the organization and use that knowledge to achieve the best performance. Technology and processes are powerful together, but without the people there is a high risk that efforts to change something in organization will not be successful. People are such factor that can break or make any KM initiatives. It is even more critical situation in nuclear knowledge management. How to develop organizational culture and individual behavior in nuclear field will be described. (author

  17. Research on the Mechanism of Cross Organizational Knowledge Sharing in BIM Competitive Environment

    Directory of Open Access Journals (Sweden)

    Zhong Wei

    2017-01-01

    Full Text Available Co-opetition under the environment of BIM implementation process because the level is not high resulting in the project BIM application value of incomplete knowledge sharing among organizations, thus establishing good knowledge can effectively solve this problem and achieve the overall benefit and benefit sharing mechanism in the project organization. This paper defines five competing modes according to the competing degree of organization between different BIM applications, including imperfect competition, competition, competition and cooperation, full cooperation and cooperation, and put forward the conceptual model and related assumptions. Analysis of the effect of path and effect of project determined in BIM application mode, the concurrence of knowledge sharing, efficiency and overall efficiency of the project within the organization through the survey and empirical results, and according to the proposed contract, the distribution of benefits and work three kinds of knowledge sharing mechanism implementation path.

  18. Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.

    Science.gov (United States)

    El-Kalioby, Mohamed; Abouelhoda, Mohamed; Krüger, Jan; Giegerich, Robert; Sczyrba, Alexander; Wall, Dennis P; Tonellato, Peter

    2012-01-01

    Bioinformatics services have been traditionally provided in the form of a web-server that is hosted at institutional infrastructure and serves multiple users. This model, however, is not flexible enough to cope with the increasing number of users, increasing data size, and new requirements in terms of speed and availability of service. The advent of cloud computing suggests a new service model that provides an efficient solution to these problems, based on the concepts of "resources-on-demand" and "pay-as-you-go". However, cloud computing has not yet been introduced within bioinformatics servers due to the lack of usage scenarios and software layers that address the requirements of the bioinformatics domain. In this paper, we provide different use case scenarios for providing cloud computing based services, considering both the technical and financial aspects of the cloud computing service model. These scenarios are for individual users seeking computational power as well as bioinformatics service providers aiming at provision of personalized bioinformatics services to their users. We also present elasticHPC, a software package and a library that facilitates the use of high performance cloud computing resources in general and the implementation of the suggested bioinformatics scenarios in particular. Concrete examples that demonstrate the suggested use case scenarios with whole bioinformatics servers and major sequence analysis tools like BLAST are presented. Experimental results with large datasets are also included to show the advantages of the cloud model. Our use case scenarios and the elasticHPC package are steps towards the provision of cloud based bioinformatics services, which would help in overcoming the data challenge of recent biological research. All resources related to elasticHPC and its web-interface are available at http://www.elasticHPC.org.

  19. A Effect on Environment and Countermeasures in accordance with a Shift to a Knowledge-Based Economy

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Ki Bok; Moon, Hyun Ju; Jeong, Hyun Keun; Kim, Tae Yol [Korea Environment Institute, Seoul (Korea)

    2000-12-01

    The importance of knowledge has been being more stressed now than any other time. How efficiently and effectively knowledge is created, spread, and applied is an important point to secure the competitiveness of an individual economic unit as well as to grow nation's economy. For that reason, the Government has been promoting various policies to accelerate a shift to a knowledge-based economy, establishing 'a Strategy for Knowledge-Based Economic Development', pan-governments level. Companies also have been positively accepting 'a Knowledge-Based Management' as a new strategy of managing companies. Accordingly, only knowledge-based industries, including a high technology manufacturing industry and an information/communication industry, are not sharply grow, but a knowledge-based activity in individual economic activities, such as R and D, has been expanding its share. As such a shift to a knowledge-based economy, it is expected that there are lots of effects in many-sided fields, society, culture, and politics, as well as economy. Based on due consideration to such various effects, the strategy for knowledge-based economic development and the policies on the related fields have to be promoted with a balance. An environmental field also cannot be exceptional. However, there has not yet been a concrete examination on which significance a shift to a knowledge-based economy environmentally has. The purpose of this study is to examine the effects on environment according to a shift to a knowledge-based economy and to find a countermeasure under the awareness of such problems. Anyhow, I hope that the results and the countermeasures from this study can contribute to achieving a shift to an environment-centered and knowledge-based economy. 82 refs., 30 figs., 10 tabs.

  20. 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…

  1. SoS Notebook: An Interactive Multi-Language Data Analysis Environment.

    Science.gov (United States)

    Peng, Bo; Wang, Gao; Ma, Jun; Leong, Man Chong; Wakefield, Chris; Melott, James; Chiu, Yulun; Du, Di; Weinstein, John N

    2018-05-22

    Complex bioinformatic data analysis workflows involving multiple scripts in different languages can be difficult to consolidate, share, and reproduce. An environment that streamlines the entire processes of data collection, analysis, visualization and reporting of such multi-language analyses is currently lacking. We developed Script of Scripts (SoS) Notebook, a web-based notebook environment that allows the use of multiple scripting language in a single notebook, with data flowing freely within and across languages. SoS Notebook enables researchers to perform sophisticated bioinformatic analysis using the most suitable tools for different parts of the workflow, without the limitations of a particular language or complications of cross-language communications. SoS Notebook is hosted at http://vatlab.github.io/SoS/ and is distributed under a BSD license. bpeng@mdanderson.org.

  2. Biowep: a workflow enactment portal for bioinformatics applications.

    Science.gov (United States)

    Romano, Paolo; Bartocci, Ezio; Bertolini, Guglielmo; De Paoli, Flavio; Marra, Domenico; Mauri, Giancarlo; Merelli, Emanuela; Milanesi, Luciano

    2007-03-08

    The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of

  3. Biowep: a workflow enactment portal for bioinformatics applications

    Directory of Open Access Journals (Sweden)

    Romano Paolo

    2007-03-01

    Full Text Available Abstract Background The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS, can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. Results We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. Conclusion We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical

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

    Science.gov (United States)

    Oshita, Kazuki; Arakawa, Kazuharu; Tomita, Masaru

    2011-04-29

    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).

  5. 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.

  6. Knowledge-based potentials in bioinformatics: From a physicist’s viewpoint

    International Nuclear Information System (INIS)

    Zheng Wei-Mou

    2015-01-01

    Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis on known native structures of proteins. Many knowledge-based potentials for proteins have been proposed. Contrary to most existing review articles which mainly describe technical details and applications of various potential models, the main foci for the discussion here are ideas and concepts involving the construction of potentials, including the relation between free energy and energy, the additivity of potentials of mean force and some key issues in potential construction. Sequence analysis is briefly viewed from an energetic viewpoint. (topical review)

  7. Implementing a Web-Based Introductory Bioinformatics Course for Non-Bioinformaticians That Incorporates Practical Exercises

    Science.gov (United States)

    Vincent, Antony T.; Bourbonnais, Yves; Brouard, Jean-Simon; Deveau, Hélène; Droit, Arnaud; Gagné, Stéphane M.; Guertin, Michel; Lemieux, Claude; Rathier, Louis; Charette, Steve J.; Lagüe, Patrick

    2018-01-01

    A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become…

  8. 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...

  9. Naturally selecting solutions: the use of genetic algorithms in bioinformatics.

    Science.gov (United States)

    Manning, Timmy; Sleator, Roy D; Walsh, Paul

    2013-01-01

    For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the most recent applications of this approach to bioinformatics based problems.

  10. Challenges for Transitioning Science Knowledge to an Operational Environment for Space Weather

    Science.gov (United States)

    Spann, James

    2012-01-01

    Effectively transitioning science knowledge to an operational environment relevant to space weather is critical to meet the civilian and defense needs, especially considering how technologies are advancing and present evolving susceptibilities to space weather impacts. The effort to transition scientific knowledge to a useful application is not a research task nor is an operational activity, but an effort that bridges the two. Successful transitioning must be an intentional effort that has a clear goal for all parties and measureable outcome and deliverable. This talk will present proven methodologies that have been demonstrated to be effective for terrestrial weather and disaster relief efforts, and how those methodologies can be applied to space weather transition efforts.

  11. Bioboxes: standardised containers for interchangeable bioinformatics software.

    Science.gov (United States)

    Belmann, Peter; Dröge, Johannes; Bremges, Andreas; McHardy, Alice C; Sczyrba, Alexander; Barton, Michael D

    2015-01-01

    Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

  12. 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…

  13. 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...

  14. 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

    As both the amount of generated biological data and the processing compute power increase, computational experimentation is no longer the exclusivity of bioinformaticians, but it is moving across all biomedical domains. For bioinformatics to realize its translational potential, domain experts need...... 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...... into their research.We review recent applications of Cytoscape, BioGPS and DAVID for data visualization, integration and functional enrichment. Moreover, we illustrate the use of Taverna, Kepler, GenePattern, and Galaxy as open-access workbenches for bioinformatics workflows. Finally, we mention services...

  15. A bioinformatics approach for precision medicine off-label drug drug selection among triple negative breast cancer patients.

    Science.gov (United States)

    Cheng, Lijun; Schneider, Bryan P; Li, Lang

    2016-07-01

    Cancer has been extensively characterized on the basis of genomics. The integration of genetic information about cancers with data on how the cancers respond to target based therapy to help to optimum cancer treatment. The increasing usage of sequencing technology in cancer research and clinical practice has enormously advanced our understanding of cancer mechanisms. The cancer precision medicine is becoming a reality. Although off-label drug usage is a common practice in treating cancer, it suffers from the lack of knowledge base for proper cancer drug selections. This eminent need has become even more apparent considering the upcoming genomics data. In this paper, a personalized medicine knowledge base is constructed by integrating various cancer drugs, drug-target database, and knowledge sources for the proper cancer drugs and their target selections. Based on the knowledge base, a bioinformatics approach for cancer drugs selection in precision medicine is developed. It integrates personal molecular profile data, including copy number variation, mutation, and gene expression. By analyzing the 85 triple negative breast cancer (TNBC) patient data in the Cancer Genome Altar, we have shown that 71.7% of the TNBC patients have FDA approved drug targets, and 51.7% of the patients have more than one drug target. Sixty-five drug targets are identified as TNBC treatment targets and 85 candidate drugs are recommended. Many existing TNBC candidate targets, such as Poly (ADP-Ribose) Polymerase 1 (PARP1), Cell division protein kinase 6 (CDK6), epidermal growth factor receptor, etc., were identified. On the other hand, we found some additional targets that are not yet fully investigated in the TNBC, such as Gamma-Glutamyl Hydrolase (GGH), Thymidylate Synthetase (TYMS), Protein Tyrosine Kinase 6 (PTK6), Topoisomerase (DNA) I, Mitochondrial (TOP1MT), Smoothened, Frizzled Class Receptor (SMO), etc. Our additional analysis of target and drug selection strategy is also fully

  16. Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

    Directory of Open Access Journals (Sweden)

    Thoraval Samuel

    2005-04-01

    Full Text Available Abstract Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. Results We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results can be reproduced or shared among users. Availability: http://if-web1.imb.uq.edu.au/Pise/5.a/gpipe.html (interactive, ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/ (download. Conclusion From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous

  17. Analyzing the field of bioinformatics with the multi-faceted topic modeling technique.

    Science.gov (United States)

    Heo, Go Eun; Kang, Keun Young; Song, Min; Lee, Jeong-Hoon

    2017-05-31

    Bioinformatics is an interdisciplinary field at the intersection of molecular biology and computing technology. To characterize the field as convergent domain, researchers have used bibliometrics, augmented with text-mining techniques for content analysis. In previous studies, Latent Dirichlet Allocation (LDA) was the most representative topic modeling technique for identifying topic structure of subject areas. However, as opposed to revealing the topic structure in relation to metadata such as authors, publication date, and journals, LDA only displays the simple topic structure. In this paper, we adopt the Tang et al.'s Author-Conference-Topic (ACT) model to study the field of bioinformatics from the perspective of keyphrases, authors, and journals. The ACT model is capable of incorporating the paper, author, and conference into the topic distribution simultaneously. To obtain more meaningful results, we use journals and keyphrases instead of conferences and bag-of-words.. For analysis, we use PubMed to collected forty-six bioinformatics journals from the MEDLINE database. We conducted time series topic analysis over four periods from 1996 to 2015 to further examine the interdisciplinary nature of bioinformatics. We analyze the ACT Model results in each period. Additionally, for further integrated analysis, we conduct a time series analysis among the top-ranked keyphrases, journals, and authors according to their frequency. We also examine the patterns in the top journals by simultaneously identifying the topical probability in each period, as well as the top authors and keyphrases. The results indicate that in recent years diversified topics have become more prevalent and convergent topics have become more clearly represented. The results of our analysis implies that overtime the field of bioinformatics becomes more interdisciplinary where there is a steady increase in peripheral fields such as conceptual, mathematical, and system biology. These results are

  18. Relationships between middle childhood outdoor experiences and an adult individual's knowledge of the environment

    Science.gov (United States)

    Gillette, Brandon A.

    During the last several decades, the nature of childhood has changed. There is not much nature in it anymore. Numerous studies in environmental education, environmental psychology, and conservation psychology show that the time children spend outdoors encourages healthy physical development, enriches creativity and imagination, and enhances classroom performance. Additional research shows that people's outdoor experiences as children, and adults can lead to more positive attitudes and behavior towards the environment, along with more environmental knowledge with which to guide public policy decisions. The overall purpose of this study was to examine the effect of middle childhood (age 6-11) outdoor experiences on an individual's current knowledge of the environment. This correlational study evaluated the following potential relationships: 1) The effect of "outdoorsiness" (defined as a fondness or enjoyment of the outdoors and related activities) on an individual's environmental knowledge; 2) The effect of gender on an individual's level of outdoorsiness; 3) The effect of setting (urban, suburban, rural, farm) on an individual's level of outdoorsiness and environmental knowledge; 4) The effect of formal [science] education on an individual's level of outdoorsiness and environmental knowledge; and 5) The effect of informal, free-choice learning on an individual's level of outdoorsiness and environmental knowledge. Outdoorsiness was measured using the Natural Experience Scale (NES), which was developed through a series of pilot surveys and field-tested in this research study. Participants included 382 undergraduate students at the University of Kansas with no preference or bias given to declared or undeclared majors. The information from this survey was used to analyze the question of whether outdoor experiences as children are related in some way to an adult's environmental knowledge after accounting for other factors of knowledge acquisition such as formal education

  19. Assimilating Text-Mining & Bio-Informatics Tools to Analyze Cellulase structures

    Science.gov (United States)

    Satyasree, K. P. N. V., Dr; Lalitha Kumari, B., Dr; Jyotsna Devi, K. S. N. V.; Choudri, S. M. Roy; Pratap Joshi, K.

    2017-08-01

    Text-mining is one of the best potential way of automatically extracting information from the huge biological literature. To exploit its prospective, the knowledge encrypted in the text should be converted to some semantic representation such as entities and relations, which could be analyzed by machines. But large-scale practical systems for this purpose are rare. But text mining could be helpful for generating or validating predictions. Cellulases have abundant applications in various industries. Cellulose degrading enzymes are cellulases and the same producing bacteria - Bacillus subtilis & fungus Pseudomonas putida were isolated from top soil of Guntur Dt. A.P. India. Absolute cultures were conserved on potato dextrose agar medium for molecular studies. In this paper, we presented how well the text mining concepts can be used to analyze cellulase producing bacteria and fungi, their comparative structures are also studied with the aid of well-establised, high quality standard bioinformatic tools such as Bioedit, Swissport, Protparam, EMBOSSwin with which a complete data on Cellulases like structure, constituents of the enzyme has been obtained.

  20. libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny

    OpenAIRE

    Butt, Davin; Roger, Andrew J; Blouin, Christian

    2005-01-01

    Background An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. Results The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used ...

  1. 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.

  2. Development and evaluation of intelligent machine tools based on knowledge evolution in M2M environment

    International Nuclear Information System (INIS)

    Kim, Dong Hoon; Song, Jun Yeob; Lee, Jong Hyun; Cha, Suk Keun

    2009-01-01

    In the near future, the foreseen improvement in machine tools will be in the form of a knowledge evolution-based intelligent device. The goal of this study is to develop intelligent machine tools having knowledge-evolution capability in Machine to Machine (M2M) wired and wireless environment. The knowledge evolution-based intelligent machine tools are expected to be capable of gathering knowledge autonomously, producing knowledge, understanding knowledge, applying reasoning to knowledge, making new decisions, dialoguing with other machines, etc. The concept of the knowledge-evolution intelligent machine originated from the process of machine control operation by the sense, dialogue and decision of a human expert. The structure of knowledge evolution in M2M and the scheme for a dialogue agent among agent-based modules such as a sensory agent, a dialogue agent and an expert system (decision support agent) are presented in this paper, and work-offset compensation from thermal change and recommendation of cutting condition are performed on-line for knowledge-evolution verification

  3. Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia.

    Science.gov (United States)

    Schneider, Maria Victoria; Griffin, Philippa C; Tyagi, Sonika; Flannery, Madison; Dayalan, Saravanan; Gladman, Simon; Watson-Haigh, Nathan; Bayer, Philipp E; Charleston, Michael; Cooke, Ira; Cook, Rob; Edwards, Richard J; Edwards, David; Gorse, Dominique; McConville, Malcolm; Powell, David; Wilkins, Marc R; Lonie, Andrew

    2017-06-30

    EMBL Australia Bioinformatics Resource (EMBL-ABR) is a developing national research infrastructure, providing bioinformatics resources and support to life science and biomedical researchers in Australia. EMBL-ABR comprises 10 geographically distributed national nodes with one coordinating hub, with current funding provided through Bioplatforms Australia and the University of Melbourne for its initial 2-year development phase. The EMBL-ABR mission is to: (1) increase Australia's capacity in bioinformatics and data sciences; (2) contribute to the development of training in bioinformatics skills; (3) showcase Australian data sets at an international level and (4) enable engagement in international programs. The activities of EMBL-ABR are focussed in six key areas, aligning with comparable international initiatives such as ELIXIR, CyVerse and NIH Commons. These key areas-Tools, Data, Standards, Platforms, Compute and Training-are described in this article. © The Author 2017. Published by Oxford University Press.

  4. Learning your way in a city: experience and gender differences in configurational knowledge of one's environment.

    Science.gov (United States)

    De Goede, Maartje; Postma, Albert

    2015-01-01

    Males tend to outperform females in their knowledge of relative and absolute distances in spatial layouts and environments. It is unclear yet in how far these differences are innate or develop through life. The aim of the present study was to investigate whether gender differences in configurational knowledge for a natural environment might be modulated by experience. In order to examine this possibility, distance as well as directional knowledge of the city of Utrecht in the Netherlands was assessed in male and female inhabitants who had different levels of familiarity with this city. Experience affected the ability to solve difficult distance knowledge problems, but only for females. While the quality of the spatial representation of metric distances improved with more experience, this effect was not different for males and females. In contrast directional configurational measures did show a main gender effect but no experience modulation. In general, it seems that we obtain different configurational aspects according to different experiential time schemes. Moreover, the results suggest that experience may be a modulating factor in the occurrence of gender differences in configurational knowledge, though this seems dependent on the type of measurement. It is discussed in how far proficiency in mental rotation ability and spatial working memory accounts for these differences.

  5. 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.

  6. Protecting innovation in bioinformatics and in-silico biology.

    Science.gov (United States)

    Harrison, Robert

    2003-01-01

    Commercial success or failure of innovation in bioinformatics and in-silico biology requires the appropriate use of legal tools for protecting and exploiting intellectual property. These tools include patents, copyrights, trademarks, design rights, and limiting information in the form of 'trade secrets'. Potentially patentable components of bioinformatics programmes include lines of code, algorithms, data content, data structure and user interfaces. In both the US and the European Union, copyright protection is granted for software as a literary work, and most other major industrial countries have adopted similar rules. Nonetheless, the grant of software patents remains controversial and is being challenged in some countries. Current debate extends to aspects such as whether patents can claim not only the apparatus and methods but also the data signals and/or products, such as a CD-ROM, on which the programme is stored. The patentability of substances discovered using in-silico methods is a separate debate that is unlikely to be resolved in the near future.

  7. Pay-as-you-go data integration for bio-informatics

    NARCIS (Netherlands)

    Wanders, B.

    2012-01-01

    Scientific research in bio-informatics is often data-driven and supported by numerous biological databases. A biological database contains factual information collected from scientific experiments and computational analyses about areas including genomics, proteomics, metabolomics, microarray gene

  8. Knowledge-based potentials in bioinformatics: From a physicist’s viewpoint

    Science.gov (United States)

    Zheng, Wei-Mou

    2015-12-01

    Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis on known native structures of proteins. Many knowledge-based potentials for proteins have been proposed. Contrary to most existing review articles which mainly describe technical details and applications of various potential models, the main foci for the discussion here are ideas and concepts involving the construction of potentials, including the relation between free energy and energy, the additivity of potentials of mean force and some key issues in potential construction. Sequence analysis is briefly viewed from an energetic viewpoint. Project supported in part by the National Natural Science Foundation of China (Grant Nos. 11175224 and 11121403).

  9. Nispero: a cloud-computing based Scala tool specially suited for bioinformatics data processing

    OpenAIRE

    Evdokim Kovach; Alexey Alekhin; Eduardo Pareja Tobes; Raquel Tobes; Eduardo Pareja; Marina Manrique

    2014-01-01

    Nowadays it is widely accepted that the bioinformatics data analysis is a real bottleneck in many research activities related to life sciences. High-throughput technologies like Next Generation Sequencing (NGS) have completely reshaped the biology and bioinformatics landscape. Undoubtedly NGS has allowed important progress in many life-sciences related fields but has also presented interesting challenges in terms of computation capabilities and algorithms. Many kinds of tasks related with NGS...

  10. Knowledge about knowledge

    International Nuclear Information System (INIS)

    Ramm, Hans Henrik

    2006-01-01

    Technology and knowledge make up the knowledge capital that has been so essential to the oil and gas industry's value creation, competitiveness and internationalization. Report prepared for the Norwegian Oil Industry Association (OLF) and The Norwegian Society of Chartered Technical and Scientific Professionals (Tekna), on the Norwegian petroleum cluster as an environment for creating knowledge capital from human capital, how fiscal and other framework conditions may influence the building of knowledge capital, the long-term perspectives for the petroleum cluster, what Norwegian society can learn from the experiences in the petroleum cluster, and the importance of gaining more knowledge about the functionality of knowledge for increased value creation (author) (ml)

  11. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal; Salama, Khaled N.; Zidan, Mohammed A.

    2012-01-01

    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

  12. [Effects of an infant/toddler health program on parenting knowledge, behavior, confidence, and home environment in low-income mothers].

    Science.gov (United States)

    Lee, Gyungjoo; Yang, Soo; Jang, Mi Heui; Yeom, Mijung

    2012-10-01

    This study was conducted to evaluate the effectiveness of a mother/infant-toddler health program developed to enhance parenting knowledge, behavior and confidence in low income mothers and home environment. A one-group pretest-posttest quasi-experimental design was used. Sixty-nine dyads of mothers and infant-toddlers (aged 0-36 months) were provided with weekly intervention for seven session. Each session consisted of three parts; first, educating to increase integrated knowledge related to the development of the infant/toddler including nutrition, first aid and home environment; second, counseling to share parenting experience among the mothers and to increase their nurturing confidence; third, playing with the infant/toddler to facilitate attachment-based parenting behavior for the mothers. Following the programs, there were significant increases in parenting knowledge on nutrition and first aid. A significant improvement was found in attachment-based parenting behavior, but not in home safety practice. Nurturing confidence was not significantly increased. The program led to more positive home environment for infant/toddler's health and development. The findings provide evidence for mother-infant/toddler health program to improve parenting knowledge, attachment-based parenting behavior and better home environment in low income mothers. Study of the long term effectiveness of this program is recommended for future research.

  13. Using social media to facilitate knowledge transfer in complex engineering environments: a primer for educators

    Science.gov (United States)

    Murphy, Glen; Salomone, Sonia

    2013-03-01

    While highly cohesive groups are potentially advantageous they are also often correlated with the emergence of knowledge and information silos based around those same functional or occupational clusters. Consequently, an essential challenge for engineering organisations wishing to overcome informational silos is to implement mechanisms that facilitate, encourage and sustain interactions between otherwise disconnected groups. This paper acts as a primer for those seeking to gain an understanding of the design, functionality and utility of a suite of software tools generically termed social media technologies in the context of optimising the management of tacit engineering knowledge. Underpinned by knowledge management theory and using detailed case examples, this paper explores how social media technologies achieve such goals, allowing for the transfer of knowledge by tapping into the tacit and explicit knowledge of disparate groups in complex engineering environments.

  14. Management Of Knowledge And System - Evolution Of Knowledge

    Directory of Open Access Journals (Sweden)

    Avishek Choudhury

    2015-08-01

    Full Text Available The study of knowledge is one of the most fundamental and necessary components in todays world. A claim to knowledge should be evaluated to determine whether or not it is knowledge in its real sense. To conduct this sort of evaluation understanding of what knowledge is and how much knowledge is possible is required. This paper provides an overview of the important aspects of knowledge and with the help of epistemology tries to answer the most fundamental questions of what is knowledge Moreover how do we know what we know The paper attempts to show the effect of culture on organizations and how foundational knowledge can help us develop logical decisions in a fluctuating environment. To manage an organization within evolving paradigm knowledge of variation acts as a necessary requirement. As Deming defined management as a prediction a leader must have skills to predict and adapt to its external environment. Most of the time organizations fail to observe the paradigm shift and couldnt adjust to the changing environment. The paper also discusses the effect of diverse culture and their respective interpretation of language. Thus the paper highlights the necessity of understanding human psychology attaining foundational knowledge and ability to validate the knowledge to establish a successful organization.

  15. A Study on Environment-Oriented Knowledge, Attitude and Behavior Level of Teacher Candidates

    Science.gov (United States)

    Akman, Ozkan; Alagoz, Bulent

    2017-01-01

    The purpose of education should be to raise people who are researchers, developer, investigating what they find, use their knowledge in their behaviors and who can interpret and put new things on them. When children are being educated, the experience should be before the occurrence of the story. First, good and bad environment should be shown,…

  16. A bioinformatics-based overview of protein Lys-Ne-acetylation

    Science.gov (United States)

    Among posttranslational modifications, there are some conceptual similarities between Lys-N'-acetylation and Ser/Thr/Tyr O-phosphorylation. Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation. T...

  17. jORCA: easily integrating bioinformatics Web Services.

    Science.gov (United States)

    Martín-Requena, Victoria; Ríos, Javier; García, Maximiliano; Ramírez, Sergio; Trelles, Oswaldo

    2010-02-15

    Web services technology is becoming the option of choice to deploy bioinformatics tools that are universally available. One of the major strengths of this approach is that it supports machine-to-machine interoperability over a network. However, a weakness of this approach is that various Web Services differ in their definition and invocation protocols, as well as their communication and data formats-and this presents a barrier to service interoperability. jORCA is a desktop client aimed at facilitating seamless integration of Web Services. It does so by making a uniform representation of the different web resources, supporting scalable service discovery, and automatic composition of workflows. Usability is at the top of the jORCA agenda; thus it is a highly customizable and extensible application that accommodates a broad range of user skills featuring double-click invocation of services in conjunction with advanced execution-control, on the fly data standardization, extensibility of viewer plug-ins, drag-and-drop editing capabilities, plus a file-based browsing style and organization of favourite tools. The integration of bioinformatics Web Services is made easier to support a wider range of users. .

  18. 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 …

  19. 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%.

  20. Nurse Knowledge, Work Environment, and Turnover in Highly Specialized Pediatric End-of-Life Care.

    Science.gov (United States)

    Lindley, Lisa C; Cozad, Melanie J

    2017-07-01

    To examine the relationship between nurse knowledge, work environment, and registered nurse (RN) turnover in perinatal hospice and palliative care organizations. Using nurse intellectual capital theory, a multivariate analysis was conducted with 2007 National Home and Hospice Care Survey data. Perinatal hospice and palliative care organizations experienced a 5% turnover rate. The professional experience of advanced practice nurses (APNs) was significantly related to turnover among RNs (β = -.032, P < .05). Compared to organizations with no APNs professional experience, clinical nurse specialists and nurse practitioners significantly reduced RN turnover by 3 percentage points. No other nurse knowledge or work environment variables were associated with RN turnover. Several of the control variables were also associated with RN turnover in the study; Organizations serving micropolitan (β = -.041, P < .05) and rural areas (β = -.037, P < .05) had lower RN turnover compared to urban areas. Organizations with a technology climate where nurses used electronic medical records had a higher turnover rate than those without (β = .036, P < .05). The findings revealed that advanced professional experience in the form of APNs was associated with reductions in RN turnover. This suggests that having a clinical nurse specialist or nurse practitioner on staff may provide knowledge and experience to other RNs, creating stability within the organization.

  1. Penalized feature selection and classification in bioinformatics

    OpenAIRE

    Ma, Shuangge; Huang, Jian

    2008-01-01

    In bioinformatics studies, supervised classification with high-dimensional input variables is frequently encountered. Examples routinely arise in genomic, epigenetic and proteomic studies. Feature selection can be employed along with classifier construction to avoid over-fitting, to generate more reliable classifier and to provide more insights into the underlying causal relationships. In this article, we provide a review of several recently developed penalized feature selection and classific...

  2. The Effects of Enhancing Prospective EFL Teachers' Knowledge Management Strategies in Virtual Learning Environments on Their Ideational Flexibility and Engagement

    Directory of Open Access Journals (Sweden)

    Ammar Abdullah Mahmoud Ismail

    2017-01-01

    Full Text Available The last few years have witnessed an increased interest in moving away from traditional language instruction settings towards more hybrid and virtual learning environments. Face-to-face interaction, guided practice, and uniformity of knowledge sources and skills are all replaced by settings where multiplicity of views from different learning communities, interconnectedness, self-directedness, and self-management of knowledge and learning are increasingly emphasized. This shift from walled-classroom instruction with its limited scope and resources to hybrid and virtual learning environments with their limitless provisions requires that learners be equipped with requisite skills and strategies to manage knowledge and handle language learning in ways commensurate with the nature and limitless possibilities of these new environments. The current study aimed at enhancing knowledge management strategies of EFL teachers in virtual learning environments and examine the impact on their ideational flexibility and engagement in language learning settings. A knowledge management model was proposed and field-test on a cohort of prospective EFL teachers in the Emirati context. Participants were prospective EFL teachers enrolled in the Methods of Teaching Courses and doing their practicum in the Emirati EFL context. Participants' ideational flexibility was tapped via a bi-methodical approach including a contextualized task and a decontextualized one. Their engagement in virtual language learning settings was tapped via an engagement scale. Results of the study indicated that enhancing prospective EFL teachers' knowledge management strategies in virtual learning environments had a significant impact on their ideational flexibility and engagement in foreign language learning settings. Details of the instructional intervention, instruments for tapping students’ ideational flexibility and engagement, and results of the study are discussed. Implications for

  3. Toward Personalized Pressure Ulcer Care Planning: Development of a Bioinformatics System for Individualized Prioritization of Clinical Pratice Guideline

    Science.gov (United States)

    2016-10-01

    AWARD NUMBER: W81XWH-15-1-0342 TITLE: Toward Personalized Pressure Ulcer Care Planning: Development of a Bioinformatics System for Individualized...Planning: Development of a Bioinformatics System for Individualized Prioritization of Clinical Pratice Guideline 5a. CONTRACT NUMBER 5b. GRANT...recommendations of CPG has been identified by experts in the field. We will use bioinformatics to enable data extraction, storage, and analysis to support

  4. Korsakow Perspective(s: Rethinking Documentary Knowledge in Digital Multilinear Environments

    Directory of Open Access Journals (Sweden)

    Franziska Weidle

    2016-12-01

    Full Text Available In “linear documentary land”, we are trained to see stories everywhere we look. As noted by Grasseni and Walter (2014, digital media affordances encourage reflections on this particular “schooling of the eye”, the power relations it is embedded in as well as the creation of counter-practices. Indeed, many artists, media practitioners and scholars advocate interactivity as a different, possibly more “authentic“, representative strategy for documentary. Drawing on my ethnographic study of the Korsakow-System, this paper analyses a software as part of a situated visual knowledge practice that challenges story as primary organizing principle in computational networked environments.

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

    Directory of Open Access Journals (Sweden)

    Swainston Neil

    2006-12-01

    Full Text Available 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 in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources. Results This paper proposes a model-driven approach for the partial generation of user interfaces for searching and browsing bioinformatics data repositories. Inspired by the Model Driven Architecture (MDA of the Object Management Group (OMG, we have developed a system that generates interfaces designed for use with bioinformatics resources. This approach helps laboratory domain experts decrease the amount of time they have to spend dealing with the repetitive aspects of user interface development. As a result, the amount of time they can spend on gathering requirements and helping develop specialised features increases. The resulting system is known as Pierre, and has been validated through its application to use cases in the life sciences, including the PEDRoDB proteomics database and the e-Fungi data warehouse. Conclusion MDAs focus on generating software from models that describe aspects of service capabilities, and can be applied to support rapid development of repository

  6. Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes.

    Science.gov (United States)

    Margaria, Tiziana; Kubczak, Christian; Steffen, Bernhard

    2008-04-25

    With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout. Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution. As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way.

  7. Evolution from Collaborative Learning to Symbiotic E-Learning: Creation of New E-Learning Environment for Knowledge Society

    Science.gov (United States)

    Songhao, He; Saito, Kenji; Maeda, Takashi; Kubo, Takara

    2011-01-01

    For people who live in the knowledge society which has rapidly been changing, learning in the widest sense becomes indispensable in all phases of working, living and playing. The construction of an environment, to meet the demands of people who need to acquire new knowledge and skills as the need arises, and enlighten each other regularly, is…

  8. Emerging role of bioinformatics tools and software in evolution of clinical research

    Directory of Open Access Journals (Sweden)

    Supreet Kaur Gill

    2016-01-01

    Full Text Available Clinical research is making toiling efforts for promotion and wellbeing of the health status of the people. There is a rapid increase in number and severity of diseases like cancer, hepatitis, HIV etc, resulting in high morbidity and mortality. Clinical research involves drug discovery and development whereas clinical trials are performed to establish safety and efficacy of drugs. Drug discovery is a long process starting with the target identification, validation and lead optimization. This is followed by the preclinical trials, intensive clinical trials and eventually post marketing vigilance for drug safety. Softwares and the bioinformatics tools play a great role not only in the drug discovery but also in drug development. It involves the use of informatics in the development of new knowledge pertaining to health and disease, data management during clinical trials and to use clinical data for secondary research. In addition, new technology likes molecular docking, molecular dynamics simulation, proteomics and quantitative structure activity relationship in clinical research results in faster and easier drug discovery process. During the preclinical trials, the software is used for randomization to remove bias and to plan study design. In clinical trials software like electronic data capture, Remote data capture and electronic case report form (eCRF is used to store the data. eClinical, Oracle clinical are software used for clinical data management and for statistical analysis of the data. After the drug is marketed the safety of a drug could be monitored by drug safety software like Oracle Argus or ARISg. Therefore, softwares are used from the very early stages of drug designing, to drug development, clinical trials and during pharmacovigilance. This review describes different aspects related to application of computers and bioinformatics in drug designing, discovery and development, formulation designing and clinical research.

  9. 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.

  10. Automatic generation of bioinformatics tools for predicting protein-ligand binding sites.

    Science.gov (United States)

    Komiyama, Yusuke; Banno, Masaki; Ueki, Kokoro; Saad, Gul; Shimizu, Kentaro

    2016-03-15

    Predictive tools that model protein-ligand binding on demand are needed to promote ligand research in an innovative drug-design environment. However, it takes considerable time and effort to develop predictive tools that can be applied to individual ligands. An automated production pipeline that can rapidly and efficiently develop user-friendly protein-ligand binding predictive tools would be useful. We developed a system for automatically generating protein-ligand binding predictions. Implementation of this system in a pipeline of Semantic Web technique-based web tools will allow users to specify a ligand and receive the tool within 0.5-1 day. We demonstrated high prediction accuracy for three machine learning algorithms and eight ligands. The source code and web application are freely available for download at http://utprot.net They are implemented in Python and supported on Linux. shimizu@bi.a.u-tokyo.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  11. Learning your way in a city: experience and gender differences in configurational knowledge of one’s environment

    Directory of Open Access Journals (Sweden)

    Maartje ede Goede

    2015-04-01

    Full Text Available Males tend to outperform females in their knowledge of relative and absolute distances in spatial layouts and environments. It is unclear yet in how far these differences are innate or develop through life. The aim of the present study was to investigate whether gender differences in configurational knowledge for a natural environment might be modulated by experience. In order to examine this possibility, distance as well as directional knowledge of the city of Utrecht in the Netherlands was assessed in male and female inhabitants who had different levels of familiarity with this city. Experience affected the ability to solve difficult distance knowledge problems, but only for females. While the quality of the spatial representation of metric distances improved with more experience, this effect was not different for males and females. In contrast directional configurational measures did show a main gender effect but no experience modulation. In general, it seems that we obtain different configurational aspects according to different experiential time schemes. Moreover, the results suggest that experience may be a modulating factor in the occurrence of gender differences in configurational knowledge, though this seems dependent on the type of measurement. It is discussed in how far proficiency in mental rotation ability and spatial working memory accounts for these differences.

  12. Learning your way in a city: experience and gender differences in configurational knowledge of one’s environment

    Science.gov (United States)

    De Goede, Maartje; Postma, Albert

    2015-01-01

    Males tend to outperform females in their knowledge of relative and absolute distances in spatial layouts and environments. It is unclear yet in how far these differences are innate or develop through life. The aim of the present study was to investigate whether gender differences in configurational knowledge for a natural environment might be modulated by experience. In order to examine this possibility, distance as well as directional knowledge of the city of Utrecht in the Netherlands was assessed in male and female inhabitants who had different levels of familiarity with this city. Experience affected the ability to solve difficult distance knowledge problems, but only for females. While the quality of the spatial representation of metric distances improved with more experience, this effect was not different for males and females. In contrast directional configurational measures did show a main gender effect but no experience modulation. In general, it seems that we obtain different configurational aspects according to different experiential time schemes. Moreover, the results suggest that experience may be a modulating factor in the occurrence of gender differences in configurational knowledge, though this seems dependent on the type of measurement. It is discussed in how far proficiency in mental rotation ability and spatial working memory accounts for these differences. PMID:25914663

  13. Staff Scientist - RNA Bioinformatics | Center for Cancer Research

    Science.gov (United States)

    The newly established RNA Biology Laboratory (RBL) at the Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH) in Frederick, Maryland is recruiting a Staff Scientist with strong expertise in RNA bioinformatics to join the Intramural Research Program’s mission of high impact, high reward science. The RBL is the equivalent of an

  14. Information Professional or IT Professional?: The Knowledge and Skills Required by Academic Librarians in the Digital Library Environment

    Science.gov (United States)

    Raju, Jaya

    2017-01-01

    As library and information science (LIS) becomes an increasingly technology-driven profession, particularly in the academic library environment, questions arise as to the extent of information technology (IT) knowledge and skills that LIS professionals require. The purpose of this paper is to ascertain what IT knowledge and skills are needed by…

  15. Bioinformatics tools for development of fast and cost effective simple ...

    African Journals Online (AJOL)

    Bioinformatics tools for development of fast and cost effective simple sequence repeat ... comparative mapping and exploration of functional genetic diversity in the ... Already, a number of computer programs have been implemented that aim at ...

  16. Virginia Bioinformatics Institute to expand cyberinfrastructure education and outreach project

    OpenAIRE

    Whyte, Barry James

    2008-01-01

    The National Science Foundation has awarded the Virginia Bioinformatics Institute at Virginia Tech $918,000 to expand its education and outreach program in Cyberinfrastructure - Training, Education, Advancement and Mentoring, commonly known as the CI-TEAM.

  17. 6th International Conference on Practical Applications of Computational Biology & Bioinformatics

    CERN Document Server

    Luscombe, Nicholas; Fdez-Riverola, Florentino; Rodríguez, Juan; Practical Applications of Computational Biology & Bioinformatics

    2012-01-01

    The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable.. The analysis of the datasets of Next Generation Sequencing needs new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Also Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. This book presents the results of the  6th International Conference on Practical Applications of Computational Biology & Bioinformatics held at University of Salamanca, Spain, 28-30th March, 2012 which brought together interdisciplinary scientists that have a strong background in the biological and computational sciences.

  18. 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.

  19. 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…

  20. Family Child Care Learning Environments: Caregiver Knowledge and Practices Related to Early Literacy and Mathematics

    Science.gov (United States)

    Phillips, Beth M.; Morse, Erika E.

    2011-01-01

    This paper presents findings from a stratified-random survey of family child care providers' backgrounds, caregiving environments, practices, attitudes, and knowledge related to language, literacy, and mathematics development for preschool children. Descriptive results are consistent with prior studies suggesting that home-based providers are…

  1. The Evaluation of Pre­-Service Preschool Teachers' Knowledge about the Concept of Environment

    Science.gov (United States)

    Ahi, Berat; Alisinanoglu, Fatma

    2015-01-01

    The purpose of the research is to evaluate pre-­service preschool teachers' knowledge about environment by analyzing their drawings about it. 70 first grade, 99 second grade, 56 third grade and 44 fourth grade, with a total of 269 students have been evaluated in this research. This qualitative research was made with social structuralism vision.…

  2. Bioinformatics for Undergraduates: Steps toward a Quantitative Bioscience Curriculum

    Science.gov (United States)

    Chapman, Barbara S.; Christmann, James L.; Thatcher, Eileen F.

    2006-01-01

    We describe an innovative bioinformatics course developed under grants from the National Science Foundation and the California State University Program in Research and Education in Biotechnology for undergraduate biology students. The project has been part of a continuing effort to offer students classroom experiences focused on principles and…

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

    African Journals Online (AJOL)

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

  4. The Effect of a Multimedia Learning Environment on the Knowledge, Attitude, Confidence, and Skill of Dental Hygiene Students

    Science.gov (United States)

    Stegeman, Cynthia A.

    2011-01-01

    The purpose of this study was to compare the effects of a student-centered, interactive, case-based, multimedia learning environment to a traditional tutorial-based, multimedia learning environment on second-year dental hygiene students (n = 29). Surveys were administered at four points to measure attainment and retention of knowledge, attitude,…

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

    Science.gov (United States)

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

    2016-11-01

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

  6. 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

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

    Science.gov (United States)

    2012-01-01

    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<0.05) gene targets in BRM indicates that nicotine exposure disrupts genes involved in neurogenesis, possibly through misregulation of nicotine-sensitive miRNAs. 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

  8. Integration of Proteomics, Bioinformatics, and Systems Biology in Traumatic Brain Injury Biomarker Discovery

    Science.gov (United States)

    Guingab-Cagmat, J.D.; Cagmat, E.B.; Hayes, R.L.; Anagli, J.

    2013-01-01

    Traumatic brain injury (TBI) is a major medical crisis without any FDA-approved pharmacological therapies that have been demonstrated to improve functional outcomes. It has been argued that discovery of disease-relevant biomarkers might help to guide successful clinical trials for TBI. Major advances in mass spectrometry (MS) have revolutionized the field of proteomic biomarker discovery and facilitated the identification of several candidate markers that are being further evaluated for their efficacy as TBI biomarkers. However, several hurdles have to be overcome even during the discovery phase which is only the first step in the long process of biomarker development. The high-throughput nature of MS-based proteomic experiments generates a massive amount of mass spectral data presenting great challenges in downstream interpretation. Currently, different bioinformatics platforms are available for functional analysis and data mining of MS-generated proteomic data. These tools provide a way to convert data sets to biologically interpretable results and functional outcomes. A strategy that has promise in advancing biomarker development involves the triad of proteomics, bioinformatics, and systems biology. In this review, a brief overview of how bioinformatics and systems biology tools analyze, transform, and interpret complex MS datasets into biologically relevant results is discussed. In addition, challenges and limitations of proteomics, bioinformatics, and systems biology in TBI biomarker discovery are presented. A brief survey of researches that utilized these three overlapping disciplines in TBI biomarker discovery is also presented. Finally, examples of TBI biomarkers and their applications are discussed. PMID:23750150

  9. Workflows for microarray data processing in the Kepler environment

    Science.gov (United States)

    2012-01-01

    Background Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. Results We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or

  10. Workflows for microarray data processing in the Kepler environment

    Directory of Open Access Journals (Sweden)

    Stropp Thomas

    2012-05-01

    Full Text Available Abstract Background Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. Results We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data and therefore are close to

  11. Workflows for microarray data processing in the Kepler environment.

    Science.gov (United States)

    Stropp, Thomas; McPhillips, Timothy; Ludäscher, Bertram; Bieda, Mark

    2012-05-17

    Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or R

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

    African Journals Online (AJOL)

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

  13. Trends in life science grid: from computing grid to knowledge grid

    Directory of Open Access Journals (Sweden)

    Konagaya Akihiko

    2006-12-01

    Full Text Available Abstract Background Grid computing has great potential to become a standard cyberinfrastructure for life sciences which often require high-performance computing and large data handling which exceeds the computing capacity of a single institution. Results This survey reviews the latest grid technologies from the viewpoints of computing grid, data grid and knowledge grid. Computing grid technologies have been matured enough to solve high-throughput real-world life scientific problems. Data grid technologies are strong candidates for realizing "resourceome" for bioinformatics. Knowledge grids should be designed not only from sharing explicit knowledge on computers but also from community formulation for sharing tacit knowledge among a community. Conclusion Extending the concept of grid from computing grid to knowledge grid, it is possible to make use of a grid as not only sharable computing resources, but also as time and place in which people work together, create knowledge, and share knowledge and experiences in a community.

  14. mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

    Science.gov (United States)

    Bokulich, Nicholas A; Rideout, Jai Ram; Mercurio, William G; Shiffer, Arron; Wolfe, Benjamin; Maurice, Corinne F; Dutton, Rachel J; Turnbaugh, Peter J; Knight, Rob; Caporaso, J Gregory

    2016-01-01

    Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e.g., raw sequence data) for each mock community data set. mockrobiota does not supply physical sample materials directly, but the data set metadata included for each mock community indicate whether physical sample materials are available. At the time of this writing, mockrobiota contains 11 mock community data sets with known species compositions, including bacterial, archaeal, and eukaryotic mock communities, analyzed by high-throughput marker gene sequencing. IMPORTANCE The availability of standard and public mock community data will facilitate ongoing method optimizations, comparisons across studies that share source data, and greater transparency and access and eliminate redundancy. These are also valuable resources for bioinformatics teaching and training. This dynamic resource is intended to expand and evolve to meet the changing needs of the omics community.

  15. 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.

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

    NARCIS (Netherlands)

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

    2017-01-01

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

  17. An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

    International Nuclear Information System (INIS)

    Taylor, Ronald C.

    2010-01-01

    Bioinformatics researchers are increasingly confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date.

  18. Neuro-symbolic representation learning on biological knowledge graphs

    KAUST Repository

    Alshahrani, Mona

    2017-04-21

    Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge.We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of SemanticWeb based knowledge bases in biology to use in machine learning and data analytics.https://github.com/bio-ontology-research-group/walking-rdf-and-owl.robert.hoehndorf@kaust.edu.sa.Supplementary data are available at Bioinformatics online.

  19. SeqHound: biological sequence and structure database as a platform for bioinformatics research

    Directory of Open Access Journals (Sweden)

    Dumontier Michel

    2002-10-01

    Full Text Available Abstract Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. Conclusions The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit.

  20. Entropy-based analysis and bioinformatics-inspired integration of global economic information transfer.

    Directory of Open Access Journals (Sweden)

    Jinkyu Kim

    Full Text Available The assessment of information transfer in the global economic network helps to understand the current environment and the outlook of an economy. Most approaches on global networks extract information transfer based mainly on a single variable. This paper establishes an entirely new bioinformatics-inspired approach to integrating information transfer derived from multiple variables and develops an international economic network accordingly. In the proposed methodology, we first construct the transfer entropies (TEs between various intra- and inter-country pairs of economic time series variables, test their significances, and then use a weighted sum approach to aggregate information captured in each TE. Through a simulation study, the new method is shown to deliver better information integration compared to existing integration methods in that it can be applied even when intra-country variables are correlated. Empirical investigation with the real world data reveals that Western countries are more influential in the global economic network and that Japan has become less influential following the Asian currency crisis.

  1. Entropy-based analysis and bioinformatics-inspired integration of global economic information transfer.

    Science.gov (United States)

    Kim, Jinkyu; Kim, Gunn; An, Sungbae; Kwon, Young-Kyun; Yoon, Sungroh

    2013-01-01

    The assessment of information transfer in the global economic network helps to understand the current environment and the outlook of an economy. Most approaches on global networks extract information transfer based mainly on a single variable. This paper establishes an entirely new bioinformatics-inspired approach to integrating information transfer derived from multiple variables and develops an international economic network accordingly. In the proposed methodology, we first construct the transfer entropies (TEs) between various intra- and inter-country pairs of economic time series variables, test their significances, and then use a weighted sum approach to aggregate information captured in each TE. Through a simulation study, the new method is shown to deliver better information integration compared to existing integration methods in that it can be applied even when intra-country variables are correlated. Empirical investigation with the real world data reveals that Western countries are more influential in the global economic network and that Japan has become less influential following the Asian currency crisis.

  2. 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

  3. Knowledge management in the engineering design environment

    Science.gov (United States)

    Briggs, Hugh C.

    2006-01-01

    The Aerospace and Defense industry is experiencing an increasing loss of knowledge through workforce reductions associated with business consolidation and retirement of senior personnel. Significant effort is being placed on process definition as part of ISO certification and, more recently, CMMI certification. The process knowledge in these efforts represents the simplest of engineering knowledge and many organizations are trying to get senior engineers to write more significant guidelines, best practices and design manuals. A new generation of design software, known as Product Lifecycle Management systems, has many mechanisms for capturing and deploying a wider variety of engineering knowledge than simple process definitions. These hold the promise of significant improvements through reuse of prior designs, codification of practices in workflows, and placement of detailed how-tos at the point of application.

  4. Cross-cultural Knowledge Management

    Directory of Open Access Journals (Sweden)

    Dorel Mihai PARASCHIV

    2009-01-01

    Full Text Available The success of international companies in providing high quality products and outstanding services is subject, on the one hand, to the increasing dynamic of the economic environment and on the other hand to the adoption of worldwide quality standards and procedures. As market place is becoming more and more global, products and services offered worldwide by international companies must face the multi-cultural environment challenges. These challenges manifest themselves not only at customer relationship level but also deep inside companies, at employee level. Important support in facing all these challenges has been provided at cognitive level by management system models and at technological level by information cutting edge technologies Business Intelligence & Knowledge Management Business Intelligence is already delivering its promised outcomes at internal business environment and, with the explosive deployment of public data bases, expand its analytical power at national, regional and international level. Quantitative measures of economic environment, wherever available, may be captured and integrated in companies’ routine analysis. As for qualitative data, some effort is still to be done in order to integrate measures of social, political, legal, natural and technological environment in companies’ strategic analysis. An increased difficulty is found in treating cultural differences, common knowledge making the most hidden part of any foreign environment. Managing cultural knowledge is crucial to success in cultivating and maintaining long-term business relationships in multicultural environments. Knowledge Management provides the long needed technological support for cross-cultural management in the tedious task of improving knowledge sharing in multi-national companies and using knowledge effectively in international joint ventures. The paper is approaching the conceptual frameworks of knowledge management and proposes an unified model

  5. 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…

  6. Content and structure of knowledge base used for virtual control of android arm motion in specified environment

    Science.gov (United States)

    Pritykin, F. N.; Nebritov, V. I.

    2018-01-01

    The paper presents the configuration of knowledge base necessary for intelligent control of android arm mechanism motion with different positions of certain forbidden regions taken into account. The present structure of the knowledge base characterizes the past experience of arm motion synthesis in the vector of velocities with due regard for the known obstacles. This structure also specifies its intrinsic properties. Knowledge base generation is based on the study of the arm mechanism instantaneous states implementations. Computational experiments connected with the virtual control of android arm motion with known forbidden regions using the developed knowledge base are introduced. Using the developed knowledge base to control virtually the arm motion reduces the time of test assignments calculation. The results of the research can be used in developing control systems of autonomous android robots in the known in advance environment.

  7. a Conceptual Framework for Virtual Geographic Environments Knowledge Engineering

    Science.gov (United States)

    You, Lan; Lin, Hui

    2016-06-01

    VGE geographic knowledge refers to the abstract and repeatable geo-information which is related to the geo-science problem, geographical phenomena and geographical laws supported by VGE. That includes expert experiences, evolution rule, simulation processes and prediction results in VGE. This paper proposes a conceptual framework for VGE knowledge engineering in order to effectively manage and use geographic knowledge in VGE. Our approach relies on previous well established theories on knowledge engineering and VGE. The main contribution of this report is following: (1) The concepts of VGE knowledge and VGE knowledge engineering which are defined clearly; (2) features about VGE knowledge different with common knowledge; (3) geographic knowledge evolution process that help users rapidly acquire knowledge in VGE; and (4) a conceptual framework for VGE knowledge engineering providing the supporting methodologies system for building an intelligent VGE. This conceptual framework systematically describes the related VGE knowledge theories and key technologies. That will promote the rapid transformation from geodata to geographic knowledge, and furtherly reduce the gap between the data explosion and knowledge absence.

  8. THE KNOWLEDGE MANAGEMENT IN INTENSIVE ENVIRONMENTS OF KNOWLEDGE: THE SMALL INCUBATED SOFTWARES COMPANIES

    Directory of Open Access Journals (Sweden)

    Greyce Krambeck

    2009-07-01

    Full Text Available This article discusses the understanding and behavior of entrepreneurs incubated for software companies (development of information systems, provide services in information technology - hardware and software, and advise on the implementation of administrative management systems in relation to knowledge, in the obtaining and facilitating the use of knowledge and availability of media. Initially, it sought a fundamental concept for the study and is based contextualise the issue, making the connection with the knowledge of the views of academic and business. After an analysis was conducted based on applied research to executives on their understanding of the concept of knowledge regarding the way in which it operates (professional and personal, concluding with the importance of knowledge for business growth from the person.

  9. Tropical Rainforests: A Case Study of UK, 13-Year-Olds' Knowledge and Understanding of These Environments

    Science.gov (United States)

    Dove, Jane

    2012-01-01

    Tropical rainforests are biologically rich ecosystems, which are threatened by a variety of different human activities. This study focuses on students' knowledge and understanding of rainforest locations, their reasons for protecting these environments and their familiarity with selected concepts about rainforest vegetation and soil. These…

  10. Rapid cloning and bioinformatic analysis of spinach Y chromosome ...

    Indian Academy of Sciences (India)

    Rapid cloning and bioinformatic analysis of spinach Y chromosome- specific EST sequences. Chuan-Liang Deng, Wei-Li Zhang, Ying Cao, Shao-Jing Wang, ... Arabidopsis thaliana mRNA for mitochondrial half-ABC transporter (STA1 gene). 389 2.31E-13. 98.96. SP3−12. Betula pendula histidine kinase 3 (HK3) mRNA, ...

  11. Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.

    Science.gov (United States)

    Kaczor-Urbanowicz, Karolina Elzbieta; Kim, Yong; Li, Feng; Galeev, Timur; Kitchen, Rob R; Gerstein, Mark; Koyano, Kikuye; Jeong, Sung-Hee; Wang, Xiaoyan; Elashoff, David; Kang, So Young; Kim, Su Mi; Kim, Kyoung; Kim, Sung; Chia, David; Xiao, Xinshu; Rozowsky, Joel; Wong, David T W

    2018-01-01

    Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva's diagnostic potential. Thus, it motivated us to perform this study. We applied principal pipelines for bioinformatic analysis of small RNA-Seq data of saliva of 98 healthy Korean volunteers including either direct or indirect mapping of the reads to the human genome using Bowtie1. Analysis of alignments to exogenous genomes by another pipeline revealed that almost all of the reads map to bacterial genomes. Thus, salivary exRNA has fundamental properties that warrant the design of unique additional steps while performing the bioinformatic analysis. Our pipelines can serve as potential guidelines for processing of RNA-Seq data of human saliva. Processing and analysis results of the experimental data generated by the exceRpt (v4.6.3) small RNA-seq pipeline (github.gersteinlab.org/exceRpt) are available from exRNA atlas (exrna-atlas.org). Alignment to exogenous genomes and their quantification results were used in this paper for the analyses of small RNAs of exogenous origin. dtww@ucla.edu. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  12. Current Knowledge in lentil genomics and its application for crop improvement

    Directory of Open Access Journals (Sweden)

    Shiv eKumar

    2015-02-01

    Full Text Available Most of the lentil growing countries face a certain set of abiotic and biotic stresses causing substantial reduction in crop growth, yield, and production. Until-to date, lentil breeders have used conventional plant breeding techniques of selection-recombination-selection cycle to develop improved cultivars. These techniques have been successful in mainstreaming some of the easy-to-manage monogenic traits. However in case of complex quantitative traits, these conventional techniques are less precise. As most of the economic traits are complex, quantitative and often influenced by environments and genotype-environment (GE interaction, the genetic improvement of these traits becomes difficult. Genomics assisted breeding is relatively powerful and fast approach to develop high yielding varieties more suitable to adverse environmental conditions. New tools such as molecular markers and bioinformatics are expected to generate new knowledge and improve our understanding on the genetics of complex traits. In the past, the limited availability of genomic resources in lentil could not allow breeders to employ these tools in mainstream breeding program. The recent application of the Next Generation Sequencing (NGS and Genotyping by sequencing (GBS technologies has facilitated to speed up the lentil genome sequencing project and large discovery of genome-wide SNP markers. Recently, several linkage maps have been developed in lentil through the use of Expressed Sequenced Tag (EST-derived Simple Sequence Repeat (SSR and Single Nucleotide Polymorphism (SNP markers. These maps have emerged as useful genomic resources to identify QTL imparting tolerance to biotic and abiotic stresses in lentil. In this review, the current knowledge on available genomic resources and its application in lentil breeding program are discussed.

  13. 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...

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

    Science.gov (United States)

    Lewis, Jamie; Bartlett, Andrew; Atkinson, Paul

    2016-01-01

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

  15. A middleware-based platform for the integration of bioinformatic services

    Directory of Open Access Journals (Sweden)

    Guzmán Llambías

    2015-08-01

    Full Text Available Performing Bioinformatic´s experiments involve an intensive access to distributed services and information resources through Internet. Although existing tools facilitate the implementation of workflow-oriented applications, they lack of capabilities to integrate services beyond low-scale applications, particularly integrating services with heterogeneous interaction patterns and in a larger scale. This is particularly required to enable a large-scale distributed processing of biological data generated by massive sequencing technologies. On the other hand, such integration mechanisms are provided by middleware products like Enterprise Service Buses (ESB, which enable to integrate distributed systems following a Service Oriented Architecture. This paper proposes an integration platform, based on enterprise middleware, to integrate Bioinformatics services. It presents a multi-level reference architecture and focuses on ESB-based mechanisms to provide asynchronous communications, event-based interactions and data transformation capabilities. The paper presents a formal specification of the platform using the Event-B model.

  16. A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Shan Li

    2014-01-01

    Full Text Available With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.

  17. Endodontic Microbiology and Pathobiology: Current State of Knowledge.

    Science.gov (United States)

    Fouad, Ashraf F

    2017-01-01

    Newer research tools and basic science knowledge base have allowed the exploration of endodontic diseases in the pulp and periapical tissues in novel ways. The use of next generation sequencing, bioinformatics analyses, genome-wide association studies, to name just a few of these innovations, has allowed the identification of hundreds of microorganisms and of host response factors. This review addresses recent advances in endodontic microbiology and the host response and discusses the potential for future innovations in this area. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Learning your way in city : experience and gender differences in configurational knowledge of one’s environment

    NARCIS (Netherlands)

    Goede, M. de; Postma, A.

    2015-01-01

    Males tend to outperform females in their knowledge of relative and absolute distances in spatial layouts and environments. It is unclear yet in how far these differences are innate or develop through life. The aim of the present study was to investigate whether gender differences in configurational

  19. Evaluation of a joint Bioinformatics and Medical Informatics international course in Peru.

    Science.gov (United States)

    Curioso, Walter H; Hansen, Jacquelyn R; Centurion-Lara, Arturo; Garcia, Patricia J; Wolf, Fredric M; Fuller, Sherrilynne; Holmes, King K; Kimball, Ann Marie

    2008-01-14

    New technologies that emerge at the interface of computational and biomedical science could drive new advances in global health, therefore more training in technology is needed among health care workers. To assess the potential for informatics training using an approach designed to foster interaction at this interface, the University of Washington and the Universidad Peruana Cayetano Heredia developed and assessed a one-week course that included a new Bioinformatics (BIO) track along with an established Medical/Public Health Informatics track (MI) for participants in Peru. We assessed the background of the participants, and measured the knowledge gained by track-specific (MI or BIO) 30-minute pre- and post-tests. Participants' attitudes were evaluated both by daily evaluations and by an end-course evaluation. Forty-three participants enrolled in the course - 20 in the MI track and 23 in the BIO track. Of 20 questions, the mean % score for the MI track increased from 49.7 pre-test (standard deviation or SD = 17.0) to 59.7 (SD = 15.2) for the post-test (P = 0.002, n = 18). The BIO track mean score increased from 33.6 pre-test to 51.2 post-test (P < 0.001, n = 21). Most comments (76%) about any aspect of the course were positive. The main perceived strength of the course was the quality of the speakers, and the main perceived weakness was the short duration of the course. Overall, the course acceptability was very good to excellent with a rating of 4.1 (scale 1-5), and the usefulness of the course was rated as very good. Most participants (62.9%) expressed a positive opinion about having had the BIO and MI tracks come together for some of the lectures. Pre- and post-test results and the positive evaluations by the participants indicate that this first joint Bioinformatics and Medical/Public Health Informatics (MI and BIO) course was a success.

  20. 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.

  1. 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...

  2. Student self-reported communication skills, knowledge and confidence across standardised patient, virtual and traditional clinical learning environments.

    Science.gov (United States)

    Quail, Michelle; Brundage, Shelley B; Spitalnick, Josh; Allen, Peter J; Beilby, Janet

    2016-02-27

    Advanced communication skills are vital for allied health professionals, yet students often have limited opportunities in which to develop them. The option of increasing clinical placement hours is unsustainable in a climate of constrained budgets, limited placement availability and increasing student numbers. Consequently, many educators are considering the potentials of alternative training methods, such as simulation. Simulations provide safe, repeatable and standardised learning environments in which students can practice a variety of clinical skills. This study investigated students' self-rated communication skill, knowledge, confidence and empathy across simulated and traditional learning environments. Undergraduate speech pathology students were randomly allocated to one of three communication partners with whom they engaged conversationally for up to 30 min: a patient in a nursing home (n = 21); an elderly trained patient actor (n = 22); or a virtual patient (n = 19). One week prior to, and again following the conversational interaction, participants completed measures of self-reported communication skill, knowledge and confidence (developed by the authors based on the Four Habit Coding Scheme), as well as the Jefferson Scale of Empathy - Health Professionals (student version). All three groups reported significantly higher communication knowledge, skills and confidence post-placement (Median d = .58), while the degree of change did not vary as a function of group membership (Median η (2)  communication skill, knowledge and confidence, though not empathy, following a brief placement in a virtual, standardised or traditional learning environment. The self-reported increases were consistent across the three placement types. It is proposed that the findings from this study provide support for the integration of more sustainable, standardised, virtual patient-based placement models into allied health training programs for the training of

  3. Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics

    Science.gov (United States)

    Palma, Jonathan P.; Benitz, William E.; Tarczy-Hornoch, Peter; Butte, Atul J.; Longhurst, Christopher A.

    2012-01-01

    The future of neonatal informatics will be driven by the availability of increasingly vast amounts of clinical and genetic data. The field of translational bioinformatics is concerned with linking and learning from these data and applying new findings to clinical care to transform the data into proactive, predictive, preventive, and participatory health. As a result of advances in translational informatics, the care of neonates will become more data driven, evidence based, and personalized. PMID:22924023

  4. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

    Science.gov (United States)

    Krampis, Konstantinos; Booth, Tim; Chapman, Brad; Tiwari, Bela; Bicak, Mesude; Field, Dawn; Nelson, Karen E

    2012-03-19

    A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly

  5. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

    Science.gov (United States)

    2012-01-01

    Background A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Results Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Conclusions Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the

  6. Multiobjective optimization in bioinformatics and computational biology.

    Science.gov (United States)

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

    2007-01-01

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

  7. 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...... analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work......Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly...

  8. Neuro-symbolic representation learning on biological knowledge graphs.

    Science.gov (United States)

    Alshahrani, Mona; Khan, Mohammad Asif; Maddouri, Omar; Kinjo, Akira R; Queralt-Rosinach, Núria; Hoehndorf, Robert

    2017-09-01

    Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of Semantic Web based knowledge bases in biology to use in machine learning and data analytics. https://github.com/bio-ontology-research-group/walking-rdf-and-owl. robert.hoehndorf@kaust.edu.sa. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  9. Managing heterogeneous knowledge: A Theory of External Knowledge Integration

    NARCIS (Netherlands)

    Kraaijenbrink, Jeroen; Wijnhoven, Alphonsus B.J.M.

    2008-01-01

    Knowledge integration has been theorised at the levels of organisations and inter-organisational dyads. However, no theory exists yet of the integration of knowledge from an organisation's environment. This paper addresses this void in the literature by presenting a theory of external knowledge

  10. Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.

    Science.gov (United States)

    Pauling, Josch; Klipp, Edda

    2016-12-22

    Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries. The computational biology and bioinformatics community has so far established methodology in genomics, transcriptomics and proteomics but there are many (combinatorial) challenges when it comes to structural diversity of lipids and their identification, quantification and interpretation. This review gives an overview and outlook on lipidomics research and illustrates ongoing computational and bioinformatics efforts. These efforts are important and necessary steps to advance the lipidomics field alongside analytic, biochemistry, biomedical and biology communities and to close the gap in available computational methodology between lipidomics and other omics sub-branches.

  11. A review of bioinformatic methods for forensic DNA analyses.

    Science.gov (United States)

    Liu, Yao-Yuan; Harbison, SallyAnn

    2018-03-01

    Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

    Science.gov (United States)

    Mayer, Gerhard; Quast, Christian; Felden, Janine; Lange, Matthias; Prinz, Manuel; Pühler, Alfred; Lawerenz, Chris; Scholz, Uwe; Glöckner, Frank Oliver; Müller, Wolfgang; Marcus, Katrin; Eisenacher, Martin

    2017-10-30

    Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Five representative scenarios for value estimation from a rough estimation to a detailed breakdown of costs are presented. To account for the diversity in bioinformatics applications and services, the notion of service-specific 'service provision units' is introduced together with the factors influencing them and the main underlying assumptions for these 'value influencing factors'. Special attention is given on how to handle personnel costs and indirect costs such as electricity. Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database analyses, one for consulting services and one for bioinformatics training events. Finally, from the discussed values, the costs of direct funding and the costs of payment of services by funded projects are calculated and compared. © The Author 2017. Published by Oxford University Press.

  13. Kubernetes as an approach for solving bioinformatic problems.

    OpenAIRE

    Markstedt, Olof

    2017-01-01

    The cluster orchestration tool Kubernetes enables easy deployment and reproducibility of life science research by utilizing the advantages of the container technology. The container technology allows for easy tool creation, sharing and runs on any Linux system once it has been built. The applicability of Kubernetes as an approach to run bioinformatic workflows was evaluated and resulted in some examples of how Kubernetes and containers could be used within the field of life science and how th...

  14. Relations among Home Literacy Environment, Child Characteristics and Print Knowledge for Preschool Children with Language Impairment

    Science.gov (United States)

    Sawyer, Brook E.; Justice, Laura M.; Guo, Ying; Logan, Jessica A. R.; Petrill, Stephen A.; Glenn-Applegate, Katherine; Kaderavek, Joan N.; Pentimonti, Jill M.

    2014-01-01

    To contribute to the modest body of work examining the home literacy environment (HLE) and emergent literacy outcomes for children with disabilities, this study addressed two aims: (a) to determine the unique contributions of the HLE on print knowledge of preschool children with language impairment and (b) to identify whether specific child…

  15. Gene-Environment Interaction Effects of Peer Deviance, Parental Knowledge and Stressful Life Events on Adolescent Alcohol Use.

    Science.gov (United States)

    Cooke, Megan E; Meyers, Jacquelyn L; Latvala, Antti; Korhonen, Tellervo; Rose, Richard J; Kaprio, Jaakko; Salvatore, Jessica E; Dick, Danielle M

    2015-10-01

    The purpose of this study was to address two methodological issues that have called into question whether previously reported gene-environment interaction (GxE) effects for adolescent alcohol use are 'real'. These issues are (1) the potential correlation between the environmental moderator and the outcome across twins and (2) non-linear transformations of the behavioral outcome. Three environments that have been previously studied (peer deviance, parental knowledge, and potentially stressful life events) were examined here. For each moderator (peer deviance, parental knowledge, and potentially stressful life events), a series of models was fit to both a raw and transformed measure of monthly adolescent alcohol use in a sample that included 825 dizygotic (DZ) and 803 monozygotic (MZ) twin pairs. The results showed that the moderating effect of peer deviance was robust to transformation, and that although the significance of moderating effects of parental knowledge and potentially stressful life events were dependent on the scale of the adolescent alcohol use outcome, the overall results were consistent across transformation. In addition, the findings did not vary across statistical models. The consistency of the peer deviance results and the shift of the parental knowledge and potentially stressful life events results between trending and significant, shed some light on why previous findings for certain moderators have been inconsistent and emphasize the importance of considering both methodological issues and previous findings when conducting and interpreting GxE analyses.

  16. The Framework of Knowledge Creation for Online Learning Environments

    Science.gov (United States)

    Huang, Hsiu­-Mei; Liaw, Shu­-Sheng

    2004-01-01

    In today's competitive global economy characterized by knowledge acquisition, the concept of knowledge management has become increasingly prevalent in academic and business practices. Knowledge creation is an important factor and remains a source of competitive advantage over knowledge management. Information technology facilitates knowledge…

  17. A User-Centric Knowledge Creation Model in a Web of Object-Enabled Internet of Things Environment

    Science.gov (United States)

    Kibria, Muhammad Golam; Fattah, Sheik Mohammad Mostakim; Jeong, Kwanghyeon; Chong, Ilyoung; Jeong, Youn-Kwae

    2015-01-01

    User-centric service features in a Web of Object-enabled Internet of Things environment can be provided by using a semantic ontology that classifies and integrates objects on the World Wide Web as well as shares and merges context-aware information and accumulated knowledge. The semantic ontology is applied on a Web of Object platform to virtualize the real world physical devices and information to form virtual objects that represent the features and capabilities of devices in the virtual world. Detailed information and functionalities of multiple virtual objects are combined with service rules to form composite virtual objects that offer context-aware knowledge-based services, where context awareness plays an important role in enabling automatic modification of the system to reconfigure the services based on the context. Converting the raw data into meaningful information and connecting the information to form the knowledge and storing and reusing the objects in the knowledge base can both be expressed by semantic ontology. In this paper, a knowledge creation model that synchronizes a service logistic model and a virtual world knowledge model on a Web of Object platform has been proposed. To realize the context-aware knowledge-based service creation and execution, a conceptual semantic ontology model has been developed and a prototype has been implemented for a use case scenario of emergency service. PMID:26393609

  18. A User-Centric Knowledge Creation Model in a Web of Object-Enabled Internet of Things Environment

    Directory of Open Access Journals (Sweden)

    Muhammad Golam Kibria

    2015-09-01

    Full Text Available User-centric service features in a Web of Object-enabled Internet of Things environment can be provided by using a semantic ontology that classifies and integrates objects on the World Wide Web as well as shares and merges context-aware information and accumulated knowledge. The semantic ontology is applied on a Web of Object platform to virtualize the real world physical devices and information to form virtual objects that represent the features and capabilities of devices in the virtual world. Detailed information and functionalities of multiple virtual objects are combined with service rules to form composite virtual objects that offer context-aware knowledge-based services, where context awareness plays an important role in enabling automatic modification of the system to reconfigure the services based on the context. Converting the raw data into meaningful information and connecting the information to form the knowledge and storing and reusing the objects in the knowledge base can both be expressed by semantic ontology. In this paper, a knowledge creation model that synchronizes a service logistic model and a virtual world knowledge model on a Web of Object platform has been proposed. To realize the context-aware knowledge-based service creation and execution, a conceptual semantic ontology model has been developed and a prototype has been implemented for a use case scenario of emergency service.

  19. A User-Centric Knowledge Creation Model in a Web of Object-Enabled Internet of Things Environment.

    Science.gov (United States)

    Kibria, Muhammad Golam; Fattah, Sheik Mohammad Mostakim; Jeong, Kwanghyeon; Chong, Ilyoung; Jeong, Youn-Kwae

    2015-09-18

    User-centric service features in a Web of Object-enabled Internet of Things environment can be provided by using a semantic ontology that classifies and integrates objects on the World Wide Web as well as shares and merges context-aware information and accumulated knowledge. The semantic ontology is applied on a Web of Object platform to virtualize the real world physical devices and information to form virtual objects that represent the features and capabilities of devices in the virtual world. Detailed information and functionalities of multiple virtual objects are combined with service rules to form composite virtual objects that offer context-aware knowledge-based services, where context awareness plays an important role in enabling automatic modification of the system to reconfigure the services based on the context. Converting the raw data into meaningful information and connecting the information to form the knowledge and storing and reusing the objects in the knowledge base can both be expressed by semantic ontology. In this paper, a knowledge creation model that synchronizes a service logistic model and a virtual world knowledge model on a Web of Object platform has been proposed. To realize the context-aware knowledge-based service creation and execution, a conceptual semantic ontology model has been developed and a prototype has been implemented for a use case scenario of emergency service.

  20. Video Bioinformatics Analysis of Human Embryonic Stem Cell Colony Growth

    Science.gov (United States)

    Lin, Sabrina; Fonteno, Shawn; Satish, Shruthi; Bhanu, Bir; Talbot, Prue

    2010-01-01

    Because video data are complex and are comprised of many images, mining information from video material is difficult to do without the aid of computer software. Video bioinformatics is a powerful quantitative approach for extracting spatio-temporal data from video images using computer software to perform dating mining and analysis. In this article, we introduce a video bioinformatics method for quantifying the growth of human embryonic stem cells (hESC) by analyzing time-lapse videos collected in a Nikon BioStation CT incubator equipped with a camera for video imaging. In our experiments, hESC colonies that were attached to Matrigel were filmed for 48 hours in the BioStation CT. To determine the rate of growth of these colonies, recipes were developed using CL-Quant software which enables users to extract various types of data from video images. To accurately evaluate colony growth, three recipes were created. The first segmented the image into the colony and background, the second enhanced the image to define colonies throughout the video sequence accurately, and the third measured the number of pixels in the colony over time. The three recipes were run in sequence on video data collected in a BioStation CT to analyze the rate of growth of individual hESC colonies over 48 hours. To verify the truthfulness of the CL-Quant recipes, the same data were analyzed manually using Adobe Photoshop software. When the data obtained using the CL-Quant recipes and Photoshop were compared, results were virtually identical, indicating the CL-Quant recipes were truthful. The method described here could be applied to any video data to measure growth rates of hESC or other cells that grow in colonies. In addition, other video bioinformatics recipes can be developed in the future for other cell processes such as migration, apoptosis, and cell adhesion. PMID:20495527

  1. Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans

    DEFF Research Database (Denmark)

    Nan, Jie; Brostromer, Erik; Liu, Xiang-Yu

    2009-01-01

    . From the interlinking structural and bioinformatics studies, we have concluded that SMU.440 could be involved in polyketide-like antibiotic resistance, providing a better understanding of this hypothetical protein. Besides, the combination of multiple methods in this study can be used as a general...

  2. Bioinformatics prediction of swine MHC class I epitopes from Porcine Reproductive and Respiratory Syndrome Virus

    DEFF Research Database (Denmark)

    Welner, Simon; Nielsen, Morten; Lund, Ole

    an effective CTL response against PRRSV, we have taken a bioinformatics approach to identify common PRRSV epitopes predicted to react broadly with predominant swine MHC (SLA) alleles. First, the genomic integrity and sequencing method was examined for 334 available complete PRRSV type 2 genomes leaving 104...... by the PopCover algorithm, providing a final list of 54 epitopes prioritized according to maximum coverage of PRRSV strains and SLA alleles. This bioinformatics approach provides a rational strategy for selecting peptides for a CTL-activating vaccine with broad coverage of both virus and swine diversity...

  3. Knowledge representation within information systems in manufacturing environments

    OpenAIRE

    Sharif, Amir M

    2004-01-01

    This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University. Representing knowledge as information content alone is insufficient in providing us with an understanding of the world around us. A combination of context as well as reasoning of the information content is fundamental to representing knowledge in an information system. Knowledge Representation is typically concerned with providing structures and theories that are used as a basis for intellige...

  4. Conference Report: "Knowledge Organization in Cooperative Learning and Working Environments". 8th Conference of the International Society for Knowledge Organization (ISKO), German Chapter

    OpenAIRE

    Doris A. Ohnesorge; H. Peter Ohly

    2003-01-01

    The report gives an overview of a conference that recognized and focused upon the fundamentals of knowledge organization as well asked questions and offered solutions for practice. The primary emphasis was given to the application of cooperative learning and working environments. The special value of this conference was the focus of the presentations and detailed discussions on current topics in the information sciences. Although the spectrum ranged from scientific to organizational environme...

  5. Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience

    Science.gov (United States)

    Panji, Sumir; Fernandes, Pedro L.; Judge, David P.; Ghouila, Amel; Salifu, Samson P.; Ahmed, Rehab; Kayondo, Jonathan; Ssemwanga, Deogratius

    2017-01-01

    Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge “Introduction to Bioinformatics” course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery–mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online “question and discussion” forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings. PMID:28981516

  6. Leveraging on Information Technology to Teach Construction Law to Built Environment Students: A Knowledge-Based System (KBS Approach

    Directory of Open Access Journals (Sweden)

    Faisal Manzoor Arain

    2009-11-01

    Full Text Available Construction law is a vital component of the body of knowledge that is needed by construction professionals in order to successfully operate in the commercial world of construction. Construction law plays an important role in shaping building projects. Construction projects are complex because they involve many human and non-human factors and variables. Teaching construction law is therefore a complex issue with several dimensions. In recent years, Information Technology (IT has become strongly established as a supporting tool for many professions, including teachers. If faculty members have a knowledge base established on similar past projects, it would assist the faculty members to present case studies and contractually based scenarios to students. This paper proposes potential utilisation of a Knowledge-based System (KBS for teaching construction law to built environment students. The KBS is primarily designed for building professionals to learn from similar past projects. The KBS is able to assist professionals by providing accurate and timelyinformation for decision making and a user-friendly tool for analysing and selecting the suggested controls for variations in educational buildings. It is recommended that the wealth of knowledge available in the KBS can be very helpful in teaching construction law to built environment students. The system presents real case studies and scenarios to students to allow them to analyse and learn construction law. The KBS could be useful to students as a general research tool because the students could populate it with their own data and use it with the reported educational projects. With further generic modifications, the KBS will also be useful for built environment students to learn about project management of building projects; thus, it will raise the overall level of professional understanding, and eventually productivity, in the construction industry.

  7. Bioinformatics and Medical Informatics: Collaborations on the Road to Genomic Medicine?

    Science.gov (United States)

    Maojo, Victor; Kulikowski, Casimir A.

    2003-01-01

    In this report, the authors compare and contrast medical informatics (MI) and bioinformatics (BI) and provide a viewpoint on their complementarities and potential for collaboration in various subfields. The authors compare MI and BI along several dimensions, including: (1) historical development of the disciplines, (2) their scientific foundations, (3) data quality and analysis, (4) integration of knowledge and databases, (5) informatics tools to support practice, (6) informatics methods to support research (signal processing, imaging and vision, and computational modeling, (7) professional and patient continuing education, and (8) education and training. It is pointed out that, while the two disciplines differ in their histories, scientific foundations, and methodologic approaches to research in various areas, they nevertheless share methods and tools, which provides a basis for exchange of experience in their different applications. MI expertise in developing health care applications and the strength of BI in biological “discovery science” complement each other well. The new field of biomedical informatics (BMI) holds great promise for developing informatics methods that will be crucial in the development of genomic medicine. The future of BMI will be influenced strongly by whether significant advances in clinical practice and biomedical research come about from separate efforts in MI and BI, or from emerging, hybrid informatics subdisciplines at their interface. PMID:12925552

  8. Acquiring Knowledge in Learning Concepts from Electrical Circuits: The Use of Multiple Representations in Technology-Based Learning Environments

    Directory of Open Access Journals (Sweden)

    Abdeljalil Métioui

    2012-04-01

    Full Text Available The constructivists approach on the conception of relative software of modelling to training and teaching of the concepts of current and voltage requires appraisal of several disciplinary fields in order to provide to the learners a training adapted to their representations. Thus, this approach requires the researchers to have adequate knowledge or skills in data processing, didactics and science content. In this regard, several researches underline that the acquisition of basic concepts that span a field of a given knowledge, must take into account the student and the scientific representations. The present research appears in this perspective, and aims to present the interactive computer environments that take into account the students (secondary and college and scientific representations related to simple electric circuits. These computer environments will help the students to analyze the functions of the electric circuits adequately.

  9. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

    Science.gov (United States)

    Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter

    2013-01-01

    Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. Contact: jison@ebi.ac.uk PMID:23479348

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

    Science.gov (United States)

    Kalas, Matús; Puntervoll, Pål; Joseph, Alexandre; Bartaseviciūte, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge

    2010-09-15

    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 of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community.

  11. 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...

  12. Bioinformatics for Next Generation Sequencing Data

    Directory of Open Access Journals (Sweden)

    Alberto Magi

    2010-09-01

    Full Text Available The emergence of next-generation sequencing (NGS platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial availability, a large number of softwares already exist for analyzing NGS data. These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection and genome browsing. This manuscript aims to guide readers in the choice of the available computational tools that can be used to face the several steps of the data analysis workflow.

  13. Analysis of Patterns of Interaction and Knowledge Construction in On-Line Learning Environments: A Methodological Strategy

    Directory of Open Access Journals (Sweden)

    Benilde García Cabrero

    2008-05-01

    Full Text Available A model of analysis of interaction and construction of knowledge in educational environments based on computer-mediated communication (CMC is proposed. This proposal considers: 1 the contextual factors that constitute the input and the scenario of interaction, 2 the interaction processes: types of interaction and its contents (Garrison, Anderson and Archer, 2000 as well as the discursive strategies (Lemke, 1997, and 3 learning results that involve the quality of the knowledge constructed by the participants (Gunawardena, Lowe and Anderson, 1997. This model was applied to the analysis of the interaction among a group of participants in two web forums (with or without the presence of a teacher, during the teaching of a PhD in Psychology program. The results show evidence of the model’s viability to describe the patterns of interaction and the levels of construction of knowledge in web forums.

  14. Gait Event Detection in Real-World Environment for Long-Term Applications: Incorporating Domain Knowledge Into Time-Frequency Analysis.

    Science.gov (United States)

    Khandelwal, Siddhartha; Wickstrom, Nicholas

    2016-12-01

    Detecting gait events is the key to many gait analysis applications that would benefit from continuous monitoring or long-term analysis. Most gait event detection algorithms using wearable sensors that offer a potential for use in daily living have been developed from data collected in controlled indoor experiments. However, for real-word applications, it is essential that the analysis is carried out in humans' natural environment; that involves different gait speeds, changing walking terrains, varying surface inclinations and regular turns among other factors. Existing domain knowledge in the form of principles or underlying fundamental gait relationships can be utilized to drive and support the data analysis in order to develop robust algorithms that can tackle real-world challenges in gait analysis. This paper presents a novel approach that exhibits how domain knowledge about human gait can be incorporated into time-frequency analysis to detect gait events from long-term accelerometer signals. The accuracy and robustness of the proposed algorithm are validated by experiments done in indoor and outdoor environments with approximately 93 600 gait events in total. The proposed algorithm exhibits consistently high performance scores across all datasets in both, indoor and outdoor environments.

  15. A Knowledge-Based Approach to Automatic Detection of Equipment Alarm Sounds in a Neonatal Intensive Care Unit Environment.

    Science.gov (United States)

    Raboshchuk, Ganna; Nadeu, Climent; Jancovic, Peter; Lilja, Alex Peiro; Kokuer, Munevver; Munoz Mahamud, Blanca; Riverola De Veciana, Ana

    2018-01-01

    A large number of alarm sounds triggered by biomedical equipment occur frequently in the noisy environment of a neonatal intensive care unit (NICU) and play a key role in providing healthcare. In this paper, our work on the development of an automatic system for detection of acoustic alarms in that difficult environment is presented. Such automatic detection system is needed for the investigation of how a preterm infant reacts to auditory stimuli of the NICU environment and for an improved real-time patient monitoring. The approach presented in this paper consists of using the available knowledge about each alarm class in the design of the detection system. The information about the frequency structure is used in the feature extraction stage, and the time structure knowledge is incorporated at the post-processing stage. Several alternative methods are compared for feature extraction, modeling, and post-processing. The detection performance is evaluated with real data recorded in the NICU of the hospital, and by using both frame-level and period-level metrics. The experimental results show that the inclusion of both spectral and temporal information allows to improve the baseline detection performance by more than 60%.

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

    Science.gov (United States)

    Ju, Feng; Zhang, Tong

    2015-11-03

    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.

  17. Shared Bioinformatics Databases within the Unipro UGENE Platform

    Directory of Open Access Journals (Sweden)

    Protsyuk Ivan V.

    2015-03-01

    Full Text Available Unipro UGENE is an open-source bioinformatics toolkit that integrates popular tools along with original instruments for molecular biologists within a unified user interface. Nowadays, most bioinformatics desktop applications, including UGENE, make use of a local data model while processing different types of data. Such an approach causes an inconvenience for scientists working cooperatively and relying on the same data. This refers to the need of making multiple copies of certain files for every workplace and maintaining synchronization between them in case of modifications. Therefore, we focused on delivering a collaborative work into the UGENE user experience. Currently, several UGENE installations can be connected to a designated shared database and users can interact with it simultaneously. Such databases can be created by UGENE users and be used at their discretion. Objects of each data type, supported by UGENE such as sequences, annotations, multiple alignments, etc., can now be easily imported from or exported to a remote storage. One of the main advantages of this system, compared to existing ones, is the almost simultaneous access of client applications to shared data regardless of their volume. Moreover, the system is capable of storing millions of objects. The storage itself is a regular database server so even an inexpert user is able to deploy it. Thus, UGENE may provide access to shared data for users located, for example, in the same laboratory or institution. UGENE is available at: http://ugene.net/download.html.

  18. Enabling knowledge processes in innovative environments

    NARCIS (Netherlands)

    Pavesi, S.

    2003-01-01

    The concept of organisational knowledge as a valuable strategic asset has become quite popular recently. Increased competition, globalisation and the emergence of new organisational models built on process-based organisational structures require organisations to create, capture, share and apply

  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. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

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

  1. Tissue damage in organic rainbow trout muscle investigated by proteomics and bioinformatics

    DEFF Research Database (Denmark)

    Wulff, Tune; Silva, T.; Nielsen, Michael Engelbrecht

    2013-01-01

    and magnitude of the cellular response, in the context of a regenerative process. Using a bioinformatics approach, the main biological function of these proteins were assigned, showing the regulation of proteins involved in processes like apoptosis, iron homeostasis and regulation of muscular structure...

  2. 3D modelling of the pathogenic Leptospira protein LipL32: A bioinformatics approach.

    Science.gov (United States)

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

    2017-12-01

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

  3. Analysis Effect of Environment Attitude, Health Consciousness and Knowledge in Developing Product Perception and Intention to Buy (A Study on Organic Food Product

    Directory of Open Access Journals (Sweden)

    Widyasari

    2010-12-01

    Full Text Available This research intends to study the factors that can affect the product perception and consumer intention in buying organic product.The study is necessary in that it explores at least some of the factors that can affect the product perception and consumer intention in buying organic product. The research results indicated that there was a positive influence of health consciousness towards environment attitude, consumer’s organic product knowledge towards organic product perception, environment attitude and consumer’s organic knowledge towards intention to buy organic product. But, there was a negative influence between environment attitude, health consciousness towards consumer’s organic product perception, and consumer’s organic product towards intention to buy organic product.

  4. Why Choose This One? Factors in Scientists' Selection of Bioinformatics Tools

    Science.gov (United States)

    Bartlett, Joan C.; Ishimura, Yusuke; Kloda, Lorie A.

    2011-01-01

    Purpose: The objective was to identify and understand the factors involved in scientists' selection of preferred bioinformatics tools, such as databases of gene or protein sequence information (e.g., GenBank) or programs that manipulate and analyse biological data (e.g., BLAST). Methods: Eight scientists maintained research diaries for a two-week…

  5. A web services choreography scenario for interoperating bioinformatics applications

    Directory of Open Access Journals (Sweden)

    Cheung David W

    2004-03-01

    with these web services using a web services choreography language (BPEL4WS. Conclusion While it is relatively straightforward to implement and publish web services, the use of web services choreography engines is still in its infancy. However, industry-wide support and push for web services standards is quickly increasing the chance of success in using web services to unify heterogeneous bioinformatics applications. Due to the immaturity of currently available web services engines, it is still most practical to implement a simple, ad-hoc XML-based workflow by hard coding the workflow as a Java application. For advanced web service users the Collaxa BPEL engine facilitates a configuration and management environment that can fully handle XML-based workflow.

  6. Tissue Banking, Bioinformatics, and Electronic Medical Records: The Front-End Requirements for Personalized Medicine

    Science.gov (United States)

    Suh, K. Stephen; Sarojini, Sreeja; Youssif, Maher; Nalley, Kip; Milinovikj, Natasha; Elloumi, Fathi; Russell, Steven; Pecora, Andrew; Schecter, Elyssa; Goy, Andre

    2013-01-01

    Personalized medicine promises patient-tailored treatments that enhance patient care and decrease overall treatment costs by focusing on genetics and “-omics” data obtained from patient biospecimens and records to guide therapy choices that generate good clinical outcomes. The approach relies on diagnostic and prognostic use of novel biomarkers discovered through combinations of tissue banking, bioinformatics, and electronic medical records (EMRs). The analytical power of bioinformatic platforms combined with patient clinical data from EMRs can reveal potential biomarkers and clinical phenotypes that allow researchers to develop experimental strategies using selected patient biospecimens stored in tissue banks. For cancer, high-quality biospecimens collected at diagnosis, first relapse, and various treatment stages provide crucial resources for study designs. To enlarge biospecimen collections, patient education regarding the value of specimen donation is vital. One approach for increasing consent is to offer publically available illustrations and game-like engagements demonstrating how wider sample availability facilitates development of novel therapies. The critical value of tissue bank samples, bioinformatics, and EMR in the early stages of the biomarker discovery process for personalized medicine is often overlooked. The data obtained also require cross-disciplinary collaborations to translate experimental results into clinical practice and diagnostic and prognostic use in personalized medicine. PMID:23818899

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

    Science.gov (United States)

    Kalaš, Matúš; Puntervoll, Pæl; Joseph, Alexandre; Bartaševičiūtė, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge

    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 of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. Availability: The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community. Contact: matus.kalas@bccs.uib.no; developers@bioxsd.org; support@bioxsd.org PMID:20823319

  8. How scientific experiments are designed: Problem solving in a knowledge-rich, error-rich environment

    Science.gov (United States)

    Baker, Lisa M.

    bias in earlier studies using science-like tasks, in which characteristics of the alternate hypothesis space may have made it unfeasible for participants to generate and test alternate hypotheses. In general, scientists and science undergraduates were found to engage in a systematic experimental design process that responded to salient features of the problem environment, including the constant potential for experimental error, availability of alternate hypotheses, and access to both theoretical knowledge and knowledge of experimental techniques.

  9. A Method of Extracting Ontology Module Using Concept Relations for Sharing Knowledge in Mobile Cloud Computing Environment

    Directory of Open Access Journals (Sweden)

    Keonsoo Lee

    2014-01-01

    Full Text Available In mobile cloud computing environment, the cooperation of distributed computing objects is one of the most important requirements for providing successful cloud services. To satisfy this requirement, all the members, who are employed in the cooperation group, need to share the knowledge for mutual understanding. Even if ontology can be the right tool for this goal, there are several issues to make a right ontology. As the cost and complexity of managing knowledge increase according to the scale of the knowledge, reducing the size of ontology is one of the critical issues. In this paper, we propose a method of extracting ontology module to increase the utility of knowledge. For the given signature, this method extracts the ontology module, which is semantically self-contained to fulfill the needs of the service, by considering the syntactic structure and semantic relation of concepts. By employing this module, instead of the original ontology, the cooperation of computing objects can be performed with less computing load and complexity. In particular, when multiple external ontologies need to be combined for more complex services, this method can be used to optimize the size of shared knowledge.

  10. A method of extracting ontology module using concept relations for sharing knowledge in mobile cloud computing environment.

    Science.gov (United States)

    Lee, Keonsoo; Rho, Seungmin; Lee, Seok-Won

    2014-01-01

    In mobile cloud computing environment, the cooperation of distributed computing objects is one of the most important requirements for providing successful cloud services. To satisfy this requirement, all the members, who are employed in the cooperation group, need to share the knowledge for mutual understanding. Even if ontology can be the right tool for this goal, there are several issues to make a right ontology. As the cost and complexity of managing knowledge increase according to the scale of the knowledge, reducing the size of ontology is one of the critical issues. In this paper, we propose a method of extracting ontology module to increase the utility of knowledge. For the given signature, this method extracts the ontology module, which is semantically self-contained to fulfill the needs of the service, by considering the syntactic structure and semantic relation of concepts. By employing this module, instead of the original ontology, the cooperation of computing objects can be performed with less computing load and complexity. In particular, when multiple external ontologies need to be combined for more complex services, this method can be used to optimize the size of shared knowledge.

  11. Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome

    DEFF Research Database (Denmark)

    Kesmir, Can; van Noort, V.; de Boer, R.J.

    2003-01-01

    not yet been quantified how different the specificity of two forms of the proteasome are. The main question, which still lacks direct evidence, is whether the immunoproteasome generates more MHC ligands. Here we use bioinformatics tools to quantify these differences and show that the immunoproteasome...

  12. In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics

    DEFF Research Database (Denmark)

    Adachi, Jun; Kumar, Chanchal; Zhang, Yanling

    2007-01-01

    , mitochondria, membrane, and cytosol of 3T3-L1 adipocytes. We identified 3,287 proteins while essentially eliminating false positives, making this one of the largest high confidence proteomes reported to date. Comprehensive bioinformatics analysis revealed that the adipocyte proteome, despite its specialized...

  13. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.

    Science.gov (United States)

    He, Yongqun; Xiang, Zuoshuang

    2010-09-27

    Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis, one of the commonest zoonotic diseases found worldwide in humans and a variety of animal species. While several animal vaccines are available, there is no effective and safe vaccine for prevention of brucellosis in humans. VIOLIN (http://www.violinet.org) is a web-based vaccine database and analysis system that curates, stores, and analyzes published data of commercialized vaccines, and vaccines in clinical trials or in research. VIOLIN contains information for 454 vaccines or vaccine candidates for 73 pathogens. VIOLIN also contains many bioinformatics tools for vaccine data analysis, data integration, and vaccine target prediction. To demonstrate the applicability of VIOLIN for vaccine research, VIOLIN was used for bioinformatics analysis of existing Brucella vaccines and prediction of new Brucella vaccine targets. VIOLIN contains many literature mining programs (e.g., Vaxmesh) that provide in-depth analysis of Brucella vaccine literature. As a result of manual literature curation, VIOLIN contains information for 38 Brucella vaccines or vaccine candidates, 14 protective Brucella antigens, and 68 host response studies to Brucella vaccines from 97 peer-reviewed articles. These Brucella vaccines are classified in the Vaccine Ontology (VO) system and used for different ontological applications. The web-based VIOLIN vaccine target prediction program Vaxign was used to predict new Brucella vaccine targets. Vaxign identified 14 outer membrane proteins that are conserved in six virulent strains from B. abortus, B. melitensis, and B. suis that are pathogenic in humans. Of the 14 membrane proteins, two proteins (Omp2b and Omp31-1) are not present in B. ovis, a Brucella species that is not pathogenic in humans. Brucella vaccine data stored in VIOLIN were compared and analyzed using the VIOLIN query system. Bioinformatics curation and ontological representation of Brucella vaccines

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

    Science.gov (United States)

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

    2016-04-30

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

  15. 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

  16. Conceptualising GP teachers' knowledge: a pedagogical content knowledge perspective.

    Science.gov (United States)

    Cantillon, Peter; de Grave, Willem

    2012-05-01

    Most teacher development initiatives focus on enhancing knowledge of teaching (pedagogy), whilst largely ignoring other important features of teacher knowledge such as subject matter knowledge and awareness of the learning context. Furthermore, teachers' ability to learn from faculty development interventions is limited by their existing (often implicit) pedagogical knowledge and beliefs. Pedagogical content knowledge (PCK) represents a model of teacher knowledge incorporating what they know about subject matter, pedagogy and context. PCK can be used to explore teachers' prior knowledge and to structure faculty development programmes so that they take account of a broader range of teachers' knowledge. We set out to examine the application of a PCK model in a general practice education setting. This study is part of a larger study that employed a mixed method approach (concept mapping, phenomenological interviews and video-stimulated recall) to explore features of GP teachers' subject matter knowledge, pedagogical knowledge and knowledge of the learning environment in the context of a general practice tutorial. This paper presents data on GP teachers' pedagogical and context knowledge. There was considerable overlap between different GP teachers' knowledge and beliefs about learners and the clinical learning environment (i.e. knowledge of context). The teachers' beliefs about learners were largely based on assumptions derived from their own student experiences. There were stark differences, however, between teachers in terms of pedagogical knowledge, particularly in terms of their teaching orientations (i.e. transmission or facilitation orientation) and this was manifest in their teaching behaviours. PCK represents a useful model for conceptualising clinical teacher prior knowledge in three domains, namely subject matter, learning context and pedagogy. It can and should be used as a simple guiding framework by faculty developers to inform the design and delivery of

  17. Impact of radioactivity on the environment: problems, state of current knowledge and approaches for identification of radioprotection criteria

    International Nuclear Information System (INIS)

    Brechignac, F.

    2001-01-01

    There is currently a revitalized concern about the potential impact of ionizing radiation on the environment that calls for the construction of a system ensuring an adequate radioprotection of the non-human biota and their associated biotopes. This paper first sets the context of the problem both, with respect to the general philosophy of environmental protection as a whole, but also with respect to the consideration of the environment achieved so far in the purpose of human radioprotection. The current accumulated knowledge on the effects of ionizing radiation to biota (fauna and flora) is then briefly reviewed, encompassing effects at individual and community/ecosystem level, situations of acute and chronic exposure to high and low doses, finally leading to the identification of the most critical gaps in scientific knowledge: effects of mixed low dose rates in chronic exposure to communities and ecosystems. The most significant current international efforts towards the identification of environmental radioprotection criteria and standards are finally presented along with some relevant national examples. (author)

  18. Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout.

    Directory of Open Access Journals (Sweden)

    Sophie Depiereux

    Full Text Available Sex steroids play a key role in triggering sex differentiation in fish, the use of exogenous hormone treatment leading to partial or complete sex reversal. This phenomenon has attracted attention since the discovery that even low environmental doses of exogenous steroids can adversely affect gonad morphology (ovotestis development and induce reproductive failure. Modern genomic-based technologies have enhanced opportunities to find out mechanisms of actions (MOA and identify biomarkers related to the toxic action of a compound. However, high throughput data interpretation relies on statistical analysis, species genomic resources, and bioinformatics tools. The goals of this study are to improve the knowledge of feminisation in fish, by the analysis of molecular responses in the gonads of rainbow trout fry after chronic exposure to several doses (0.01, 0.1, 1 and 10 μg/L of ethynylestradiol (EE2 and to offer target genes as potential biomarkers of ovotestis development. We successfully adapted a bioinformatics microarray analysis workflow elaborated on human data to a toxicogenomic study using rainbow trout, a fish species lacking accurate functional annotation and genomic resources. The workflow allowed to obtain lists of genes supposed to be enriched in true positive differentially expressed genes (DEGs, which were subjected to over-representation analysis methods (ORA. Several pathways and ontologies, mostly related to cell division and metabolism, sexual reproduction and steroid production, were found significantly enriched in our analyses. Moreover, two sets of potential ovotestis biomarkers were selected using several criteria. The first group displayed specific potential biomarkers belonging to pathways/ontologies highlighted in the experiment. Among them, the early ovarian differentiation gene foxl2a was overexpressed. The second group, which was highly sensitive but not specific, included the DEGs presenting the highest fold change and

  19. OralCard: a bioinformatic tool for the study of oral proteome.

    Science.gov (United States)

    Arrais, Joel P; Rosa, Nuno; Melo, José; Coelho, Edgar D; Amaral, Diana; Correia, Maria José; Barros, Marlene; Oliveira, José Luís

    2013-07-01

    The molecular complexity of the human oral cavity can only be clarified through identification of components that participate within it. However current proteomic techniques produce high volumes of information that are dispersed over several online databases. Collecting all of this data and using an integrative approach capable of identifying unknown associations is still an unsolved problem. This is the main motivation for this work. We present the online bioinformatic tool OralCard, which comprises results from 55 manually curated articles reflecting the oral molecular ecosystem (OralPhysiOme). It comprises experimental information available from the oral proteome both of human (OralOme) and microbial origin (MicroOralOme) structured in protein, disease and organism. This tool is a key resource for researchers to understand the molecular foundations implicated in biology and disease mechanisms of the oral cavity. The usefulness of this tool is illustrated with the analysis of the oral proteome associated with diabetes melitus type 2. OralCard is available at http://bioinformatics.ua.pt/oralcard. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Efficient Feature Selection and Classification of Protein Sequence Data in Bioinformatics

    Science.gov (United States)

    Faye, Ibrahima; Samir, Brahim Belhaouari; Md Said, Abas

    2014-01-01

    Bioinformatics has been an emerging area of research for the last three decades. The ultimate aims of bioinformatics were to store and manage the biological data, and develop and analyze computational tools to enhance their understanding. The size of data accumulated under various sequencing projects is increasing exponentially, which presents difficulties for the experimental methods. To reduce the gap between newly sequenced protein and proteins with known functions, many computational techniques involving classification and clustering algorithms were proposed in the past. The classification of protein sequences into existing superfamilies is helpful in predicting the structure and function of large amount of newly discovered proteins. The existing classification results are unsatisfactory due to a huge size of features obtained through various feature encoding methods. In this work, a statistical metric-based feature selection technique has been proposed in order to reduce the size of the extracted feature vector. The proposed method of protein classification shows significant improvement in terms of performance measure metrics: accuracy, sensitivity, specificity, recall, F-measure, and so forth. PMID:25045727

  1. MOWServ: a web client for integration of bioinformatic resources

    Science.gov (United States)

    Ramírez, Sergio; Muñoz-Mérida, Antonio; Karlsson, Johan; García, Maximiliano; Pérez-Pulido, Antonio J.; Claros, M. Gonzalo; Trelles, Oswaldo

    2010-01-01

    The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user’s tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/. PMID:20525794

  2. Bioprospecting and Functional Analysis of Neglected Environments

    DEFF Research Database (Denmark)

    Vogt, Josef Korbinian

    on Biological Diversity (explained in Chapter 3). Proteolytic enzymes – described in Chapter 4 – are the target for bioprospecting due to their high market value. Section II describes methods used for the analysis of metagenomic and RNA-seq datasets, including Manuscript I, which includes the taxonomic...... of arctic marine metagenomes reveals bacterial strategies for deep sea persistence (Manuscript II). Furthermore, this extreme environment is a fertile ground to mine for novel proteolytic enzymes. Manuscript III presents a bioinformatics approach to identify sequences for potential commercialization...

  3. Single-Cell Transcriptomics Bioinformatics and Computational Challenges

    Directory of Open Access Journals (Sweden)

    Lana Garmire

    2016-09-01

    Full Text Available The emerging single-cell RNA-Seq (scRNA-Seq technology holds the promise to revolutionize our understanding of diseases and associated biological processes at an unprecedented resolution. It opens the door to reveal the intercellular heterogeneity and has been employed to a variety of applications, ranging from characterizing cancer cells subpopulations to elucidating tumor resistance mechanisms. Parallel to improving experimental protocols to deal with technological issues, deriving new analytical methods to reveal the complexity in scRNA-Seq data is just as challenging. Here we review the current state-of-the-art bioinformatics tools and methods for scRNA-Seq analysis, as well as addressing some critical analytical challenges that the field faces.

  4. Does Environmental Knowledge Inhibit Hominin Dispersal?

    Science.gov (United States)

    Wren, Colin D; Costopoulos, Andre

    2015-07-01

    We investigated the relationship between the dispersal potential of a hominin population, its local-scale foraging strategies, and the characteristics of the resource environment using an agent-based modeling approach. In previous work we demonstrated that natural selection can favor a relatively low capacity for assessing and predicting the quality of the resource environment, especially when the distribution of resources is highly clustered. That work also suggested that the more knowledge foraging populations had about their environment, the less likely they were to abandon the landscape they know and disperse into novel territory. The present study gives agents new individual and social strategies for learning about their environment. For both individual and social learning, natural selection favors decreased levels of environmental knowledge, particularly in low-heterogeneity environments. Social acquisition of detailed environmental knowledge results in crowding of agents, which reduces available reproductive space and relative fitness. Agents with less environmental knowledge move away from resource clusters and into areas with more space available for reproduction. These results suggest that, rather than being a requirement for successful dispersal, environmental knowledge strengthens the ties to particular locations and significantly reduces the dispersal potential as a result. The evolved level of environmental knowledge in a population depends on the characteristics of the resource environment and affects the dispersal capacity of the population.

  5. Synergy between Medical Informatics and Bioinformatics: Facilitating Genomic Medicine for Future Health Care

    Czech Academy of Sciences Publication Activity Database

    Martin-Sanchez, F.; Iakovidis, I.; Norager, S.; Maojo, V.; de Groen, P.; Van der Lei, J.; Jones, T.; Abraham-Fuchs, K.; Apweiler, R.; Babic, A.; Baud, R.; Breton, V.; Cinquin, P.; Doupi, P.; Dugas, M.; Eils, R.; Engelbrecht, R.; Ghazal, P.; Jehenson, P.; Kulikowski, C.; Lampe, K.; De Moor, G.; Orphanoudakis, S.; Rossing, N.; Sarachan, B.; Sousa, A.; Spekowius, G.; Thireos, G.; Zahlmann, G.; Zvárová, Jana; Hermosilla, I.; Vicente, F. J.

    2004-01-01

    Roč. 37, - (2004), s. 30-42 ISSN 1532-0464 Institutional research plan: CEZ:AV0Z1030915 Keywords : bioinformatics * medical informatics * genomics * genomic medicine * biomedical informatics Subject RIV: BD - Theory of Information Impact factor: 1.013, year: 2004

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  7. Strategies for Using Peer-Assisted Learning Effectively in an Undergraduate Bioinformatics Course

    Science.gov (United States)

    Shapiro, Casey; Ayon, Carlos; Moberg-Parker, Jordan; Levis-Fitzgerald, Marc; Sanders, Erin R.

    2013-01-01

    This study used a mixed methods approach to evaluate hybrid peer-assisted learning approaches incorporated into a bioinformatics tutorial for a genome annotation research project. Quantitative and qualitative data were collected from undergraduates who enrolled in a research-based laboratory course during two different academic terms at UCLA.…

  8. Fostering accurate HIV/AIDS knowledge among unmarried youths in Cameroon: do family environment and peers matter?

    Science.gov (United States)

    Tsala Dimbuene, Zacharie; Kuate Defo, Barthelemy

    2011-05-19

    respondents reported accurate knowledge about HIV transmission routes and prevention strategies. Findings showed that the role of family environment as source of accurate HIV knowledge transmission routes and prevention strategies is of paramount significance; however, families have been poorly integrated in the design and implementation of the first generation of HIV interventions. There is an urgent need that policymakers work together with families to improve the efficiency of these interventions. Peer influences is likely controversial because of the double positive effect of peer-to-peer communication on both accurate and inaccurate knowledge of HIV transmission routes.

  9. Combining multiple decisions: applications to bioinformatics

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  10. Bioinformatics Analysis Reveals Genes Involved in the Pathogenesis of Ameloblastoma and Keratocystic Odontogenic Tumor.

    Science.gov (United States)

    Santos, Eliane Macedo Sobrinho; Santos, Hércules Otacílio; Dos Santos Dias, Ivoneth; Santos, Sérgio Henrique; Batista de Paula, Alfredo Maurício; Feltenberger, John David; Sena Guimarães, André Luiz; Farias, Lucyana Conceição

    2016-01-01

    Pathogenesis of odontogenic tumors is not well known. It is important to identify genetic deregulations and molecular alterations. This study aimed to investigate, through bioinformatic analysis, the possible genes involved in the pathogenesis of ameloblastoma (AM) and keratocystic odontogenic tumor (KCOT). Genes involved in the pathogenesis of AM and KCOT were identified in GeneCards. Gene list was expanded, and the gene interactions network was mapped using the STRING software. "Weighted number of links" (WNL) was calculated to identify "leader genes" (highest WNL). Genes were ranked by K-means method and Kruskal-Wallis test was used (Preview data was used to corroborate the bioinformatics data. CDK1 was identified as leader gene for AM. In KCOT group, results show PCNA and TP53 . Both tumors exhibit a power law behavior. Our topological analysis suggested leader genes possibly important in the pathogenesis of AM and KCOT, by clustering coefficient calculated for both odontogenic tumors (0.028 for AM, zero for KCOT). The results obtained in the scatter diagram suggest an important relationship of these genes with the molecular processes involved in AM and KCOT. Ontological analysis for both AM and KCOT demonstrated different mechanisms. Bioinformatics analyzes were confirmed through literature review. These results may suggest the involvement of promising genes for a better understanding of the pathogenesis of AM and KCOT.

  11. Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow

    DEFF Research Database (Denmark)

    Deshmukh, Atul S; Cox, Juergen; Jensen, Lars Juhl

    2015-01-01

    , in principle, allows an unbiased and comprehensive analysis of cellular secretomes; however, the distinction of bona fide secreted proteins from proteins released upon lysis of a small fraction of dying cells remains challenging. Here we applied highly sensitive MS and streamlined bioinformatics to analyze......-resistant conditions. Our study demonstrates an efficient combined experimental and bioinformatics workflow to identify putative secreted proteins from insulin-resistant skeletal muscle cells, which could easily be adapted to other cellular models....

  12. The effect of the work environment and performance-based self-esteem on cognitive stress symptoms among Danish knowledge workers.

    Science.gov (United States)

    Albertsen, Karen; Rugulies, Reiner; Garde, Anne Helene; Burr, Hermann

    2010-02-01

    Interpersonal relations at work as well as individual factors seem to play prominent roles in the modern labour market, and arguably also for the change in stress symptoms. The aim was to examine whether exposures in the psychosocial work environment predicted symptoms of cognitive stress in a sample of Danish knowledge workers (i.e. employees working with sign, communication or exchange of knowledge) and whether performance-based self-esteem had a main effect, over and above the work environmental factors. 349 knowledge workers, selected from a national, representative cohort study, were followed up with two data collections, 12 months apart. We used data on psychosocial work environment factors and cognitive stress symptoms measured with the Copenhagen Psychosocial Questionnaire (COPSOQ), and a measurement of performance-based self-esteem. Effects on cognitive stress symptoms were analyzed with a GLM procedure with and without adjustment for baseline level. Measures at baseline of quantitative demands, role conflicts, lack of role clarity, recognition, predictability, influence and social support from management were positively associated with cognitive stress symptoms 12 months later. After adjustment for baseline level of cognitive stress symptoms, follow-up level was only predicted by lack of predictability. Performance-based self-esteem was prospectively associated with cognitive stress symptoms and had an independent effect above the psychosocial work environment factors on the level of and changes in cognitive stress symptoms. The results suggest that both work environmental and individual characteristics should be taken into account in order to capture sources of stress in modern working life.

  13. 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...

  14. Sharing and Cultivating Tacit Knowledge in an Online Learning Environment

    Science.gov (United States)

    Tee, Meng Yew; Karney, Dennis

    2010-01-01

    Research on knowledge cultivation often focuses on explicit forms of knowledge. However, knowledge can also take a tacit form--a form that is often difficult or impossible to tease out, even when it is considered critical in an educational context. A review of the literature revealed that few studies have examined tacit knowledge issues in online…

  15. Can Mobile Technology Enable Knowledge Communication in a Learning Environment?

    DEFF Research Database (Denmark)

    Kampf, Constance; Islas Sedano, Carolina

    2008-01-01

    this mobile phone game to help next years' students navigated the CampusNet system in order to study for the exam.  The CampusNet system can be seen as a knowledge management technology situated within the social context of the Project Management course, and so the examples offered, in effect, demonstrate...... To be effective, knowledge management systems need to encompass both social processes and technical components (McDermott 2000),   On the other hand, knowledge communication as a concept has emerged not from the inspiration of technology, but partly from the social-technical challenge of dealing...... with technology in knowledge management systems.  So, is knowledge communication a process that can be technologically enabled?  In this presentation, we explore the possibilities of socio-technical interaction for knowledge communication through the use of a mobile phone game as a knowledge communication tool...

  16. Functionality and Evolutionary History of the Chaperonins in Thermophilic Archaea. A Bioinformatical Perspective

    Science.gov (United States)

    Karlin, Samuel

    2004-01-01

    We used bioinformatics methods to study phylogenetic relations and differentiation patterns of the archaeal chaperonin 60 kDa heat-shock protein (HSP60) genes in support of the study of differential expression patterns of the three chaperonin genes encoded in Sulfolobus shibatae.

  17. Cluster Flow: A user-friendly bioinformatics workflow tool [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Philip Ewels

    2016-12-01

    Full Text Available Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at http://clusterflow.io.

  18. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Fabrizio Fierro

    2017-09-01

    Full Text Available Human G-protein coupled receptors (hGPCRs constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation.

  19. MAPI: towards the integrated exploitation of bioinformatics Web Services.

    Science.gov (United States)

    Ramirez, Sergio; Karlsson, Johan; Trelles, Oswaldo

    2011-10-27

    Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).

  20. PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.

    Science.gov (United States)

    Anslan, Sten; Bahram, Mohammad; Hiiesalu, Indrek; Tedersoo, Leho

    2017-11-01

    High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24 hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable. © 2017 John Wiley & Sons Ltd.