WorldWideScience

Sample records for bioinformatics resource center

  1. Wrapping and interoperating bioinformatics resources using CORBA.

    Science.gov (United States)

    Stevens, R; Miller, C

    2000-02-01

    Bioinformaticians seeking to provide services to working biologists are faced with the twin problems of distribution and diversity of resources. Bioinformatics databases are distributed around the world and exist in many kinds of storage forms, platforms and access paradigms. To provide adequate services to biologists, these distributed and diverse resources have to interoperate seamlessly within single applications. The Common Object Request Broker Architecture (CORBA) offers one technical solution to these problems. The key component of CORBA is its use of object orientation as an intermediate form to translate between different representations. This paper concentrates on an explanation of object orientation and how it can be used to overcome the problems of distribution and diversity by describing the interfaces between objects.

  2. The European Bioinformatics Institute's data resources.

    Science.gov (United States)

    Brooksbank, Catherine; Camon, Evelyn; Harris, Midori A; Magrane, Michele; Martin, Maria Jesus; Mulder, Nicola; O'Donovan, Claire; Parkinson, Helen; Tuli, Mary Ann; Apweiler, Rolf; Birney, Ewan; Brazma, Alvis; Henrick, Kim; Lopez, Rodrigo; Stoesser, Guenter; Stoehr, Peter; Cameron, Graham

    2003-01-01

    As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics Institute (EBI) hosts six core databases, which store information on DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), protein structure (MSD), whole genomes (Ensembl) and gene expression (ArrayExpress). But just as a cell would be useless if it couldn't transcribe DNA or translate RNA, our resources would be compromised if each existed in isolation. We have therefore developed a range of tools that not only facilitate the deposition and retrieval of biological information, but also allow users to carry out searches that reflect the interconnectedness of biological information. The EBI's databases and tools are all available on our website at www.ebi.ac.uk. PMID:12519944

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes...... to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials....... Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database...

  4. ENVIRONMENTAL BIOINFORMATICS AND COMPUTATIONAL TOXICOLOGY CENTER

    Science.gov (United States)

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

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

    Institute of Scientific and Technical Information of China (English)

    Trias Thireou; George Spyrou; Vassilis Atlamazoglou

    2007-01-01

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

  6. 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...

  7. 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…

  8. Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools

    Directory of Open Access Journals (Sweden)

    Daisuke Kihara

    2006-01-01

    Full Text Available The immensely popular fields of cancer research and bioinformatics overlap in many different areas, e.g. large data repositories that allow for users to analyze data from many experiments (data handling, databases, pattern mining, microarray data analysis, and interpretation of proteomics data. There are many newly available resources in these areas that may be unfamiliar to most cancer researchers wanting to incorporate bioinformatics tools and analyses into their work, and also to bioinformaticians looking for real data to develop and test algorithms. This review reveals the interdependence of cancer research and bioinformatics, and highlight the most appropriate and useful resources available to cancer researchers. These include not only public databases, but general and specific bioinformatics tools which can be useful to the cancer researcher. The primary foci are function and structure prediction tools of protein genes. The result is a useful reference to cancer researchers and bioinformaticians studying cancer alike.

  9. The European Bioinformatics Institute’s data resources

    OpenAIRE

    Brooksbank, Catherine; Cameron, Graham; Thornton, Janet

    2009-01-01

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

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

    Science.gov (United States)

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

  11. 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

  12. 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%.

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

    Science.gov (United States)

    Hu, Rongdong; Liu, Guangming; Jiang, Jingfei; Wang, Lixin

    2015-01-01

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

  14. 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, gene

  15. 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

    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...

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

    OpenAIRE

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  18. National Sexual Violence Resource Center (NSVRC)

    Data.gov (United States)

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

  19. A model nursing computer resource center.

    Science.gov (United States)

    Mueller, Sheryl S; Pullen, Richard L; McGee, K Sue

    2002-01-01

    Nursing graduates are required to demonstrate computer technology skills and critical reflective thinking skills in the workplace. The authors discuss a model computer resource center that enhances the acquisition of these requisite skills by students in both an associate degree and vocational nursing program. The computer resource center maximizes student learning and promotes faculty effectiveness and efficiency by a "full-service" approach to computerized testing, information technology instruction, online research, and interactive computer program practice. PMID:12023644

  20. 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...

  1. Introducing Bioinformatics into the Biology Curriculum: Exploring the National Center for Biotechnology Information.

    Science.gov (United States)

    Smith, Thomas M.; Emmeluth, Donald S.

    2002-01-01

    Explains the potential of computer technology in science education and argues for integrating bioinformatics into the biology curriculum. Describes three modules designed to introduce students to technological advancements in biology. Aims to develop a better understanding of molecular biology among students. (YDS)

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

    OpenAIRE

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Mark W. Tanner

    2010-09-01

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

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

    Science.gov (United States)

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

  5. Illinois trauma centers and community violence resources

    Directory of Open Access Journals (Sweden)

    Bennet Butler

    2014-01-01

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

  6. Illinois trauma centers and community violence resources

    OpenAIRE

    Bennet Butler; Ogo Agubuzu; Luke Hansen; Marie Crandall

    2014-01-01

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

  7. The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud.

    Science.gov (United States)

    Karimi, Kamran; Vize, Peter D

    2014-01-01

    As a model organism database, Xenbase has been providing informatics and genomic data on Xenopus (Silurana) tropicalis and Xenopus laevis frogs for more than a decade. The Xenbase database contains curated, as well as community-contributed and automatically harvested literature, gene and genomic data. A GBrowse genome browser, a BLAST+ server and stock center support are available on the site. When this resource was first built, all software services and components in Xenbase ran on a single physical server, with inherent reliability, scalability and inter-dependence issues. Recent advances in networking and virtualization techniques allowed us to move Xenbase to a virtual environment, and more specifically to a private cloud. To do so we decoupled the different software services and components, such that each would run on a different virtual machine. In the process, we also upgraded many of the components. The resulting system is faster and more reliable. System maintenance is easier, as individual virtual machines can now be updated, backed up and changed independently. We are also experiencing more effective resource allocation and utilization. Database URL: www.xenbase.org.

  8. Marshall Space Flight Center Telescience Resource Kit

    Science.gov (United States)

    Wade, Gina

    2016-01-01

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

  9. A Resource Center for Informal Science Education

    Science.gov (United States)

    Dickow, B.

    2011-12-01

    Informal science education (ISE) is playing an increasingly important role in how and where the public engages with science. A growing body of research is showing that people learn the majority of their science knowledge outside of school (Falk & Dierking, 2010). The ISE field includes a wide variety of sources, including the internet, TV programs, magazines, hobby clubs and museums, all sectors of the informal science education field. These experiences touch large numbers of people throughout their lifetimes. If you would like to share your research with the public, ISE can be an effective conduit for meaningful science communication. However, because the ISE field is so diverse, it can be overwhelming with its multiple entry points. If you already are part of an ISE initiative, knowing how to access the most useful resources easily can also be daunting. CAISE, the Center for Advancement of Informal Science Education, is a resource center for the ISE field funded by the National Science Foundation (NSF). CAISE can help connect you to the knowledge and people of ISE, through its website, products and in-person convenings. The proposed CAISE presentation will outline the diversity of the field and concisely present data that will make the case for the impact of ISE. We will focus on examples of successful programs that connect science with the public and that bring together AGU's science research community with practitioners and researchers within ISE. Pathways to various ISE resources in the form of current CAISE initiatives will be described as well. The presentation will include an interview section in which a CAISE staff member will ask questions of a scientist involved in an ISE initiative in order to detail one example of how ISE can be a valuable tool for engaging the public in science. Time for audience Q&A also will be included in the session.

  10. Virtualized cloud data center networks issues in resource management

    CERN Document Server

    Tsai, Linjiun

    2016-01-01

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

  11. 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.

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

    Science.gov (United States)

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

    2016-06-01

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

  13. National Maternal and Child Oral Health Resource Center

    Science.gov (United States)

    ... OHRC on Twitter Tweets by @OHRC_GU With funding from the Maternal and Child Health Bureau, Health Resources and Services Administration National Maternal and Child Oral Health Resource Center • Georgetown ...

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

    Science.gov (United States)

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

    2011-01-01

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

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

    OpenAIRE

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

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Schmid Amy K

    2007-11-01

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

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

    Science.gov (United States)

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

    2012-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Tennis Joseph T

    2009-09-01

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

  19. NASA Center for Computational Sciences: History and Resources

    Science.gov (United States)

    2000-01-01

    The Nasa Center for Computational Sciences (NCCS) has been a leading capacity computing facility, providing a production environment and support resources to address the challenges facing the Earth and space sciences research community.

  20. Natural Resources at Kennedy Space Center

    Science.gov (United States)

    Phillips, Lynne

    2015-01-01

    Informative presentation on the purpose and need for an Ecological Program at the Kennedy Space Center. Includes the federal laws mandating the program followed by a description of many of the long term monitoring projects. Projects include wildlife surveying by observation as well as interactive surveys to collect basic animal data for analysis of trends in habitat use and ecosystem health. The program is designed for a broad range in audience from elementary to college level.

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

    Science.gov (United States)

    Javid, Mahnaz A.

    1998-01-01

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

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

    OpenAIRE

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

    2006-01-01

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

  3. Multi-Cultural Resource Center Materials Handbook, Grades K-3.

    Science.gov (United States)

    Gillespie, Mary F.; Barrientos, Anita

    This annotated bibliography cites multicultural materials whose themes correlate with basic concepts taught in the primary grades. The items are in the Multi-Cultural Resource Center of the Toledo, Ohio public schools. The purpose of the bibliography is to help teachers integrate materials into their classroom. Films, filmstrips, books, study…

  4. Building an Information Resource Center for Competitive Intelligence.

    Science.gov (United States)

    Martin, J. Sperling

    1992-01-01

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

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

    Science.gov (United States)

    2011-08-30

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

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

    Science.gov (United States)

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

    1999-01-01

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

  7. The NIH-NIAID Filariasis Research Reagent Resource Center.

    Directory of Open Access Journals (Sweden)

    Michelle L Michalski

    2011-11-01

    Full Text Available Filarial worms cause a variety of tropical diseases in humans; however, they are difficult to study because they have complex life cycles that require arthropod intermediate hosts and mammalian definitive hosts. Research efforts in industrialized countries are further complicated by the fact that some filarial nematodes that cause disease in humans are restricted in host specificity to humans alone. This potentially makes the commitment to research difficult, expensive, and restrictive. Over 40 years ago, the United States National Institutes of Health-National Institute of Allergy and Infectious Diseases (NIH-NIAID established a resource from which investigators could obtain various filarial parasite species and life cycle stages without having to expend the effort and funds necessary to maintain the entire life cycles in their own laboratories. This centralized resource (The Filariasis Research Reagent Resource Center, or FR3 translated into cost savings to both NIH-NIAID and to principal investigators by freeing up personnel costs on grants and allowing investigators to divert more funds to targeted research goals. Many investigators, especially those new to the field of tropical medicine, are unaware of the scope of materials and support provided by the FR3. This review is intended to provide a short history of the contract, brief descriptions of the fiilarial species and molecular resources provided, and an estimate of the impact the resource has had on the research community, and describes some new additions and potential benefits the resource center might have for the ever-changing research interests of investigators.

  8. Amarillo National Resource Center for Plutonium 1999 plan

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-01-30

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

  9. Amarillo National Resource Center for Plutonium 1999 plan

    International Nuclear Information System (INIS)

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

  10. Strategies for developing biostatistics resources in an academic health center.

    Science.gov (United States)

    Welty, Leah J; Carter, Rickey E; Finkelstein, Dianne M; Harrell, Frank E; Lindsell, Christopher J; Macaluso, Maurizio; Mazumdar, Madhu; Nietert, Paul J; Oster, Robert A; Pollock, Brad H; Roberson, Paula K; Ware, James H

    2013-04-01

    Biostatistics--the application of statistics to understanding health and biology-provides powerful tools for developing research questions, designing studies, refining measurements, analyzing data, and interpreting findings. Biostatistics plays an important role in health-related research, yet biostatistics resources are often fragmented, ad hoc, or oversubscribed within academic health centers (AHCs). Given the increasing complexity and quantity of health-related data, the emphasis on accelerating clinical and translational science, and the importance of conducting reproducible research, the need for the thoughtful development of biostatistics resources within AHCs is growing.In this article, the authors identify strategies for developing biostatistics resources in three areas: (1) recruiting and retaining biostatisticians, (2) efficiently using biostatistics resources, and (3) improving biostatistical contributions to science. AHCs should consider these three domains in building strong biostatistics resources, which they can leverage to support a broad spectrum of research. For each of the three domains, the authors describe the advantages and disadvantages of AHCs creating centralized biostatistics units rather than dispersing such resources across clinical departments or other research units. They also address the challenges that biostatisticians face in contributing to research without sacrificing their individual professional growth or the trajectory of their research teams. The authors ultimately recommend that AHCs create centralized biostatistics units because this approach offers distinct advantages both to investigators who collaborate with biostatisticians as well as to the biostatisticians themselves, and it is better suited to accomplish the research and education missions of AHCs.

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

    Science.gov (United States)

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

    2013-11-01

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

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

    Science.gov (United States)

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

    2013-11-01

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

  13. Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis: EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

    Directory of Open Access Journals (Sweden)

    Planas Josep V

    2008-10-01

    Full Text Available Abstract Background The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species. Results Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis, larval stages (pre-metamorphosis, metamorphosis, juvenile stages (post-metamorphosis, abnormal fish, and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs. Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34% had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data. Conclusion New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions.

  14. Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

    Science.gov (United States)

    Cerdà, Joan; Mercadé, Jaume; Lozano, Juan José; Manchado, Manuel; Tingaud-Sequeira, Angèle; Astola, Antonio; Infante, Carlos; Halm, Silke; Viñas, Jordi; Castellana, Barbara; Asensio, Esther; Cañavate, Pedro; Martínez-Rodríguez, Gonzalo; Piferrer, Francesc; Planas, Josep V; Prat, Francesc; Yúfera, Manuel; Durany, Olga; Subirada, Francesc; Rosell, Elisabet; Maes, Tamara

    2008-01-01

    Background The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species. Results Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis), larval stages (pre-metamorphosis, metamorphosis), juvenile stages (post-metamorphosis, abnormal fish), and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs). Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34%) had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data. Conclusion New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions. PMID:18973667

  15. 75 FR 7487 - National Center for Research Resources; Notice of Closed Meetings

    Science.gov (United States)

    2010-02-19

    ....gov . Name of Committee: National Center for Research Resources Special Emphasis Panel; COBRE III...: National Center for Research Resources Special Emphasis Panel; RCMI COBRE. Date: March 17-18, 2010. Time:...

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

    Science.gov (United States)

    Varga, Z M

    2016-01-01

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

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

    Science.gov (United States)

    Varga, Zoltán M

    2011-01-01

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

  18. Education resources of the National Center for Biotechnology Information.

    Science.gov (United States)

    Cooper, Peter S; Lipshultz, Dawn; Matten, Wayne T; McGinnis, Scott D; Pechous, Steven; Romiti, Monica L; Tao, Tao; Valjavec-Gratian, Majda; Sayers, Eric W

    2010-11-01

    The National Center for Biotechnology Information (NCBI) hosts 39 literature and molecular biology databases containing almost half a billion records. As the complexity of these data and associated resources and tools continues to expand, so does the need for educational resources to help investigators, clinicians, information specialists and the general public make use of the wealth of public data available at the NCBI. This review describes the educational resources available at NCBI via the NCBI Education page (www.ncbi.nlm.nih.gov/Education/). These resources include materials designed for new users, such as About NCBI and the NCBI Guide, as well as documentation, Frequently Asked Questions (FAQs) and writings on the NCBI Bookshelf such as the NCBI Help Manual and the NCBI Handbook. NCBI also provides teaching materials such as tutorials, problem sets and educational tools such as the Amino Acid Explorer, PSSM Viewer and Ebot. NCBI also offers training programs including the Discovery Workshops, webinars and tutorials at conferences. To help users keep up-to-date, NCBI produces the online NCBI News and offers RSS feeds and mailing lists, along with a presence on Facebook, Twitter and YouTube.

  19. CAISE: A NSF Resource Center for Informal Science Education

    Science.gov (United States)

    Dickow, Benjamin

    2012-01-01

    Informal science education (ISE) is playing an increasingly important role in how and where the public engages with science. A growing body of research is showing that people learn the majority of their science knowledge outside of school (Falk & Dierking, 2010). The ISE field includes a wide variety of sources, including the internet, TV programs, magazines, hobby clubs and museums. These experiences touch large numbers of people throughout their lifetimes. If you would like to share your research with the public, ISE can be an effective conduit for meaningful science communication. However, because the ISE field is so diverse, it can be overwhelming with its multiple entry points. If you already are part of an ISE initiative, knowing how to access the most useful resources easily can also be daunting. CAISE, the Center for Advancement of Informal Science Education, is a resource center for the ISE field funded by the National Science Foundation (NSF). CAISE can help connect you to the knowledge and people of ISE, through its website, products and in-person convenings. The proposed CAISE presentation will outline the diversity of the field and concisely present data that will make the case for the impact of ISE. We will focus on examples of successful programs that connect science with the public and that bring together AAS's science research community with practitioners and researchers within ISE. Pathways to various ISE resources in the form of current CAISE initiatives will be described as well. The presentation will include an interview section in which a CAISE staff member will ask questions of a scientist involved in an ISE initiative in order to detail one example of how ISE can be a valuable tool for engaging the public in science. Time for audience Q&A also will be included in the session.

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

    International Nuclear Information System (INIS)

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

  1. Bioinformatics in Africa: The Rise of Ghana?

    Directory of Open Access Journals (Sweden)

    Thomas K Karikari

    2015-09-01

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

  2. Eukaryotic Pathogen Database Resources (EuPathDB)

    Data.gov (United States)

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

  3. Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy.

    Science.gov (United States)

    Türei, Dénes; Földvári-Nagy, László; Fazekas, Dávid; Módos, Dezső; Kubisch, János; Kadlecsik, Tamás; Demeter, Amanda; Lenti, Katalin; Csermely, Péter; Vellai, Tibor; Korcsmáros, Tamás

    2015-01-01

    Autophagy is a complex cellular process having multiple roles, depending on tissue, physiological, or pathological conditions. Major post-translational regulators of autophagy are well known, however, they have not yet been collected comprehensively. The precise and context-dependent regulation of autophagy necessitates additional regulators, including transcriptional and post-transcriptional components that are listed in various datasets. Prompted by the lack of systems-level autophagy-related information, we manually collected the literature and integrated external resources to gain a high coverage autophagy database. We developed an online resource, Autophagy Regulatory Network (ARN; http://autophagy-regulation.org), to provide an integrated and systems-level database for autophagy research. ARN contains manually curated, imported, and predicted interactions of autophagy components (1,485 proteins with 4,013 interactions) in humans. We listed 413 transcription factors and 386 miRNAs that could regulate autophagy components or their protein regulators. We also connected the above-mentioned autophagy components and regulators with signaling pathways from the SignaLink 2 resource. The user-friendly website of ARN allows researchers without computational background to search, browse, and download the database. The database can be downloaded in SQL, CSV, BioPAX, SBML, PSI-MI, and in a Cytoscape CYS file formats. ARN has the potential to facilitate the experimental validation of novel autophagy components and regulators. In addition, ARN helps the investigation of transcription factors, miRNAs and signaling pathways implicated in the control of the autophagic pathway. The list of such known and predicted regulators could be important in pharmacological attempts against cancer and neurodegenerative diseases.

  4. Resource allocation in academic health centers: creating common metrics.

    Science.gov (United States)

    Joiner, Keith A; Castellanos, Nathan; Wartman, Steven A

    2011-09-01

    Optimizing resource allocation is essential for effective academic health center (AHC) management, yet guidelines and principles for doing so in the research and educational arenas remain limited. To address this issue, the authors analyzed responses to the 2007-2008 Association of Academic Health Centers census using ratio analysis. The concept was to normalize data from an individual institution to that same institution, by creating a ratio of two separate values from the institution (e.g., total faculty FTEs/total FTEs). The ratios were then compared across institutions. Generally, this strategy minimizes the effect of institution size on the responses, size being the predominant limitation of using absolute values for developing meaningful metrics. In so doing, ratio analysis provides a range of responses that can be displayed in graphical form to determine the range and distribution of values. The data can then be readily scrutinized to determine where any given institution falls within the distribution. Staffing ratios and operating ratios from up to 54 institutions are reported. For ratios including faculty numbers in the numerator or denominator, the range of values is wide and minimally discriminatory, reflecting heterogeneity across institutions in faculty definitions. Values for financial ratios, in particular total payroll expense/total operating expense, are more tightly clustered, reflecting in part the use of units with a uniform definition (i.e., dollars), and emphasizing the utility of such ratios in decision guidelines. The authors describe how to apply these insights to develop metrics for resource allocation in the research and educational arenas. PMID:21785307

  5. Resource allocation in academic health centers: creating common metrics.

    Science.gov (United States)

    Joiner, Keith A; Castellanos, Nathan; Wartman, Steven A

    2011-09-01

    Optimizing resource allocation is essential for effective academic health center (AHC) management, yet guidelines and principles for doing so in the research and educational arenas remain limited. To address this issue, the authors analyzed responses to the 2007-2008 Association of Academic Health Centers census using ratio analysis. The concept was to normalize data from an individual institution to that same institution, by creating a ratio of two separate values from the institution (e.g., total faculty FTEs/total FTEs). The ratios were then compared across institutions. Generally, this strategy minimizes the effect of institution size on the responses, size being the predominant limitation of using absolute values for developing meaningful metrics. In so doing, ratio analysis provides a range of responses that can be displayed in graphical form to determine the range and distribution of values. The data can then be readily scrutinized to determine where any given institution falls within the distribution. Staffing ratios and operating ratios from up to 54 institutions are reported. For ratios including faculty numbers in the numerator or denominator, the range of values is wide and minimally discriminatory, reflecting heterogeneity across institutions in faculty definitions. Values for financial ratios, in particular total payroll expense/total operating expense, are more tightly clustered, reflecting in part the use of units with a uniform definition (i.e., dollars), and emphasizing the utility of such ratios in decision guidelines. The authors describe how to apply these insights to develop metrics for resource allocation in the research and educational arenas.

  6. The secondary metabolite bioinformatics portal

    DEFF Research Database (Denmark)

    Weber, Tilmann; Kim, Hyun Uk

    2016-01-01

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

  7. Argonne Laboratory Computing Resource Center - FY2004 Report.

    Energy Technology Data Exchange (ETDEWEB)

    Bair, R.

    2005-04-14

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

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

    Institute of Scientific and Technical Information of China (English)

    Antonio d'Acierno; Angelo Facchiano; Anna Marabotti

    2009-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Nelson Rex T

    2010-06-01

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

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

    Science.gov (United States)

    2010-01-01

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

  11. 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...

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

    Directory of Open Access Journals (Sweden)

    Eliane Gasparino

    2008-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Shankavaram Uma

    2006-04-01

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

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

    Science.gov (United States)

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

    2008-01-01

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

  15. Flow cytometry bioinformatics.

    Directory of Open Access Journals (Sweden)

    Kieran O'Neill

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

  16. An Introduction to Bioinformatics

    Institute of Scientific and Technical Information of China (English)

    SHENG Qi-zheng; De Moor Bart

    2004-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-09-01

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

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

    Data.gov (United States)

    National Aeronautics and Space Administration — The Earth Resources Observation and Science (EROS) Center manages this collection of Landsat 7 scenes created for aesthetic purposes rather than scientific...

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

    Science.gov (United States)

    Manczuk, Suzanne

    1999-01-01

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

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

    Science.gov (United States)

    Berrong, Joseph M.; And Others

    1982-01-01

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

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

    Science.gov (United States)

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

    2016-03-01

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

  3. 15 CFR 291.4 - National industry-specific pollution prevention and environmental compliance resource centers.

    Science.gov (United States)

    2010-01-01

    ... § 291.4 National industry-specific pollution prevention and environmental compliance resource centers... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false National industry-specific pollution prevention and environmental compliance resource centers. 291.4 Section 291.4 Commerce and Foreign...

  4. Deep Learning in Bioinformatics

    OpenAIRE

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2016-01-01

    In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current res...

  5. 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

  6. Natural Resource Program Center FY 2011 Annual Report

    Data.gov (United States)

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

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

    OpenAIRE

    Mihaela Pitea

    2013-01-01

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

  8. Introduction to Bioinformatics

    OpenAIRE

    Thampi, Sabu M.

    2009-01-01

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

  9. Educational Resources Information Center (ERIC) File Partition Study: Final Report.

    Science.gov (United States)

    Hull, Cynthia C.; Wanger, Judith

    A study to provide the National Center for Educational Communication (NCE) with information that could be useful in making the ERIC data base more relevant to the needs of educators and more efficiently usable by them is discussed. Specific purposes of this project were to use an empirical field-survey study as an armature around which to: (1)…

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

    Data.gov (United States)

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

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

    Data.gov (United States)

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

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-11-01

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

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

    Data.gov (United States)

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

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

    Data.gov (United States)

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

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-06-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Ngo, Thi Phuong Le

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-31

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

  19. Chemistry in Bioinformatics

    OpenAIRE

    Mitchell John; Murray-Rust Peter; Rzepa Henry

    2005-01-01

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

  20. Assessment of water resources for nuclear energy centers

    International Nuclear Information System (INIS)

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

  1. Assessment of water resources for nuclear energy centers

    Energy Technology Data Exchange (ETDEWEB)

    Samuels, G.

    1976-09-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  3. National Training Center Fort Irwin expansion area aquatic resources survey

    Energy Technology Data Exchange (ETDEWEB)

    Cushing, C.E.; Mueller, R.P.

    1996-02-01

    Biologists from Pacific Northwest National Laboratory (PNNL) were requested by personnel from Fort Irwin to conduct a biological reconnaissance of the Avawatz Mountains northeast of Fort Irwin, an area for proposed expansion of the Fort. Surveys of vegetation, small mammals, birds, reptiles, amphibians, and aquatic resources were conducted during 1995 to characterize the populations and habitats present with emphasis on determining the presence of any species of special concern. This report presents a description of the sites sampled, a list of the organisms found and identified, and a discussion of relative abundance. Taxonomic identifications were done to the lowest level possible commensurate with determining the status of the taxa relative to its possible listing as a threatened, endangered, or candidate species. Consultation with taxonomic experts was undertaken for the Coleoptera ahd Hemiptera. In addition to listing the macroinvertebrates found, the authors also present a discussion related to the possible presence of any threatened or endangered species or species of concern found in Sheep Creek Springs, Tin Cabin Springs, and the Amargosa River.

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

    Science.gov (United States)

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

    2008-01-01

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

  5. 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. PMID:21036947

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

    CERN Document Server

    Meyer, J; The ATLAS collaboration; Weber, P

    2011-01-01

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

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

    CERN Document Server

    Meyer, J; The ATLAS collaboration; Weber, P

    2010-01-01

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

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

    Science.gov (United States)

    Watkins, A. H.

    1975-01-01

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

  9. 2011 Year in review--Earth Resources Observation and Science Center

    Science.gov (United States)

    Johnson, Rebecca, (compiler)

    2012-01-01

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

  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. Bioinformatics and School Biology

    Science.gov (United States)

    Dalpech, Roger

    2006-01-01

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

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

    Science.gov (United States)

    Zainudin, Fadzliaton; Ismail, Kamarulzaman

    2010-01-01

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

  13. 34 CFR 656.3 - What activities define a comprehensive or undergraduate National Resource Center?

    Science.gov (United States)

    2010-07-01

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

  14. Turning Russian specialized microbial culture collections into resource centers for biotechnology.

    Science.gov (United States)

    Ivshina, Irena B; Kuyukina, Maria S

    2013-11-01

    Specialized nonmedical microbial culture collections contain unique bioresources that could be useful for biotechnology companies. Cooperation between collections and companies has suffered from shortcomings in infrastructure and legislation, hindering access to holdings. These challenges may be overcome by the transformation of collections into national bioresource centers and integration into international microbial resource networks.

  15. Final Technical Report of the Illinois Regional Resource Center. June 1, 1974 Through November 30, 1977.

    Science.gov (United States)

    Berjohn, Harold; Boker-Pfeiffer, Dea

    The final technical report on the Illinois Regional Resource Center (RRC) details project activities (1974 to 1977) concerning the programing and assessment of unexplained or undiagnosed handicaps. Summaries and evaluation information are presented on the following RRC efforts: state program development (including technical assistance activities);…

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

    Science.gov (United States)

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

    2008-01-01

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

  17. An Experimental Learning Resources Center and a New Curriculum in the Social Sciences.

    Science.gov (United States)

    Leeb, David

    At Mercer County Community College (New Jersey) an experimental learning resources center and a new curriculum in the social sciences were developed having primary objectives of: (1) keeping more minority-group students in school, (2) reducing their withdrawal rate, (3) developing assessment techniques accommodating inner-city populations, (4)…

  18. 75 FR 3741 - National Center for Research Resources; Notice of Closed Meetings

    Science.gov (United States)

    2010-01-22

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Center for Research Resources; Notice of Closed...: February 17-18, 2010. Time: 8 a.m. to 5 p.m. Agenda: To provide concept review of proposed...

  19. 75 FR 48365 - Solicitation for a Cooperative Agreement-NIC Cost Containment Online Resource Center Project

    Science.gov (United States)

    2010-08-10

    ... National Institute of Corrections Solicitation for a Cooperative Agreement--NIC Cost Containment Online...: Solicitation for cooperative agreement. SUMMARY: The National Institute of Corrections (NIC) is soliciting.... The NIC Cost Containment Online Resource Center (CCORC) will be housed on the NIC Web site and...

  20. Resources

    Science.gov (United States)

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

  1. In the Spotlight: Bioinformatics

    Science.gov (United States)

    Wang, May Dongmei

    2016-01-01

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

  2. 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.

  3. Feature selection in bioinformatics

    Science.gov (United States)

    Wang, Lipo

    2012-06-01

    In bioinformatics, there are often a large number of input features. For example, there are millions of single nucleotide polymorphisms (SNPs) that are genetic variations which determine the dierence between any two unrelated individuals. In microarrays, thousands of genes can be proled in each test. It is important to nd out which input features (e.g., SNPs or genes) are useful in classication of a certain group of people or diagnosis of a given disease. In this paper, we investigate some powerful feature selection techniques and apply them to problems in bioinformatics. We are able to identify a very small number of input features sucient for tasks at hand and we demonstrate this with some real-world data.

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

    Science.gov (United States)

    David, John; Irizarry, Kristopher J L

    2009-01-01

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

  5. In the Spotlight: Bioinformatics

    OpenAIRE

    Wang, May Dongmei

    2012-01-01

    During 2012, next generation sequencing (NGS) has attracted great attention in the biomedical research community, especially for personalized medicine. Also, third generation sequencing has become available. Therefore, state-of-art sequencing technology and analysis are reviewed in this Bioinformatics spotlight on 2012. Next-generation sequencing (NGS) is high-throughput nucleic acid sequencing technology with wide dynamic range and single base resolution. The full promise of NGS depends on t...

  6. 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.

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

    International Nuclear Information System (INIS)

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

  8. Mental health resources for LGBT collegians: a content analysis of college counseling center Web sites.

    Science.gov (United States)

    Wright, Paul J; McKinley, Christopher J

    2011-01-01

    This study content analyzed a randomly selected stratified national sample of 203 four-year United States colleges' counseling center Web sites to assess the degree to which such sites feature information and reference services for lesbian, gay, bisexual, and transgender (LGBT) collegians. Results revealed that LGBT-targeted communications were infrequent. For instance, fewer than one third of counseling center Web sites described individual counseling opportunities for LGBT students, fewer than 11% mentioned group counseling opportunities, and fewer than 6% offered a university crafted pamphlet with information about LGBT issues and resources. Findings are interpreted within the context of prior LGBT student health research.

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-03-01

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

  10. Western Mineral and Environmental Resources Science Center--providing comprehensive earth science for complex societal issues

    Science.gov (United States)

    Frank, David G.; Wallace, Alan R.; Schneider, Jill L.

    2010-01-01

    Minerals in the environment and products manufactured from mineral materials are all around us and we use and come into contact with them every day. They impact our way of life and the health of all that lives. Minerals are critical to the Nation's economy and knowing where future mineral resources will come from is important for sustaining the Nation's economy and national security. The U.S. Geological Survey (USGS) Mineral Resources Program (MRP) provides scientific information for objective resource assessments and unbiased research results on mineral resource potential, production and consumption statistics, as well as environmental consequences of mining. The MRP conducts this research to provide information needed for land planners and decisionmakers about where mineral commodities are known and suspected in the earth's crust and about the environmental consequences of extracting those commodities. As part of the MRP scientists of the Western Mineral and Environmental Resources Science Center (WMERSC or 'Center' herein) coordinate the development of national, geologic, geochemical, geophysical, and mineral-resource databases and the migration of existing databases to standard models and formats that are available to both internal and external users. The unique expertise developed by Center scientists over many decades in response to mineral-resource-related issues is now in great demand to support applications such as public health research and remediation of environmental hazards that result from mining and mining-related activities. Western Mineral and Environmental Resources Science Center Results of WMERSC research provide timely and unbiased analyses of minerals and inorganic materials to (1) improve stewardship of public lands and resources; (2) support national and international economic and security policies; (3) sustain prosperity and improve our quality of life; and (4) protect and improve public health, safety, and environmental quality. The MRP

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

    International Nuclear Information System (INIS)

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

  12. Evaluation of a fungal collection as certified reference material producer and as a biological resource center.

    Science.gov (United States)

    Forti, Tatiana; Souto, Aline da S S; do Nascimento, Carlos Roberto S; Nishikawa, Marilia M; Hubner, Marise T W; Sabagh, Fernanda P; Temporal, Rosane Maria; Rodrigues, Janaína M; da Silva, Manuela

    2016-01-01

    Considering the absence of standards for culture collections and more specifically for biological resource centers in the world, in addition to the absence of certified biological material in Brazil, this study aimed to evaluate a Fungal Collection from Fiocruz, as a producer of certified reference material and as Biological Resource Center (BRC). For this evaluation, a checklist based on the requirements of ABNT ISO GUIA34:2012 correlated with the ABNT NBR ISO/IEC17025:2005, was designed and applied. Complementing the implementation of the checklist, an internal audit was performed. An evaluation of this Collection as a BRC was also conducted following the requirements of the NIT-DICLA-061, the Brazilian internal standard from Inmetro, based on ABNT NBR ISO/IEC 17025:2005, ABNT ISO GUIA 34:2012 and OECD Best Practice Guidelines for BRCs. This was the first time that the NIT DICLA-061 was applied in a culture collection during an internal audit. The assessments enabled the proposal for the adequacy of this Collection to assure the implementation of the management system for their future accreditation by Inmetro as a certified reference material producer as well as its future accreditation as a Biological Resource Center according to the NIT-DICLA-061. PMID:26991280

  13. Evaluation of a fungal collection as certified reference material producer and as a biological resource center

    Directory of Open Access Journals (Sweden)

    Tatiana Forti

    2016-06-01

    Full Text Available Abstract Considering the absence of standards for culture collections and more specifically for biological resource centers in the world, in addition to the absence of certified biological material in Brazil, this study aimed to evaluate a Fungal Collection from Fiocruz, as a producer of certified reference material and as Biological Resource Center (BRC. For this evaluation, a checklist based on the requirements of ABNT ISO GUIA34:2012 correlated with the ABNT NBR ISO/IEC17025:2005, was designed and applied. Complementing the implementation of the checklist, an internal audit was performed. An evaluation of this Collection as a BRC was also conducted following the requirements of the NIT-DICLA-061, the Brazilian internal standard from Inmetro, based on ABNT NBR ISO/IEC 17025:2005, ABNT ISO GUIA 34:2012 and OECD Best Practice Guidelines for BRCs. This was the first time that the NIT DICLA-061 was applied in a culture collection during an internal audit. The assessments enabled the proposal for the adequacy of this Collection to assure the implementation of the management system for their future accreditation by Inmetro as a certified reference material producer as well as its future accreditation as a Biological Resource Center according to the NIT-DICLA-061.

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

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-07-01

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

  16. Bioinformatic methods in protein characterization

    OpenAIRE

    Kallberg, Yvonne

    2002-01-01

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

  17. Bioinformatics and Computational Core Technology Center

    Data.gov (United States)

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

  18. Pattern recognition in bioinformatics.

    Science.gov (United States)

    de Ridder, Dick; de Ridder, Jeroen; Reinders, Marcel J T

    2013-09-01

    Pattern recognition is concerned with the development of systems that learn to solve a given problem using a set of example instances, each represented by a number of features. These problems include clustering, the grouping of similar instances; classification, the task of assigning a discrete label to a given instance; and dimensionality reduction, combining or selecting features to arrive at a more useful representation. The use of statistical pattern recognition algorithms in bioinformatics is pervasive. Classification and clustering are often applied to high-throughput measurement data arising from microarray, mass spectrometry and next-generation sequencing experiments for selecting markers, predicting phenotype and grouping objects or genes. Less explicitly, classification is at the core of a wide range of tools such as predictors of genes, protein function, functional or genetic interactions, etc., and used extensively in systems biology. A course on pattern recognition (or machine learning) should therefore be at the core of any bioinformatics education program. In this review, we discuss the main elements of a pattern recognition course, based on material developed for courses taught at the BSc, MSc and PhD levels to an audience of bioinformaticians, computer scientists and life scientists. We pay attention to common problems and pitfalls encountered in applications and in interpretation of the results obtained.

  19. Agile parallel bioinformatics workflow management using Pwrake

    Directory of Open Access Journals (Sweden)

    Tanaka Masahiro

    2011-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Débora Sommer

    2008-12-01

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

  1. Human resources management in fitness centers and their relationship with the organizational performance

    Directory of Open Access Journals (Sweden)

    Jerónimo García Fernández

    2014-12-01

    Full Text Available Purpose: Human capital is essential in organizations providing sports services. However, there are few studies that examine what practices are carried out and whether they, affect sports organizations achieve better results are. Therefore the aim of this paper is to analyze the practices of human resource management in private fitness centers and the relationship established with organizational performance.Design/methodology/approach: Questionnaire to 101 managers of private fitness centers in Spain, performing exploratory and confirmatory factor analysis, and linear regressions between the variables.Findings: In organizations of fitness, the findings show that training practices, reward, communication and selection are positively correlated with organizational performance.Research limitations/implications: The fact that you made a convenience sampling in a given country and reduce the extrapolation of the results to the market.Originality/value: First, it represents a contribution to the fact that there are no studies analyzing the management of human resources in sport organizations from the point of view of the top leaders. On the other hand, allows fitness center managers to adopt practices to improve organizational performance.

  2. Bioinformatics analyses for signal transduction networks

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

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

  3. 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…

  4. A qualitative evaluation of school-based family resource and youth service centers.

    Science.gov (United States)

    Kalafat, J; Illback, R J

    1998-08-01

    As part of the Kentucky Education Reform Act, school-based Family Resource/Youth Service Centers were commissioned to address those poverty-related issues that attenuate children and youths' coming to school prepared to learn. The centers had flexible mandates and were to adapt their service profiles to local urban, suburban and rural communities. A variety of grounded, inductive qualitative strategies were employed in an implementation evaluation that yielded profiles or domains of program elements, and descriptions of implementation strategies and impact on participants. These program descriptors were considered accurate by program personnel, formed the basis for training new program coordinators, and have served as reliable predictors of educational outcomes for program participants, thus affirming the utility of the qualitative evaluation approaches. PMID:9772732

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

    Directory of Open Access Journals (Sweden)

    Quan Liang

    2014-07-01

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

  6. Medical Image Resource Center--making electronic teaching files from PACS.

    Science.gov (United States)

    Lim, C C Tchoyoson; Yang, Guo Liang; Nowinski, Wieslaw L; Hui, Francis

    2003-12-01

    A picture archive and communications system (PACS) is a rich source of images and data suitable for creating electronic teaching files (ETF). However, the potential for PACS to support nonclinical applications has not been fully realized: at present there is no mechanism for PACS to identify and store teaching files; neither is there a standardized method for sharing such teaching images. The Medical Image Resource Center (MIRC) is a new central image repository that defines standards for data exchange among different centers. We developed an ETF server that retrieves digital imaging and communication in medicine (DICOM) images from PACS, and enables users to create teaching files that conform to the new MIRC schema. We test-populated our ETF server with illustrative images from the clinical case load of the National Neuroscience Institute, Singapore. Together, PACS and MIRC have the potential to benefit radiology teaching and research.

  7. 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...

  8. Bioinformatics meets parasitology.

    Science.gov (United States)

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

    2012-05-01

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

  9. Engineering BioInformatics

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

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

  10. Virtual bioinformatics distance learning suite*.

    Science.gov (United States)

    Tolvanen, Martti; Vihinen, Mauno

    2004-05-01

    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 over the Internet. Currently, we provide two fully computer-based courses, "Introduction to Bioinformatics" and "Bioinformatics in Functional Genomics." Here we will discuss the application of distance learning in bioinformatics training and our experiences gained during the 3 years that we have run the courses, with about 400 students from a number of universities. The courses are available at bioinf.uta.fi.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Monica Molino

    2016-07-01

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

  14. Science center capabilities to monitor and investigate Michigan’s water resources, 2016

    Science.gov (United States)

    Giesen, Julia A.; Givens, Carrie E.

    2016-09-06

    Michigan faces many challenges related to water resources, including flooding, drought, water-quality degradation and impairment, varying water availability, watershed-management issues, stormwater management, aquatic-ecosystem impairment, and invasive species. Michigan’s water resources include approximately 36,000 miles of streams, over 11,000 inland lakes, 3,000 miles of shoreline along the Great Lakes (MDEQ, 2016), and groundwater aquifers throughout the State.The U.S. Geological Survey (USGS) works in cooperation with local, State, and other Federal agencies, as well as tribes and universities, to provide scientific information used to manage the water resources of Michigan. To effectively assess water resources, the USGS uses standardized methods to operate streamgages, water-quality stations, and groundwater stations. The USGS also monitors water quality in lakes and reservoirs, makes periodic measurements along rivers and streams, and maintains all monitoring data in a national, quality-assured, hydrologic database.The USGS in Michigan investigates the occurrence, distribution, quantity, movement, and chemical and biological quality of surface water and groundwater statewide. Water-resource monitoring and scientific investigations are conducted statewide by USGS hydrologists, hydrologic technicians, biologists, and microbiologists who have expertise in data collection as well as various scientific specialties. A support staff consisting of computer-operations and administrative personnel provides the USGS the functionality to move science forward. Funding for USGS activities in Michigan comes from local and State agencies, other Federal agencies, direct Federal appropriations, and through the USGS Cooperative Matching Funds, which allows the USGS to partially match funding provided by local and State partners.This fact sheet provides an overview of the USGS current (2016) capabilities to monitor and study Michigan’s vast water resources. More

  15. Optimal scheduling of logistical support for medical resources order and shipment in community health service centers

    Directory of Open Access Journals (Sweden)

    Ming Liu

    2015-11-01

    Full Text Available Purpose: This paper aims to propose an optimal scheduling for medical resources order and shipment in community health service centers (CHSCs.Design/methodology/approach: This paper presents two logistical support models for scheduling medical resources in CHSCs. The first model is a deterministic planning model (DM, which systematically considers the demands for various kinds of medical resources, the lead time of supplier, the storage capacity and other constraints, as well as the integrated shipment planning in the dimensions of time and space. The problem is a multi-commodities flow problem and is formulated as a mixed 0-1 integer programming model. Considering the demand for medical resources is always stochastic in practice, the second model is constructed as a stochastic programming model (SM. A solution procedure is developed to solve the proposed two models and a simulation-based evaluation method is proposed to compare the performances of the proposed models. Findings andFindings: The main contributions of this paper includes the following two aspects: (1 While most research on medical resources optimization studies a static problem taking no consideration of the time evolution and especially the dynamic demand for such resources, the proposed models in our paper integrate time-space network technique, which can find the optimal scheduling of logistical support for medical resources order and shipment in CHSCs effectively. (2 The logistics plans in response to the deterministic demand and the time-varying demand are constructed as 0-1 mixed integer programming model and stochastic integer programming model, respectively. The optimal solutions not only minimize the operation cost of the logistics system, but also can improve the order and shipment operation in practice.Originality/value: Currently, medical resources in CHSCs are purchased by telephone or e-mail. The important parameters in decision making, i.e. order/shipment frequency

  16. Human Resources Center: An Innovation in Education; General Job Functions (Unofficial); General Plan for Curriculum Organization; Early Childhood Education.

    Science.gov (United States)

    Pontiac City School District, MI.

    The Human Resources Center in Pontiac, Michigan is an educational institution designed to help develop talents and human potential from early childhood through adulthood. The Center offers a new approach to the problems of urban communities through comprehensive planning; education is made to serve a broader role than it has in the past.…

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

    Science.gov (United States)

    Lowe, Karen

    2003-01-01

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

  18. The Contribution of Background Variables, Internal and External Resources to Life Satisfaction among Adolescents in Residential Treatment Centers

    Science.gov (United States)

    Lipschitz-Elhawi, Racheli; Itzhaky, Haya; Michal, Hefetz

    2008-01-01

    The article deals with the contribution of background variables (gender, years of residence in a treatment center, and family status), internal resource (self-esteem), and external resources (peer, family and significant other support, sense of belonging to the community) to life satisfaction among adolescents living in residential treatment…

  19. Translational bioinformatics in psychoneuroimmunology: methods and applications.

    Science.gov (United States)

    Yan, Qing

    2012-01-01

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

  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. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! PMID:27471065

  2. ASD: a bioinformatics resource on alternative splicing

    OpenAIRE

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

    2005-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Bair, R. B. (CLS-CI)

    2011-05-13

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

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

    Science.gov (United States)

    Ahmed, Abdalla

    2016-01-01

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

  5. Analysis of metagenomics next generation sequence data for fungal ITS barcoding: Do you need advance bioinformatics experience?

    Directory of Open Access Journals (Sweden)

    Abdalla Osman Abdalla Ahmed

    2016-07-01

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

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

    Science.gov (United States)

    Ahmed, Abdalla

    2016-01-01

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

  7. Application Of Data Mining In Bioinformatics

    OpenAIRE

    KHALID RAZA

    2012-01-01

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

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

    Science.gov (United States)

    Tatusova, Tatiana

    2016-01-01

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

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

    Science.gov (United States)

    Tatusova, Tatiana

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  11. Clustering Techniques in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Muhammad Ali Masood

    2015-01-01

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

  12. 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…

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

    Science.gov (United States)

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

    2015-12-01

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

  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. An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

    Science.gov (United States)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-05-31

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-06-30

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

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

    Science.gov (United States)

    Logan, W. S.

    2015-12-01

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

  19. Generations of interdisciplinarity in bioinformatics

    Science.gov (United States)

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

    2016-01-01

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

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

    International Nuclear Information System (INIS)

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

  1. Training Experimental Biologists in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Pedro Fernandes

    2012-01-01

    Full Text Available Bioinformatics, for its very nature, is devoted to a set of targets that constantly evolve. Training is probably the best response to the constant need for the acquisition of bioinformatics skills. It is interesting to assess the effects of training in the different sets of researchers that make use of it. While training bench experimentalists in the life sciences, we have observed instances of changes in their attitudes in research that, if well exploited, can have beneficial impacts in the dialogue with professional bioinformaticians and influence the conduction of the research itself.

  2. Drug targets for lymphatic filariasis: A bioinformatics approach

    Directory of Open Access Journals (Sweden)

    Om Prakash Sharma

    2013-08-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

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

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

    Science.gov (United States)

    Meyer, Nadean

    2011-01-01

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

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  6. Bioinformatics interoperability: all together now !

    NARCIS (Netherlands)

    Meganck, B.; Mergen, P.; Meirte, D.

    2009-01-01

    The following text presents some personal ideas about the way (bio)informatics2 is heading, along with some examples of how our institution – the Royal Museum for Central Africa (RMCA) – is gearing up for these new times ahead. It tries to find the important trends amongst the buzzwords, and to demo

  7. Visualising "Junk" DNA through Bioinformatics

    Science.gov (United States)

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

    2005-01-01

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

  8. 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...

  9. 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…

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

    Directory of Open Access Journals (Sweden)

    Alameddine Mohamad

    2012-11-01

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Bishop, John B.

    2010-01-01

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

  14. Application of bioinformatics in tropical medicine

    Institute of Scientific and Technical Information of China (English)

    Wiwanitkit V

    2008-01-01

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

  15. The NIH-NIAID Schistosomiasis Resource Center at the Biomedical Research Institute: Molecular Redux

    Science.gov (United States)

    Cody, James J.; Ittiprasert, Wannaporn; Miller, André N.; Henein, Lucie; Mentink-Kane, Margaret M.; Hsieh, Michael H.

    2016-01-01

    Schistosomiasis remains a health burden in many parts of the world. The complex life cycle of Schistosoma parasites and the economic and societal conditions present in endemic areas make the prospect of eradication unlikely in the foreseeable future. Continued and vigorous research efforts must therefore be directed at this disease, particularly since only a single World Health Organization (WHO)-approved drug is available for treatment. The National Institutes of Health (NIH)–National Institute of Allergy and Infectious Diseases (NIAID) Schistosomiasis Resource Center (SRC) at the Biomedical Research Institute provides investigators with the critical raw materials needed to carry out this important research. The SRC makes available, free of charge (including international shipping costs), not only infected host organisms but also a wide array of molecular reagents derived from all life stages of each of the three main human schistosome parasites. As the field of schistosomiasis research rapidly advances, it is likely to become increasingly reliant on omics, transgenics, epigenetics, and microbiome-related research approaches. The SRC has and will continue to monitor and contribute to advances in the field in order to support these research efforts with an expanding array of molecular reagents. In addition to providing investigators with source materials, the SRC has expanded its educational mission by offering a molecular techniques training course and has recently organized an international schistosomiasis-focused meeting. This review provides an overview of the materials and services that are available at the SRC for schistosomiasis researchers, with a focus on updates that have occurred since the original overview in 2008. PMID:27764112

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

    Science.gov (United States)

    Goodyear, Leslie

    2012-01-01

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

  17. 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.

  18. An introduction to proteome bioinformatics.

    Science.gov (United States)

    Jones, Andrew R; Hubbard, Simon J

    2010-01-01

    This book is part of the Methods in Molecular Biology series, and provides a general overview of computational approaches used in proteome research. In this chapter, we give an overview of the scope of the book in terms of current proteomics experimental techniques and the reasons why computational approaches are needed. We then give a summary of each chapter, which together provide a picture of the state of the art in proteome bioinformatics research.

  19. 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.

  20. 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.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  3. David Grant Medical Center energy use baseline and integrated resource assessment

    Energy Technology Data Exchange (ETDEWEB)

    Richman, E.E.; Hoshide, R.K.; Dittmer, A.L.

    1993-04-01

    The US Air Mobility Command (AMC) has tasked Pacific Northwest Laboratory (PNL) with supporting the US Department of Energy (DOE) Federal Energy Management Program's (FEMP) mission to identify, evaluate, and assist in acquiring all cost-effective energy resource opportunities (EROs) at the David Grant Medical Center (DGMC). This report describes the methodology used to identify and evaluate the EROs at DGMC, provides a life-cycle cost (LCC) analysis for each ERO, and prioritizes any life-cycle cost-effective EROs based on their net present value (NPV), value index (VI), and savings to investment ratio (SIR or ROI). Analysis results are presented for 17 EROs that involve energy use in the areas of lighting, fan and pump motors, boiler operation, infiltration, electric load peak reduction and cogeneration, electric rate structures, and natural gas supply. Typical current energy consumption is approximately 22,900 MWh of electricity (78,300 MBtu), 87,600 kcf of natural gas (90,300 MBtu), and 8,300 gal of fuel oil (1,200 MBtu). A summary of the savings potential by energy-use category of all independent cost-effective EROs is shown in a table. This table includes the first cost, yearly energy consumption savings, and NPV for each energy-use category. The net dollar savings and NPV values as derived by the life-cycle cost analysis are based on the 1992 federal discount rate of 4.6%. The implementation of all EROs could result in a yearly electricity savings of more than 6,000 MWh or 26% of current yearly electricity consumption. More than 15 MW of billable load (total billed by the utility for a 12-month period) or more than 34% of current billed demand could also be saved. Corresponding natural gas savings would be 1,050 kcf (just over 1% of current consumption). Total yearly net energy cost savings for all options would be greater than $343,340. This value does not include any operations and maintenance (O M) savings.

  4. David Grant Medical Center energy use baseline and integrated resource assessment

    Energy Technology Data Exchange (ETDEWEB)

    Richman, E.E.; Hoshide, R.K.; Dittmer, A.L.

    1993-04-01

    The US Air Mobility Command (AMC) has tasked Pacific Northwest Laboratory (PNL) with supporting the US Department of Energy (DOE) Federal Energy Management Program`s (FEMP) mission to identify, evaluate, and assist in acquiring all cost-effective energy resource opportunities (EROs) at the David Grant Medical Center (DGMC). This report describes the methodology used to identify and evaluate the EROs at DGMC, provides a life-cycle cost (LCC) analysis for each ERO, and prioritizes any life-cycle cost-effective EROs based on their net present value (NPV), value index (VI), and savings to investment ratio (SIR or ROI). Analysis results are presented for 17 EROs that involve energy use in the areas of lighting, fan and pump motors, boiler operation, infiltration, electric load peak reduction and cogeneration, electric rate structures, and natural gas supply. Typical current energy consumption is approximately 22,900 MWh of electricity (78,300 MBtu), 87,600 kcf of natural gas (90,300 MBtu), and 8,300 gal of fuel oil (1,200 MBtu). A summary of the savings potential by energy-use category of all independent cost-effective EROs is shown in a table. This table includes the first cost, yearly energy consumption savings, and NPV for each energy-use category. The net dollar savings and NPV values as derived by the life-cycle cost analysis are based on the 1992 federal discount rate of 4.6%. The implementation of all EROs could result in a yearly electricity savings of more than 6,000 MWh or 26% of current yearly electricity consumption. More than 15 MW of billable load (total billed by the utility for a 12-month period) or more than 34% of current billed demand could also be saved. Corresponding natural gas savings would be 1,050 kcf (just over 1% of current consumption). Total yearly net energy cost savings for all options would be greater than $343,340. This value does not include any operations and maintenance (O&M) savings.

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

    Directory of Open Access Journals (Sweden)

    Katayama Toshiaki

    2010-08-01

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

  6. 75 FR 79072 - Notice of Funding Availability for the Small Business Transportation Resource Center Program

    Science.gov (United States)

    2010-12-17

    ... as Disadvantaged Business Enterprises (DBE) and the development of programs to encourage, stimulate.... Department of Commerce's Minority Business Development Centers (MBDCs), Small Business Development Centers... proof of tax-exempt status; (B) Have at least one year of documented and continuous experience prior...

  7. Impact of Information Technology, Clinical Resource Constraints, and Patient-Centered Practice Characteristics on Quality of Care

    Directory of Open Access Journals (Sweden)

    JongDeuk Baek

    2015-02-01

    Full Text Available Objective: Factors in the practice environment, such as health information technology (IT infrastructure, availability of other clinical resources, and financial incentives, may influence whether practices are able to successfully implement the patient-centered medical home (PCMH model and realize its benefits. This study investigates the impacts of those PCMH-related elements on primary care physicians’ perception of quality of care. Methods: A multiple logistic regression model was estimated using the 2004 to 2005 CTS Physician Survey, a national sample of salaried primary care physicians (n = 1733. Results: The patient-centered practice environment and availability of clinical resources increased physicians’ perceived quality of care. Although IT use for clinical information access did enhance physicians’ ability to provide high quality of care, a similar positive impact of IT use was not found for e-prescribing or the exchange of clinical patient information. Lack of resources was negatively associated with physician perception of quality of care. Conclusion: Since health IT is an important foundation of PCMH, patient-centered practices are more likely to have health IT in place to support care delivery. However, despite its potential to enhance delivery of primary care, simply making health IT available does not necessarily translate into physicians’ perceptions that it enhances the quality of care they provide. It is critical for health-care managers and policy makers to ensure that primary care physicians fully recognize and embrace the use of new technology to improve both the quality of care provided and the patient outcomes.

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

    CERN Document Server

    Buyya, Rajkumar; Abawajy, Jemal

    2010-01-01

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

  9. Developing expertise in bioinformatics for biomedical research in Africa

    OpenAIRE

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

    2015-01-01

    Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases) that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are help...

  10. Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

    Science.gov (United States)

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

    2016-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Baseler Michael W

    2007-11-01

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

  12. Bioinformatic science and devices for computer analysis and visualization of macromolecules

    Directory of Open Access Journals (Sweden)

    Yu.B. Porozov

    2010-06-01

    Full Text Available The goals and objectives of bioinformatic science are presented in the article. The main methods and approaches used in computer biology are highlighted. Areas in which bioinformatic science can greatly facilitate and speed up the work of practical biologist and pharmacologist are revealed. The features of both the basic packages and software devices for complete, thorough analysis of macromolecules and for development and modeling of ligands and binding centers are described

  13. 75 FR 5296 - Office of Postsecondary Education; Overview Information; National Resource Centers (NRC) Program...

    Science.gov (United States)

    2010-02-02

    ... Science, Communication, Journalism and Schools of Education in order to strengthen international... Science, Communication, Journalism, or Education. Program Authority: 20 U.S.C. 1122. Applicable... into the International Resource Information System (IRIS) online data and reporting system....

  14. St. Edward Mercy Medical Center, Fort Smith, AR. Human resource planning identifies institutional need, available personnel.

    Science.gov (United States)

    Keith, J M

    1981-04-01

    Human resource planning, which allows health care facilities to identify future staffing needs and to project staffing availability, will increase as institutions seek to balance quality, costs, employees' needs.

  15. A User-Centered Design Approach to Develop a Web-Based Instructional Resource System for Homeland Education

    Directory of Open Access Journals (Sweden)

    Chaoyun Liang

    2009-03-01

    Full Text Available Under the national educational policy of Nine-Year Integrated Curriculum, elementary and junior high school teachers are expected to design their own instructional materials, and to teach their courses which could be linked to students’ daily lives. The policy also allocates funding to create a variety of web-based instructional resource systems in order to assist these teachers in preparing their classes. Upon the basis of a user-centered design approach, this study is aimed at constructing a set of suggestions of planning, designing, and developing a web-based instructional resource system for the homeland education. This research team takes Nei-Li area in Taiwan as an example to develop such a system, and constructs a user-centered design model. The study results indicate that, unlike the traditional instructional design approach, the proposed model takes into account the user’s needs, the capability of the project team, the resource availability for implementation, the national educational reform policy, the development of information technology industry, and the socio-cultural context of a community at the initial phase. In addition, the development process is divided into two courses, one for contents design while the other for system construction, both of which are implemented at the same time.

  16. 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.

  17. Tribal Business Information Centers: A Wealth of New Resources for Indian Communities.

    Science.gov (United States)

    Wakshul, Barbra

    1996-01-01

    Quanah Crossland Stamps, assistant administrator of the Small Business Administration, describes a pilot program establishing 17 reservation-based Tribal Business Information Centers (TBICs) in North Dakota, South Dakota, Montana, Wyoming, and the Navajo Nation. Managed by tribal colleges, TBICs offer business workshops, access to computer…

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

    Directory of Open Access Journals (Sweden)

    Hüser Andrea T

    2007-11-01

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

  19. Center for fetal monkey gene transfer for heart, lung, and blood diseases: an NHLBI resource for the gene therapy community.

    Science.gov (United States)

    Tarantal, Alice F; Skarlatos, Sonia I

    2012-11-01

    The goals of the National Heart, Lung, and Blood Institute (NHLBI) Center for Fetal Monkey Gene Transfer for Heart, Lung, and Blood Diseases are to conduct gene transfer studies in monkeys to evaluate safety and efficiency; and to provide NHLBI-supported investigators with expertise, resources, and services to actively pursue gene transfer approaches in monkeys in their research programs. NHLBI-supported projects span investigators throughout the United States and have addressed novel approaches to gene delivery; "proof-of-principle"; assessed whether findings in small-animal models could be demonstrated in a primate species; or were conducted to enable new grant or IND submissions. The Center for Fetal Monkey Gene Transfer for Heart, Lung, and Blood Diseases successfully aids the gene therapy community in addressing regulatory barriers, and serves as an effective vehicle for advancing the field.

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-09-01

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

  1. 78 FR 41817 - Notice of Funding Availability for the Small Business Transportation Resource Center Program

    Science.gov (United States)

    2013-07-11

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

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

    Science.gov (United States)

    Milligan, Colleen K.

    2006-01-01

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

  3. Virus variation resources at the National Center for Biotechnology Information: dengue virus

    Directory of Open Access Journals (Sweden)

    Rozanov Michael

    2009-04-01

    Full Text Available Abstract Background There is an increasing number of complete and incomplete virus genome sequences available in public databases. This large body of sequence data harbors information about epidemiology, phylogeny, and virulence. Several specialized databases, such as the NCBI Influenza Virus Resource or the Los Alamos HIV database, offer sophisticated query interfaces along with integrated exploratory data analysis tools for individual virus species to facilitate extracting this information. Thus far, there has not been a comprehensive database for dengue virus, a significant public health threat. Results We have created an integrated web resource for dengue virus. The technology developed for the NCBI Influenza Virus Resource has been extended to process non-segmented dengue virus genomes. In order to allow efficient processing of the dengue genome, which is large in comparison with individual influenza segments, we developed an offline pre-alignment procedure which generates a multiple sequence alignment of all dengue sequences. The pre-calculated alignment is then used to rapidly create alignments of sequence subsets in response to user queries. This improvement in technology will also facilitate the incorporation of additional virus species in the future. The set of virus-specific databases at NCBI, which will be referred to as Virus Variation Resources (VVR, allow users to build complex queries against virus-specific databases and then apply exploratory data analysis tools to the results. The metadata is automatically collected where possible, and extended with data extracted from the literature. Conclusion The NCBI Dengue Virus Resource integrates dengue sequence information with relevant metadata (sample collection time and location, disease severity, serotype, sequenced genome region and facilitates retrieval and preliminary analysis of dengue sequences using integrated web analysis and visualization tools.

  4. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Directory of Open Access Journals (Sweden)

    Michael Römer

    Full Text Available Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  5. 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/.

  6. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Science.gov (United States)

    Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

    2016-01-01

    Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/. PMID:26882475

  7. Best practices in bioinformatics training for life scientists.

    Science.gov (United States)

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

    2013-09-01

    The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists. PMID:23803301

  8. Best practices in bioinformatics training for life scientists.

    Science.gov (United States)

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

    2013-09-01

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

  9. 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.

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

    Science.gov (United States)

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

    2006-01-01

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

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

    Science.gov (United States)

    Naimiy, Hamid M. K. Al

    2015-08-01

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

  12. Bioinformatics and Microarray Data Analysis on the Cloud.

    Science.gov (United States)

    Calabrese, Barbara; Cannataro, Mario

    2016-01-01

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

  13. [Laboral health in Penitentiary Center of Chile: a look from policies of human resources].

    Science.gov (United States)

    Güilgüiruca R, M; Herrera-Bascur, J

    2015-01-01

    This article examines the influence of human resources policies on occupational health variables, such as engagement and job satisfaction, with regard to Chilean prison employees. 80 workers at the Women's Prison of Iquique were evaluated and results show that 77% and 88 % have a moderate to high score in terms of engagement and job satisfaction respectively. The 24% variation in engagement of the workers studied can be explained by policies aimed at promoting personal interests, while 32% of the variation in job satisfaction could be explained by policies of self-efficacy and personal interests. The above data permits the assertion to be made that human resources policies have a role that is relevant and necessary to modify and improve the occupational health conditions of these public sector workers.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-15

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

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

    OpenAIRE

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

    2012-01-01

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

  16. 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…

  17. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

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

  18. 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…

  19. 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.

  20. Rapid Development of Bioinformatics Education in China

    Science.gov (United States)

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

    2003-01-01

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

  1. 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.

  2. 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.

  3. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-04-01

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

  5. Resource Management in Internet-Oriented Data Centers%面向Internet数据中心的资源管理

    Institute of Scientific and Technical Information of China (English)

    张伟; 宋莹; 阮利; 祝明发; 肖利民

    2012-01-01

    Internet data centers are developing towards a diversified, intelligent, automated, large-scaled, and standardized direction. With the increasing of scale and complexity, it brings great challenges in how to effectively manage resources. Currently, resource management has become a major issue in Internet data centers, and its importance and urgency cannot be ignored. This paper analyzes two major challenges of resource management with which the Internet data center is facing: (1) meeting the compatibility of concurrent and multiple application SLAs (service level agreements); (2) improving the energy efficiency of system service. Based on the challenges, this paper thoroughly analyzes and summarizes the related work of resource management guaranteeing the SLA, reducing power, and incorporating the objectives of guaranteeing the SLA and reducing power simultaneously during the last ten years. Finally, the paper summaraizes the research and points out future research directions.%Internet数据中心向多元化、智能化、自动化、规模化与标准化道路发展,其规模越来越大、越来越复杂,这为如何有效管理资源带来极大的冲击与挑战.当前,资源管理已成为Internet数据中心亟待解决的重要问题,其重要性与紧迫性已不容忽视.分析了Internet数据中心资源管理面临的两大挑战:(1)满足并发多应用SLAs(servicelevel agreements)的兼容性;(2)提高系统服务的能量有效性.以挑战为主线,对近十几年来国内外在满足SLA、降低功耗、同时满足SLA和降低功耗方面所取得的资源管理研究成果进行了全面的概括总结和分析,最后进行总结并对未来的研究发展趋势提出观点.

  6. [Post-translational modification (PTM) bioinformatics in China: progresses and perspectives].

    Science.gov (United States)

    Zexian, Liu; Yudong, Cai; Xuejiang, Guo; Ao, Li; Tingting, Li; Jianding, Qiu; Jian, Ren; Shaoping, Shi; Jiangning, Song; Minghui, Wang; Lu, Xie; Yu, Xue; Ziding, Zhang; Xingming, Zhao

    2015-07-01

    Post-translational modifications (PTMs) are essential for regulating conformational changes, activities and functions of proteins, and are involved in almost all cellular pathways and processes. Identification of protein PTMs is the basis for understanding cellular and molecular mechanisms. In contrast with labor-intensive and time-consuming experiments, the PTM prediction using various bioinformatics approaches can provide accurate, convenient, and efficient strategies and generate valuable information for further experimental consideration. In this review, we summarize the current progresses made by Chineses bioinformaticians in the field of PTM Bioinformatics, including the design and improvement of computational algorithms for predicting PTM substrates and sites, design and maintenance of online and offline tools, establishment of PTM-related databases and resources, and bioinformatics analysis of PTM proteomics data. Through comparing similar studies in China and other countries, we demonstrate both advantages and limitations of current PTM bioinformatics as well as perspectives for future studies in China.

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

    Directory of Open Access Journals (Sweden)

    E. Erdogan

    2008-01-01

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

  8. Website for avian flu information and bioinformatics

    Institute of Scientific and Technical Information of China (English)

    GAO; George; Fu

    2009-01-01

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

  9. Website for avian flu information and bioinformatics

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-22

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

  12. 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.

  13. Fort Collins Science Center Ecosystem Dynamics branch--interdisciplinary research for addressing complex natural resource issues across landscapes and time

    Science.gov (United States)

    Bowen, Zachary H.; Melcher, Cynthia P.; Wilson, Juliette T.

    2013-01-01

    The Ecosystem Dynamics Branch of the Fort Collins Science Center offers an interdisciplinary team of talented and creative scientists with expertise in biology, botany, ecology, geology, biogeochemistry, physical sciences, geographic information systems, and remote-sensing, for tackling complex questions about natural resources. As demand for natural resources increases, the issues facing natural resource managers, planners, policy makers, industry, and private landowners are increasing in spatial and temporal scope, often involving entire regions, multiple jurisdictions, and long timeframes. Needs for addressing these issues include (1) a better understanding of biotic and abiotic ecosystem components and their complex interactions; (2) the ability to easily monitor, assess, and visualize the spatially complex movements of animals, plants, water, and elements across highly variable landscapes; and (3) the techniques for accurately predicting both immediate and long-term responses of system components to natural and human-caused change. The overall objectives of our research are to provide the knowledge, tools, and techniques needed by the U.S. Department of the Interior, state agencies, and other stakeholders in their endeavors to meet the demand for natural resources while conserving biodiversity and ecosystem services. Ecosystem Dynamics scientists use field and laboratory research, data assimilation, and ecological modeling to understand ecosystem patterns, trends, and mechanistic processes. This information is used to predict the outcomes of changes imposed on species, habitats, landscapes, and climate across spatiotemporal scales. The products we develop include conceptual models to illustrate system structure and processes; regional baseline and integrated assessments; predictive spatial and mathematical models; literature syntheses; and frameworks or protocols for improved ecosystem monitoring, adaptive management, and program evaluation. The descriptions

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-22

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

  15. Experiences with workflows for automating data-intensive bioinformatics.

    Science.gov (United States)

    Spjuth, Ola; Bongcam-Rudloff, Erik; Hernández, Guillermo Carrasco; Forer, Lukas; Giovacchini, Mario; Guimera, Roman Valls; Kallio, Aleksi; Korpelainen, Eija; Kańduła, Maciej M; Krachunov, Milko; Kreil, David P; Kulev, Ognyan; Łabaj, Paweł P; Lampa, Samuel; Pireddu, Luca; Schönherr, Sebastian; Siretskiy, Alexey; Vassilev, Dimitar

    2015-01-01

    High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out data management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However, workflow systems can incur significant development and administration overhead so bioinformatics pipelines are often still built without them. We present the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead. The organizations are working on similar problems, but we have addressed them with different strategies and solutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution. PMID:26282399

  16. 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.

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

    Science.gov (United States)

    Broussard, Brenda S; Broussard, Anne B

    2010-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Maarten van Zonneveld

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

    Thompson, H. Wendell, Sr.

    2005-01-01

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

  2. The research subject advocate at minority Clinical Research Centers: an added resource for protection of human subjects.

    Science.gov (United States)

    Easa, David; Norris, Keith; Hammatt, Zoë; Kim, Kari; Hernandez, Esther; Kato, Kambrie; Balaraman, Venkataraman; Ho, Tammy; Shomaker, Samuel

    2005-01-01

    In early 2001, the National Institutes of Health (NIH) created the research subject advocate (RSA) position as an additional resource for human subjects protection at NIH-funded Clinical Research Centers (CRCs) to enhance the protection of human participants in clinical research studies. We describe the RSA position in the context of clinical research, with a particular emphasis on the role of the RSA in two of the five CRCs funded by the NIH Research Centers in Minority Institutions (RCMI) program. Through participation in protocol development, informed consent procedures, study implementation and follow-up with adverse events, the RSA works closely with research investigators and their staff to protect study participants. The RSA also conducts workshops, training and education sessions, and consultation with investigators to foster enhanced communication and adherence to ethical standards and safety regulations. Although we cannot yet provide substantive evidence of positive outcomes, this article illuminates the value of the RSA position in ensuring that safety of research participants is accorded the highest priority at CRCs. On the basis of initial results, we conclude that the RSA is an effective mechanism for achieving the NIH goal of maintaining the utmost scrutiny of protocols involving human subjects.

  3. Fish bone foreign body presenting with an acute fulminating retropharyngeal abscess in a resource-challenged center: a case report

    Directory of Open Access Journals (Sweden)

    Oyewole Ezekiel O

    2011-04-01

    Full Text Available Abstract Introduction A retropharyngeal abscess is a potentially life-threatening infection in the deep space of the neck, which can compromise the airway. Its management requires highly specialized care, including surgery and intensive care, to reduce mortality. This is the first case of a gas-forming abscess reported from this region, but not the first such report in the literature. Case presentation We present a case of a 16-month-old Yoruba baby girl with a gas-forming retropharyngeal abscess secondary to fish bone foreign body with laryngeal spasm that was managed in the recovery room. We highlight specific problems encountered in the management of this case in a resource-challenged center such as ours. Conclusion We describe an unusual presentation of a gas-forming organism causing a retropharyngeal abscess in a child. The patient's condition was treated despite the challenges of inadequate resources for its management. We recommend early recognition through adequate evaluation of any oropharyngeal injuries or infection and early referral to the specialist with prompt surgical intervention.

  4. Integrative Bioinformatics for Genomics and Proteomics

    OpenAIRE

    Wu, C.H.

    2011-01-01

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

  5. 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....

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

    OpenAIRE

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

    2009-01-01

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

  7. Coronavirus Genomics and Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Kwok-Yung Yuen

    2010-08-01

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

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

    Science.gov (United States)

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

    2016-04-01

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

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

    Institute of Scientific and Technical Information of China (English)

    岳秉飞

    2003-01-01

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

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

    CERN Multimedia

    2003-01-01

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

  11. Resources.

    Science.gov (United States)

    Stewart, John; MacDonald, Ian

    1980-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Sukman T. Putra

    2015-12-01

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

  13. Models@Home: distributed computing in bioinformatics using a screensaver based approach.

    NARCIS (Netherlands)

    Krieger, E.; Vriend, G.

    2002-01-01

    MOTIVATION: Due to the steadily growing computational demands in bioinformatics and related scientific disciplines, one is forced to make optimal use of the available resources. A straightforward solution is to build a network of idle computers and let each of them work on a small piece of a scienti

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

    Science.gov (United States)

    Cianfrani, C. M.

    2009-12-01

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

  15. Human Resource Center Directory.

    Science.gov (United States)

    Southwestern Cooperative Educational Lab., Albuquerque, NM.

    A reference bank of persons with expertise in educational, socioeconomic, and cultural matters as they relate to non-English speaking Spanish-surnamed adults has been compiled. Approximately 700 persons residing in 33 states, Washington, D.C., Puerto Rico, the Virgin Islands, and Italy are listed. A brief resume of each person listed includes…

  16. 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.

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

    Science.gov (United States)

    Yan, Qing

    2010-01-01

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

  18. 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.

  19. Revitalizing an Urban Community College Women's Resource Center: Kingsborough Community College--The City University of New York.

    Science.gov (United States)

    Miller, Estelle

    This article describes the creation, administration, and services of an urban community college women's center. Information is provided on the center's advisory board charged with broadening the base of support, advising on policy formation, long-term planning, and program development. Strategies utilized to promote the center (e.g., publications,…

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

    Science.gov (United States)

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

    2014-12-01

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

  1. Evolution of web services in bioinformatics

    NARCIS (Netherlands)

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

    2005-01-01

    Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to be complex and in order to understand them, it is often necessary to link many data sets and use more than one tool. Therefore, bioinformatic

  2. A bioinformatics approach to marker development

    NARCIS (Netherlands)

    Tang, J.

    2008-01-01

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

  3. "Extreme Programming" in a Bioinformatics Class

    Science.gov (United States)

    Kelley, Scott; Alger, Christianna; Deutschman, Douglas

    2009-01-01

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

  4. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    NARCIS (Netherlands)

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of pr

  5. 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. PMID:26473029

  6. 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:…

  7. 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…

  8. 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…

  9. 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...

  10. Bioinformatic analysis of the nucleolus

    DEFF Research Database (Denmark)

    Leung, Anthony K L; Andersen, Jens S; Mann, Matthias;

    2003-01-01

    The nucleolus is a plurifunctional, nuclear organelle, which is responsible for ribosome biogenesis and many other functions in eukaryotes, including RNA processing, viral replication and tumour suppression. Our knowledge of the human nucleolar proteome has been expanded dramatically by the two...... novel or uncharacterized proteins. This review focuses on how to apply the derived knowledge of this newly recognized nucleolar proteome, such as their amino acid/peptide composition and their homologies across species, to explore the function and dynamics of the nucleolus, and suggests ways to identify......, in silico, possible functions of the novel/uncharacterized proteins and potential interaction networks within the human nucleolus, or between the nucleolus and other nuclear organelles, by drawing resources from the public domain....

  11. MAPI: towards the integrated exploitation of bioinformatics Web Services

    Directory of Open Access Journals (Sweden)

    Karlsson Johan

    2011-10-01

    Full Text Available Abstract Background Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. Results To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. Conclusions The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others.

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

  13. 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

  14. Explain bioinformatics to your grandmother!

    Directory of Open Access Journals (Sweden)

    Virginie Bernard

    2013-10-01

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

  15. 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…

  16. A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway

    Directory of Open Access Journals (Sweden)

    Mitali Bhattacharjee

    2012-01-01

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

  17. REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa M R; Verbitskiy, Daniil; Brennicke, Axel; Quagliariello, Carla

    2011-03-01

    RNA editing is a post-transcriptional molecular process whereby the information in a genetic message is modified from that in the corresponding DNA template by means of nucleotide substitutions, insertions and/or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. RNA editing events have been annotated in primary databases as GenBank and at more sophisticated level in the specialized databases REDIdb, dbRES and EdRNA. At present, REDIdb is the only freely available database that focuses on the organellar RNA editing process and annotates each editing modification in its biological context. Here we present an updated and upgraded release of REDIdb with a web-interface refurbished with graphical and computational facilities that improve RNA editing investigations. Details of the REDIdb features and novelties are illustrated and compared to other RNA editing databases. REDIdb is freely queried at http://biologia.unical.it/py_script/REDIdb/.

  18. BIOINFORMATIC RESOURCES FOR SOYBEAN GENETIC AND GENOMIC RESEARCH

    Science.gov (United States)

    In the last 10 years, soybean researchers have produced huge amounts of sequence-based data. The molecular genetic map has expanded to include over 2,000 RFLP, RAPD, SSR and SNP markers. Over a thousand QTL have been mapped representing ~90 agronomically important traits. Over 350,000 Expressed S...

  19. Technical Perspectives on Knowledge Management in Bioinformatics Workflow Systems

    Directory of Open Access Journals (Sweden)

    Walaa N. Ismail

    2015-01-01

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

  20. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal

    2012-07-28

    Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we introduce our Adaptive Hybrid Multiprocessor technique to accelerate the implementation of the Smith-Waterman algorithm. Our technique utilizes both the graphics processing unit (GPU) and the central processing unit (CPU). It adapts to the implementation according to the number of CPUs given as input by efficiently distributing the workload between the processing units. Using existing resources (GPU and CPU) in an efficient way is a novel approach. The peak performance achieved for the platforms GPU + CPU, GPU + 2CPUs, and GPU + 3CPUs is 10.4 GCUPS, 13.7 GCUPS, and 18.6 GCUPS, respectively (with the query length of 511 amino acid). © 2010 IEEE.

  1. ASSESSMENT OF REQUIREMENT OF THE POPULATION IN THE ORGAN TRANSPLANTATION, THE DONOR RESOURCE AND PLANNING OF THE EFFECTIVE NETWORK OF THE MEDICAL ORGANIZATIONS (THE CENTERS OF TRANSPLANTATION

    Directory of Open Access Journals (Sweden)

    S. V. Gautier

    2013-01-01

    Full Text Available Aim. To estimate the requirement of the population of the Russian Federation for an organ transplantation and donor resource, to offer approach to planning of an effective network of the medical organizations (the centers of transplantation. Materials and methods. The analysis and comparison of statistical data on population, number of the patients receiving a dialysis, data about medical care on an organ transplantation in Russia and foreign countries is made. Results. On the basis of what the assessment of requirement of the population of the Russian Federation in an organ transplantation and donor resource is carried out, approach to planning of an effective network of the medical organizations (the centers of transplantation and scenarios of development of organ do- nation and transplantation in Russia is offered. Conclusion. To provide the population of the Russian Federation with medical care on an organ transplantation according to real requirement and donor resource, in each region of the Russian Federation have to be organized deceased organ donation and transplantation of a cadaveric kidney. But the transplantation of extrarenal organs is better to develop in the federal centers of hi-tech medical care with donor providing from territories of adjacent regions. 

  2. Alzheimer - resources

    Science.gov (United States)

    Resources - Alzheimer ... The following organizations are good resources for information on Alzheimer disease : Alzheimer's Association -- www.alz.org Alzheimer's Disease Education and Referral Center -- www.nia.nih.gov/alzheimers ...

  3. Infertility - resources

    Science.gov (United States)

    Resources - infertility ... The following organizations are good resources for information on infertility : Centers for Disease Control and Prevention -- www.cdc/gov/reproductivehealth/infertility March of Dimes -- www.marchofdimes.com/ ...

  4. SIDS - resources

    Science.gov (United States)

    Resources - SIDS ... The following organizations are good resources for information on SIDS : American SIDS Institute -- www.sids.org Centers for Disease Control and Prevention -- www.cdc.gov/sids National ...

  5. Bioinformatics Approaches for Human Gut Microbiome Research

    Directory of Open Access Journals (Sweden)

    Zhijun Zheng

    2016-07-01

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

  6. 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.

  7. Discovery and Classification of Bioinformatics Web Services

    Energy Technology Data Exchange (ETDEWEB)

    Rocco, D; Critchlow, T

    2002-09-02

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

  8. Bioinformatics for saffron (Crocus sativus L. improvement

    Directory of Open Access Journals (Sweden)

    Ghulam A. Parray

    2009-02-01

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

  9. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    OpenAIRE

    Hasan, L.

    2011-01-01

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

  10. Genome bioinformatics of tomato and potato

    OpenAIRE

    Datema, E.

    2011-01-01

    In the past two decades genome sequencing has developed from a laborious and costly technology employed by large international consortia to a widely used, automated and affordable tool used worldwide by many individual research groups. Genome sequences of many food animals and crop plants have been deciphered and are being exploited for fundamental research and applied to improve their breeding programs. The developments in sequencing technologies have also impacted the associated bioinformat...

  11. Chapter 16: Text Mining for Translational Bioinformatics

    OpenAIRE

    Bretonnel Cohen, K; Hunter, Lawrence E.

    2013-01-01

    Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. P...

  12. Adapting bioinformatics curricula for big data

    OpenAIRE

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

    2015-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these...

  13. [Applied problems of mathematical biology and bioinformatics].

    Science.gov (United States)

    Lakhno, V D

    2011-01-01

    Mathematical biology and bioinformatics represent a new and rapidly progressing line of investigations which emerged in the course of work on the project "Human genome". The main applied problems of these sciences are grug design, patient-specific medicine and nanobioelectronics. It is shown that progress in the technology of mass sequencing of the human genome has set the stage for starting the national program on patient-specific medicine.

  14. VLSI Microsystem for Rapid Bioinformatic Pattern Recognition

    Science.gov (United States)

    Fang, Wai-Chi; Lue, Jaw-Chyng

    2009-01-01

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

  15. Adapting bioinformatics curricula for big data.

    Science.gov (United States)

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

    2016-01-01

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

  16. Bioinformatics Approach in Plant Genomic Research.

    Science.gov (United States)

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

    2016-08-01

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

  17. Bioinformatics tools for analysing viral genomic data.

    Science.gov (United States)

    Orton, R J; Gu, Q; Hughes, J; Maabar, M; Modha, S; Vattipally, S B; Wilkie, G S; Davison, A J

    2016-04-01

    The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing.

  18. 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.

  19. 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.

  20. Chapter 16: text mining for translational bioinformatics.

    Directory of Open Access Journals (Sweden)

    K Bretonnel Cohen

    2013-04-01

    Full Text Available 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.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    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...... within convenient, integrated “workbench” environments. Resource descriptions are the core element of registry and workbench systems, which are used to both help the user find and comprehend available software tools, data resources, and Web Services, and to localise, execute and combine them...

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

    OpenAIRE

    Mochida, Keiichi; Shinozaki, Kazuo

    2011-01-01

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

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

    Science.gov (United States)

    Gyamfi, Alexander

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S; Slezak, T

    2005-04-05

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

  6. USDA Stakeholder Workshop on Animal Bioinformatics: Summary and Recommendations.

    Science.gov (United States)

    Hamernik, Debora L; Adelson, David L

    2003-01-01

    An electronic workshop was conducted on 4 November-13 December 2002 to discuss current issues and needs in animal bioinformatics. The electronic (e-mail listserver) format was chosen to provide a relatively speedy process that is broad in scope, cost-efficient and easily accessible to all participants. Approximately 40 panelists with diverse species and discipline expertise communicated through the panel e-mail listserver. The panel included scientists from academia, industry and government, in the USA, Australia and the UK. A second 'stakeholder' e-mail listserver was used to obtain input from a broad audience with general interests in animal genomics. The objectives of the electronic workshop were: (a) to define priorities for animal genome database development; and (b) to recommend ways in which the USDA could provide leadership in the area of animal genome database development. E-mail messages from panelists and stakeholders are archived at http://genome.cvm.umn.edu/bioinfo/. Priorities defined for animal genome database development included: (a) data repository; (b) tools for genome analysis; (c) annotation; (d) practical application of genomic data; and (e) a biological framework for DNA sequence. A stable source of funding, such as the USDA Agricultural Research Service (ARS), was recommended to support maintenance of data repositories and data curation. Continued support for competitive grants programs within the USDA Cooperative State Research, Education and Extension Service (CSREES) was recommended for tool development and hypothesis-driven research projects in genome analysis. Additional stakeholder input will be required to continuously refine priorities and maximize the use of limited resources for animal bioinformatics within the USDA. PMID:18629125

  7. USDA Stakeholder Workshop on Animal Bioinformatics: Summary and Recommendations

    Directory of Open Access Journals (Sweden)

    David L. Adelson

    2006-04-01

    Full Text Available An electronic workshop was conducted on 4 November–13 December 2002 to discuss current issues and needs in animal bioinformatics. The electronic (e-mail listserver format was chosen to provide a relatively speedy process that is broad in scope, cost-efficient and easily accessible to all participants. Approximately 40 panelists with diverse species and discipline expertise communicated through the panel e-mail listserver. The panel included scientists from academia, industry and government, in the USA, Australia and the UK. A second ‘stakeholder’ e-mail listserver was used to obtain input from a broad audience with general interests in animal genomics. The objectives of the electronic workshop were: (a to define priorities for animal genome database development; and (b to recommend ways in which the USDA could provide leadership in the area of animal genome database development. E-mail messages from panelists and stakeholders are archived at http://genome.cvm.umn.edu/bioinfo/. Priorities defined for animal genome database development included: (a data repository; (b tools for genome analysis; (c annotation; (d practical application of genomic data; and (e a biological framework for DNA sequence. A stable source of funding, such as the USDA Agricultural Research Service (ARS, was recommended to support maintenance of data repositories and data curation. Continued support for competitive grants programs within the USDA Cooperative State Research, Education and Extension Service (CSREES was recommended for tool development and hypothesis-driven research projects in genome analysis. Additional stakeholder input will be required to continuously refine priorities and maximize the use of limited resources for animal bioinformatics within the USDA.

  8. Translational Bioinformatics:Past, Present, and Future

    Institute of Scientific and Technical Information of China (English)

    Jessica D. Tenenbaum

    2016-01-01

    Though a relatively young discipline, translational bioinformatics (TBI) has become a key component of biomedical research in the era of precision medicine. Development of high-throughput technologies and electronic health records has caused a paradigm shift in both healthcare and biomedical research. Novel tools and methods are required to convert increasingly voluminous datasets into information and actionable knowledge. This review provides a definition and contex-tualization of the term TBI, describes the discipline’s brief history and past accomplishments, as well as current foci, and concludes with predictions of future directions in the field.

  9. 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.

  10. 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.

  11. How to operate an Energy Advisory Service. Volume II. New York Institute of Technology Energy Information Center and Referral Service resource material. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Spak, G.T.

    1978-06-01

    The NYIT Energy Information Center is a comprehensive information service covering every aspect of energy conservation and related technology, including conservation programs and practices, alternative energy systems, energy legislation, and public policy development in the United States and abroad. Materials in the Center can be located through a Card Catalog System and a Vertical File System. The Card Catalog System has entries which organize books and other printed materials according to authors/titles and according to the subject headings developed by the Library of Congress. The Vertical System contains pamphlets, newsclips, reprints, studies, announcements, product specifications and other ephemeral literature, and is organized according to subject headings based on the emerging vocabulary of the energy literature. The key to vertical file resources is the Thesaurus of Descriptors which is given. The Thesaurus includes all subject headings found in the Vertical File as well as other cross referenced terms likely to come to mind when seeking information on a specific energy area.

  12. The Effects of International Trade on Resource Misallocation : Trade Partner Matters (Replaced by CentER DP 2012-046)

    NARCIS (Netherlands)

    Curuk, M.

    2011-01-01

    This paper suggests that contingent on the productivity level of the trade partner; international trade may create resource misallocation in less productive countries. It theoretically shows how productivity spillovers induced by trade with more productive countries and heterogeneity in pro- ductivi

  13. 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…

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

    Directory of Open Access Journals (Sweden)

    Prantar Chakrabarti

    2012-12-01

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

  15. 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

  16. 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.

  17. The Genome Atlas Resource

    OpenAIRE

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

    2010-01-01

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

  18. Discussion on Resources Sharing Model of Experimental Teaching Demonstration Center%实验教学示范中心资源共享模式探析

    Institute of Scientific and Technical Information of China (English)

    熊梦辉

    2011-01-01

    The construction of experimental teaching demonstration center improve the experimental teaching level, and meet the social needs of application-oriented talents. However its potential can still be improved such as; the efficiency of the opening and share with high quality resource,and its radiation effect,the using efficiency in education. By analyzing the contents of resources of experimental teaching demonstration center, experimental equipments and fields, experimental content, teaching idea, then the author discussed how to promote the opening and sharing of these resources. And put forward the opinion like the rent of field,substitut-teach the exchange of the teacher,network share,so as to enhance the experimenaal teaching. At last the author gave an example of Guangdong Province on how to share high quality resources of experimental teaching demonstration center.%高校实验教学示范中心建设有效地提高了实验教学水平,满足了应用性人才培养的社会需求,但其潜力还有待进一步的挖掘,如何实现这些优质资源的有效开放与共享,充分发挥其示范辐射效应,提高教育投入的使用效益?示范中心所拥有的场地设备、人才队伍、教学理念、教学改革、管理制度等均是可以实现共享的优质资源.分析探讨了从教学场地设备、实验教学师资、实验教学理念等方面加强实验教学示范中心优质资源的开放与共享,提出场地租借、代开实验、课程共享、师资交流、网络共享等资源共享的模式,介绍了广东省成立实验教学示范中心联席会、建设开放共享信息平台等促进优质教学资源有效共享的措施.

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

    Science.gov (United States)

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

    2011-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Nomi L Harris

    2016-02-01

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

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

    Institute of Scientific and Technical Information of China (English)

    Ravi Shankar

    2011-01-01

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

  2. 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…

  3. 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…

  4. 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…

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

    Science.gov (United States)

    Glaspie, Henry W; Oshiro Wong, Celeste M

    2015-03-01

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

  6. Academic Training - Bioinformatics: Decoding the Genome

    CERN Multimedia

    Chris Jones

    2006-01-01

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

  7. Bioinformatic and Biometric Methods in Plant Morphology

    Directory of Open Access Journals (Sweden)

    Surangi W. Punyasena

    2014-08-01

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

  8. Bioinformatics analysis of estrogen-responsive genes

    Science.gov (United States)

    Handel, Adam E.

    2016-01-01

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

  9. Bioinformatics Analysis of Estrogen-Responsive Genes.

    Science.gov (United States)

    Handel, Adam E

    2016-01-01

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

  10. Combining multiple decisions: applications to bioinformatics

    International Nuclear Information System (INIS)

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

  11. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    Next generation sequencing (NGS) has revolutionized the field of genomics and its wide range of applications has resulted in the genome-wide analysis of hundreds of species and the development of thousands of computational tools. This thesis represents my work on NGS analysis of four species, Lotus...... japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... agricultural and biological importance. Its capacity to form symbiotic relationships with rhizobia and microrrhizal fungi has fascinated researchers for years. Lotus has a small genome of approximately 470 Mb and a short life cycle of 2 to 3 months, which has made Lotus a model legume plant for many molecular...

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

    Directory of Open Access Journals (Sweden)

    Kristina M. Obom

    2009-12-01

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

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

    OpenAIRE

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

    2009-01-01

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

  14. 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.

  15. 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.

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

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2016-06-01

    Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression. PMID:27281025

  17. Hydrologic Engineering Center

    Data.gov (United States)

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

  18. Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya marker-assisted selection and population genetic studies.

    Directory of Open Access Journals (Sweden)

    Newton Medeiros Vidal

    Full Text Available Carica papaya (papaya is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns. A total of 116,453 (72.6% of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement. Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes, achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12. The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

  19. Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies.

    Science.gov (United States)

    Vidal, Newton Medeiros; Grazziotin, Ana Laura; Ramos, Helaine Christine Cancela; Pereira, Messias Gonzaga; Venancio, Thiago Motta

    2014-01-01

    Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

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

    Directory of Open Access Journals (Sweden)

    K. Stephen Suh

    2013-01-01

    Full Text Available 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.

  1. 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.

  2. Diabetes - resources

    Science.gov (United States)

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

  3. Arthritis - resources

    Science.gov (United States)

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

  4. Hemophilia - resources

    Science.gov (United States)

    Resources - hemophilia ... The following organizations provide further information on hemophilia : Centers for Disease Control and Prevention -- www.cdc.gov/ncbddd/hemophilia/index.html National Heart, Lung, and Blood Institute -- www.nhlbi.nih.gov/ ...

  5. Diabetes - resources

    Science.gov (United States)

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

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

    Institute of Scientific and Technical Information of China (English)

    汪正康; 周鹏; 肖俊超; 武延军

    2015-01-01

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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  8. Survey of MapReduce frame operation in bioinformatics.

    Science.gov (United States)

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

    2014-07-01

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

  9. Survey of MapReduce frame operation in bioinformatics.

    Science.gov (United States)

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

    2014-07-01

    Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics. PMID:23396756

  10. 数据中心硬件资源的虚拟化建设%The Virtual Construction Hardware Resources Data Center

    Institute of Scientific and Technical Information of China (English)

    李志飞; 宿建波; 郑确

    2015-01-01

    为了实现企业信息化水平的进一步跨越,雅砻江水域水电开发有限公司(以下简称雅砻江公司)数据中心开展了硬件资源的虚拟化建设,并在此基础上实现了企业云管理平台的搭建,大幅提高了硬件资源的利用率和安全性。%In order to further across the implementation of enterprise informationization level, the Yalong River Hydropower Development Company Limited domain (hereinafter referred to as the Yalong company) data center to carry out the virtual construction of hardware resources, and on the basis of this implementation to build enterprise cloud management platform, a substantial increase in the rate and safety of the use of hardware resources.

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

    Institute of Scientific and Technical Information of China (English)

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

    2002-01-01

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

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

    Science.gov (United States)

    Brown, James A L

    2016-05-01

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

  13. Evolution of web services in bioinformatics.

    Science.gov (United States)

    Neerincx, Pieter B T; Leunissen, Jack A M

    2005-06-01

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

  14. Bioinformatics in cancer therapy and drug design

    International Nuclear Information System (INIS)

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

  15. Victim assistance - resources

    Science.gov (United States)

    Rape - resources; Resources - rape ... The following organizations are good resources for information on domestic violence and rape : Administration for Children and Families -- www.acf.hhs.gov National Center for Victims of ...

  16. 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. PMID:27383682

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

    CERN Document Server

    Maji, Pradipta

    2014-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  19. Creating Bioinformatic Workflows within the BioExtract Server

    Science.gov (United States)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows generally require access to multiple, distributed data sources and analytic tools. The requisite data sources may include large public data repositories, community...

  20. Survey of Natural Language Processing Techniques in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Zhiqiang Zeng

    2015-01-01

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

  1. 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

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

    OpenAIRE

    Ilzins, Olaf; Isea, Raul; Hoebeke, Johan

    2016-01-01

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

  3. Training community resource center and clinic personnel to prompt patients in listing questions for doctors: Follow-up interviews about barriers and facilitators to the implementation of consultation planning

    Directory of Open Access Journals (Sweden)

    Sepucha Karen

    2008-01-01

    Full Text Available Abstract Background Visit preparation interventions help patients prepare to meet with a medical provider. Systematic reviews have found some positive effects, but there are no reports describing implementation experiences. Consultation Planning (CP is a visit preparation technique in which a trained coach or facilitator elicits and documents patient questions for an upcoming medical appointment. We integrated CP into a university breast cancer clinic beginning in 1998. Representatives of other organizations expressed interest in CP, so we invited them to training workshops in 2000, 2001, and 2002. Objectives In order to learn from experience and generate hypotheses, we asked: 1 How many trainees implemented CP? 2 What facilitated implementation? 3 How have trainees, patients, physicians, and administrative leaders of implementing organizations reacted to CP? 4 What were the barriers to implementation? Methods We attempted to contact 32 trainees and scheduled follow-up, semi-structured, audio-recorded telephone interviews with 18. We analyzed quantitative data by tabulating frequencies and qualitative data by coding transcripts and identifying themes. Results Trainees came from two different types of organizations, clinics (which provide medical care versus resource centers (which provide patient support services but not medical care. We found that: 1 Fourteen of 21 respondents, from five of eight resource centers, implemented CP. Four of the five implementing resource centers were rural. 2 Implementers identified the championing of CP by an internal staff member as a critical success factor. 3 Implementers reported that modified CP has been productive. 4 Four respondents, from two resource centers and two clinics, did not implement CP, reporting resource limitations or conflicting priorities as the critical barriers. Conclusion CP training workshops have been associated with subsequent CP implementations at resource centers but not clinics. We

  4. UCSF Center for HIV Information

    Science.gov (United States)

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

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

    Science.gov (United States)

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

    2016-07-01

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

  6. Automatic Discovery and Inferencing of Complex Bioinformatics Web Interfaces

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-12-22

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

  7. 厦门市医院承办社区卫生服务中心人力资源现状调查%Investigation on human resources of municipal hospital delivered community health center in Xiamen

    Institute of Scientific and Technical Information of China (English)

    林民强

    2014-01-01

    Objectives:To learn status quo and problems on human resources of municipal hospital delivered community health center in Xiamen and give evidence on human resources reform in community health center. Methods:Self designed questionnaire was used in 15 municipal hospital delivered community health centers to investigate human resources status. Data were analyzed by Excel. Results:Problems in Xiamen community health centers can be described as insufficient and under qualified of human resources. Primary education and title staffs are still the main body. Conclusions:It needs to transfer the conception of high value on hospital and look down upon community health center, make active human resources policy, strengthen integrated hospital and community health center management and continuous improve community health center human resources training to promote human resources' capacity in community health center.%目的:了解厦门市医院承办社区卫生服务中心人力资源的现状及存在问题,为社区卫生服务中心人力资源的改革发展提供依据。方法:采用自制调查问卷,对2012年厦门市15家医院承办社区卫生服务中心人员状况进行调查,运用Excel进行数据统计分析。结果:厦门市社区卫生服务中心人力资源总量不足,人员的质量较差,仍以低学历和低职称人员为主。结论:通过转变“重医院、轻社区”观念、制定积极的人才政策、强化医院-社区一体化管理、不断完善社区人才的培养政策等策略加强社区卫生服务中心人才队伍建设,提高其卫生服务水平。

  8. 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

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

    Institute of Scientific and Technical Information of China (English)

    袁芳; 闫术卓; 邵正隆; 俞春; 宋树仁

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Sílvia Sunyer Lazaro

    2007-07-01

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

  11. The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond1

    Science.gov (United States)

    Mueller, Lukas A.; Solow, Teri H.; Taylor, Nicolas; Skwarecki, Beth; Buels, Robert; Binns, John; Lin, Chenwei; Wright, Mark H.; Ahrens, Robert; Wang, Ying; Herbst, Evan V.; Keyder, Emil R.; Menda, Naama; Zamir, Dani; Tanksley, Steven D.

    2005-01-01

    The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such as potato (Solanum tuberosum), eggplant (Solanum melongena), pepper (Capsicum annuum), and tomato (Solanum lycopersicum). The aim of SGN is to relate these species to one another using a comparative genomics approach and to tie them to the other dicots through the fully sequenced genome of Arabidopsis (Arabidopsis thaliana). SGN currently houses map and marker data for Solanaceae species, a large expressed sequence tag collection with computationally derived unigene sets, an extensive database of phenotypic information for a mutagenized tomato population, and associated tools such as real-time quantitative trait loci. Recently, the International Solanaceae Project (SOL) was formed as an umbrella organization for Solanaceae research in over 30 countries to address important questions in plant biology. The first cornerstone of the SOL project is the sequencing of the entire euchromatic portion of the tomato genome. SGN is collaborating with other bioinformatics centers in building the bioinformatics infrastructure for the tomato sequencing project and implementing the bioinformatics strategy of the larger SOL project. The overarching goal of SGN is to make information available in an intuitive comparative format, thereby facilitating a systems approach to investigations into the basis of adaptation and phenotypic diversity in the Solanaceae family, other species in the Asterid clade such as coffee (Coffea arabica), Rubiaciae, and beyond. PMID:16010005

  12. Application of bioinformatics in plant breeding

    NARCIS (Netherlands)

    Vassilev, D.; Leunissen, J.; Atanassov, A.; Nenov, A.; Dimov, G.

    2005-01-01

    The goal of plant genomics is to understand the genetic and molecular basis of all biological processes in plants that are relevant to the specie. This understanding is fundamental to allow efficient exploitation of plants as biological resources in the development of new cultivars with improved qua

  13. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

    Science.gov (United States)

    Thorvaldsdottir, Helga; Liefeld, Ted; Ocana, Marco; Borges-Rivera, Diego; Pochet, Nathalie; Robinson, James T.; Demchak, Barry; Hull, Tim; Ben-Artzi, Gil; Blankenberg, Daniel; Barber, Galt P.; Lee, Brian T.; Kuhn, Robert M.; Nekrutenko, Anton; Segal, Eran; Ideker, Trey; Reich, Michael; Regev, Aviv; Chang, Howard Y.; Mesirov, Jill P.

    2015-01-01

    Integrative analysis of multiple data types to address complex biomedical questions requires the use of multiple software tools in concert and remains an enormous challenge for most of the biomedical research community. Here we introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource. Seeded as a collaboration of six of the most popular genomics analysis tools, GenomeSpace now supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate the ability of non-programming users’ to leverage GenomeSpace in integrative analysis, it offers a growing set of ‘recipes’, short workflows involving a few tools and steps to guide investigators through high utility analysis tasks. PMID:26780094

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

    Institute of Scientific and Technical Information of China (English)

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

    2010-01-01

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

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

    Science.gov (United States)

    Bülow, Lorenz; Hehl, Reinhard

    2016-01-01

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

  16. Probabilistic models and machine learning in structural bioinformatics

    DEFF Research Database (Denmark)

    Hamelryck, Thomas

    2009-01-01

    and experimental determination of macromolecular structure that are based on such methods. These developments include generative models of protein structure, the estimation of the parameters of energy functions that are used in structure prediction, the superposition of macromolecules and structure determination......Structural bioinformatics is concerned with the molecular structure of biomacromolecules on a genomic scale, using computational methods. Classic problems in structural bioinformatics include the prediction of protein and RNA structure from sequence, the design of artificial proteins or enzymes......, and the automated analysis and comparison of biomacromolecules in atomic detail. The determination of macromolecular structure from experimental data (for example coming from nuclear magnetic resonance, X-ray crystallography or small angle X-ray scattering) has close ties with the field of structural bioinformatics...

  17. The Genome Atlas Resource

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  18. Approaches in integrative bioinformatics towards the virtual cell

    CERN Document Server

    Chen, Ming

    2014-01-01

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

  19. Bioinformatic scaling of allosteric interactions in biomedical isozymes

    Science.gov (United States)

    Phillips, J. C.

    2016-09-01

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

  20. High-performance computational solutions in protein bioinformatics

    CERN Document Server

    Mrozek, Dariusz

    2014-01-01

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

  1. 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

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

    Science.gov (United States)

    Seto, Donald

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

  3. Squid – a simple bioinformatics grid

    Directory of Open Access Journals (Sweden)

    de Miranda Antonio B

    2005-08-01

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

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

    Institute of Scientific and Technical Information of China (English)

    解海美; 陈进

    2014-01-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

  6. BioRuby: Bioinformatics software for the Ruby programming language

    NARCIS (Netherlands)

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

    2010-01-01

    The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it suppor

  7. 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…

  8. 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...

  9. Bioinformatics Assisted Gene Discovery and Annotation of Human Genome

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

  10. Setubal named deputy director at Virginia Bioinformatics Institute

    OpenAIRE

    Whyte, Barry James

    2005-01-01

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

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

    Science.gov (United States)

    Suplatov, Dmitry; Voevodin, Vladimir; Švedas, Vytas

    2015-03-01

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

  12. Incorporation of Bioinformatics Exercises into the Undergraduate Biochemistry Curriculum

    Science.gov (United States)

    Feig, Andrew L.; Jabri, Evelyn

    2002-01-01

    The field of bioinformatics is developing faster than most biochemistry textbooks can adapt. Supplementing the undergraduate biochemistry curriculum with data-mining exercises is an ideal way to expose the students to the common databases and tools that take advantage of this vast repository of biochemical information. An integrated collection of…

  13. 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…

  14. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

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

  15. Bioinformatics analysis of two-component regulatory systems in Staphylococcus epidermidis

    Institute of Scientific and Technical Information of China (English)

    QIN Zhiqiang; ZHONG Yang; ZHANG Jian; HE Youyu; WU Yang; JIANG Juan; CHEN Jiemin; LUO Xiaomin; QU Di

    2004-01-01

    Sixteen pairs of two-component regulatory systems are identified in the genome of Staphylococcus epidermidis ATCC12228 strain, which is newly sequenced by our laboratory for Medical Molecular Virology and Chinese National Human Genome Center at Shanghai, by using bioinformatics analysis. Comparative analysis of the twocomponent regulatory systems in S. epidermidis and that of S.aureus and Bacillus subtilis shows that these systems may regulate some important biological functions, e.g. growth,biofilm formation, and expression of virulence factors in S.epidermidis. Two conserved domains, i.e. HATPase_c and REC domains, are found in all 16 pairs of two-component proteins.Homologous modelling analysis indicates that there are 4similar HATPase_c domain structures of histidine kinases and 13 similar REC domain structures of response regulators,and there is one AMP-PNP binding pocket in the HATPase_c domain and three active aspartate residues in the REC domain. Preliminary experiment reveals that the bioinformatics analysis of the conserved domain structures in the two-component regulatory systems in S. epidermidis may provide useful information for discovery of potential drug target.

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Rocco, D; Critchlow, T J

    2003-05-01

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

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

    Science.gov (United States)

    McKenna, Neil J

    2011-08-01

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

  19. Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.

    Science.gov (United States)

    Liu, Bo; Madduri, Ravi K; Sotomayor, Borja; Chard, Kyle; Lacinski, Lukasz; Dave, Utpal J; Li, Jianqiang; Liu, Chunchen; Foster, Ian T

    2014-06-01

    Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach.

  20. Heart disease - resources

    Science.gov (United States)

    Resources - heart disease ... The following organizations are good resources for information on heart disease: American Heart Association -- www.heart.org Centers for Disease Control and Prevention -- www.cdc.gov/heartdisease

  1. 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

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

    OpenAIRE

    Espinosa, Judith M; White, Mary E

    2001-01-01

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

  3. 现代数据中心网络资源管理技术分析与综述%Analysis and survey of resource management on modern data center networks

    Institute of Scientific and Technical Information of China (English)

    邓罡; 龚正虎; 王宏; 陈琳; 刘志宏

    2014-01-01

    Data center is the basic facility of Internet and cloud computing. Since network resource is critical resource in data center thorough study and analysis of its management, which can help to improve data center’s performance, save costs and expenses, and is of great significance. However, as the structure characteristic and application mode are pro-found changing, it brings tremendous challenges to modern data center network resource management. Currently, lots of studies have been made in this field. In order to have an overall perspective of current research, some of the most impor-tant aspects were summarized and analyzed, which are automatic address configuration, congestion control, network traf-fic management and virtualization management. They are also the hotspots in current academe. Based on the comprehen-sive comparison and analysis, some trends of the future data center network resource management were pointed out in the end.%现代数据中心网络结构特征和应用模式的深刻变革,给网络资源管理带来了全新的挑战。地址自动配置技术、传输控制技术、流量管理技术以及虚拟化管理技术等是现代数据中心网络资源管理的重要内容,也是近年来学术界研究的重要方向。结合当前的研究现状,对以上几个方面的最新研究成果进行分析综述,并就网络资源管理未来的发展趋势进行展望。

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

    Science.gov (United States)

    Nehm, Ross H.; Budd, Ann F.

    2006-01-01

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

  5. LEARNING HORMONE ACTION MECHANISMS WITH BIOINFORMATICS

    Directory of Open Access Journals (Sweden)

    João Carlos Sousa

    2007-05-01

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

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

    Science.gov (United States)

    Shachak, Aviv; Ophir, Ron; Rubin, Eitan

    2005-01-01

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

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

    Science.gov (United States)

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

    2007-01-01

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

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

    Science.gov (United States)

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

    2007-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    邱大平; 贾勤

    2012-01-01

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

  10. Health Center Controlled Network

    Data.gov (United States)

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

  11. Contact Center Manager Administration (CCMA)

    Data.gov (United States)

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Slezak, T; Wolinsky, M

    2002-10-31

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

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

    Science.gov (United States)

    Ju, Feng; Zhang, Tong

    2015-11-01

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

  14. TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services.

    Science.gov (United States)

    Katayama, Toshiaki; Nakao, Mitsuteru; Takagi, Toshihisa

    2010-07-01

    Web services have become widely used in bioinformatics analysis, but there exist incompatibilities in interfaces and data types, which prevent users from making full use of a combination of these services. Therefore, we have developed the TogoWS service to provide an integrated interface with advanced features. In the TogoWS REST (REpresentative State Transfer) API (application programming interface), we introduce a unified access method for major database resources through intuitive URIs that can be used to search, retrieve, parse and convert the database entries. The TogoWS SOAP API resolves compatibility issues found on the server and client-side SOAP implementations. The TogoWS service is freely available at: http://togows.dbcls.jp/.

  15. 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.

  16. 基于人类遗传资源收集、保藏及生物信息学技术的遗传病致病基因定位与克隆%Mapping and identification of disease responsible genes based on genetic resource reservation and bioinformatics approach

    Institute of Scientific and Technical Information of China (English)

    夏家辉; 夏昆; 潘乾; 龙志高; 戴和平; 邬玲仟; 梁德生; 蔡芳

    2006-01-01

    @@ Mapping and identification of disease associated genes will demonstrate the genetic basis for the human genetic disorders, and provide the fundamental data for elucidation of pathogenesis mechanism of the disorders. Genetic resources, including pedigree information, blood sample, and tissues, etc., are essential materials for finding of the linked locus and gene for certain genetic disease. Genome wide scanning, positional cloning and candidate approach are most widely used methods or strategy, by which, thousands of diseases responsible genes have been identified. National laboratory of medical genetics of China (NLMG) has initiated the study on genetic resources collection, mapping and identification of disease associated gene since 1970s, here we summarize the major findings in this area achieved by NLMG.

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

    Science.gov (United States)

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

    2009-02-01

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

  18. 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.

  19. 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.

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

    Institute of Scientific and Technical Information of China (English)

    Xiao Li; Yizheng Zhang

    2003-01-01

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

  1. Security in SPGBP – Simulation of Protein Generation Bioinformatic Project

    Directory of Open Access Journals (Sweden)

    Toma Cristian

    2010-06-01

    Full Text Available Bioinformatics has known a rapid growth in the last decade, along with the development of the genomic projects worldwide. The Human Genome Project alone offers the sequences for 70 000 – 100 000 genes, as terra bytes of information. The major challenge nowadays is to process this huge amount of data. This paper comes to suggest a solution for the retrieval and processing of biological data. The main objective of this section is to point a direction in the development of tools that enable manipulation and efficient access to different types of biological data. Also, the major challenge is to use security in the proposed distributed architecture and to import concepts from bioinformatics into cryptography and IT&C security.

  2. Bioinformatics Analysis of Zinc Transporter from Baoding Alfalfa

    Institute of Scientific and Technical Information of China (English)

    Haibo WANG; Junyun GUO

    2012-01-01

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

  3. 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...

  4. 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.

  5. 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.

  6. 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.  .

  7. Promoting synergistic research and education in genomics and bioinformatics

    OpenAIRE

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

    2008-01-01

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

  8. BioJava: an open-source framework for bioinformatics

    OpenAIRE

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

    2008-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Aidan Budd

    2015-02-01

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

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

    Science.gov (United States)

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

    2015-02-01

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

  11. Drug targets for lymphatic filariasis: A bioinformatics approach

    OpenAIRE

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

    2013-01-01

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

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

    OpenAIRE

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

    2007-01-01

    Abstract Background Cell specific gene expression is largely regulated by different combinations of transcription factors that bind cis-elements in the upstream promoter sequence. However, experimental detection of cis-elements is difficult, expensive, and time-consuming. This provides a motivation for developing bioinformatic methods to identify cis-elements that could prioritize future experimental studies. Here, we use motif discovery algorithms to predict transcription factor binding site...

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

    OpenAIRE

    Nora Khaldi

    2012-01-01

    ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational b...

  14. 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.

  15. A comparison of common programming languages used in bioinformatics

    Directory of Open Access Journals (Sweden)

    Gillings Michael R

    2008-02-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Muhammad Zakarya

    2011-11-01

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

  19. 区域性数字化教育资源中心建设研究--以珠海市为例%Study on the Construction of Regional Digital Education Resource Center-- A case study of Zhuhai city

    Institute of Scientific and Technical Information of China (English)

    郭玲

    2014-01-01

    In the process of deepening the construction of learning -type City of Zhuhai, relying on community college construction of lifelong education system in Zhuhai, by integrating the educational resources, it is a strategic development target for Zhuhai education information to achieve integration of academic education and the integration of non-diploma education. Based on the analysis of the present situation of the construction of digital educational resources in Zhuhai, on the basis of Zhuhai education resources construction in the plight of around regional digitized education resource center progressive service oriented management thinking, as well as the characteristics of the region and culture, this paper explored the application mode of digital education resource center.%在深化珠海学习型城市的建设过程中,依托珠海社区大学构建终身教育体系,整合教育资源以实现学历教育与非学历教育的一体化融合已成为珠海教育信息化的战略发展目标。本文在对珠海目前数字化教育资源建设的现状分析的基础上,针对面临的困境,围绕区域性数字化教育资源中心逐步面向服务的管理方式展开思考,结合本地区特色,对区域性数字化教育资源中心的应用模式进行了探索。

  20. Elastic resource adjustment method for cloud computing data center%面向云计算数据中心的弹性资源调整方法

    Institute of Scientific and Technical Information of China (English)

    申京; 吴晨光; 郝洋; 殷波; 蔺艳斐

    2015-01-01

    To make resources purchase plan of service which has a variety of service quality requirements, this paper proposes an application performance oriented-cloud computing elastic resources adjustment method through the platform as a service and infrastructure as a service to sign agreement on allocation of resources based on Service-Level Agreement. Using the automatic scaling algorithm,this method adjusts virtual machine resources of load demand in the vertical level. In order to dynamically adjust allocation of resources to meet the needs of application service level,the cloud computing resources utilization rate is optimized. Simulation results are provided to show the effectiveness of the proposed method.%为了制定多种业务质量要求服务的资源购买方案,通过平台服务商与基础设施服务商之间签订基于服务等级协议的资源分配协议,提出一种面向应用性能的云计算弹性资源调整方法。该方法利用自动伸缩算法,在垂直层次上对负载需求的波动进行虚拟机资源调整,以实现动态调整分配资源量来满足应用的服务级别的需求,优化云计算资源利用率。最后通过仿真验证该算法的有效性。

  1. Effect of Availability of Teaching and Learning Resources on the Implementation of Inclusive Education in Pre-School Centers in Nyamira North Sub-County, Nyamira County, Kenya

    Science.gov (United States)

    Okongo, Rachel Bosibori; Ngao, Gladys; Rop, Naftal K.; Nyongesa, Wesonga Justus

    2015-01-01

    Inclusive education is a process of adjusting the home, school and the larger community to accommodate persons with special needs. In respect to pre-school learners, it is a means by which centers accommodate all learners regardless of their physical, intellectual, social, emotional, linguistic challenges. UNICEF notes that some 150 million…

  2. Instructional Media Initiatives: Focusing on the Educational Resources Center at Thirteen/wnet, New York, New York-- Slavery and the Making of America

    Science.gov (United States)

    Donlevy, Jim

    2005-01-01

    Slavery and the Making of America, a four-part series from PBS, is airing throughout the United States during February 2005. This landmark series examines the history of slavery in the United States and the significant role it played in shaping the development of the Nation. This article describes the series, including online resources, and…

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    樊志平

    2014-01-01

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

  5. Bioinformatics in microbial biotechnology – a mini review

    Directory of Open Access Journals (Sweden)

    Bansal Arvind K

    2005-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Jaschob Daniel

    2012-07-01

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

  7. Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer.

    Directory of Open Access Journals (Sweden)

    İrem Çelen

    Full Text Available Given the wealth of bioinformatics resources and the growing complexity of biological information, it is valuable to integrate data from disparate sources to gain insight into the role of genes/proteins in health and disease. We have developed a bioinformatics framework that combines literature mining with information from biomedical ontologies and curated databases to create knowledge "maps" of genes/proteins of interest. We applied this approach to the study of beta-catenin, a cell adhesion molecule and transcriptional regulator implicated in cancer. The knowledge map includes post-translational modifications (PTMs, protein-protein interactions, disease-associated mutations, and transcription factors co-activated by beta-catenin and their targets and captures the major processes in which beta-catenin is known to participate. Using the map, we generated testable hypotheses about beta-catenin biology in normal and cancer cells. By focusing on proteins participating in multiple relation types, we identified proteins that may participate in feedback loops regulating beta-catenin transcriptional activity. By combining multiple network relations with PTM proteoform-specific functional information, we proposed a mechanism to explain the observation that the cyclin dependent kinase CDK5 positively regulates beta-catenin co-activator activity. Finally, by overlaying cancer-associated mutation data with sequence features, we observed mutation patterns in several beta-catenin PTM sites and PTM enzyme binding sites that varied by tissue type, suggesting multiple mechanisms by which beta-catenin mutations can contribute to cancer. The approach described, which captures rich information for molecular species from genes and proteins to PTM proteoforms, is extensible to other proteins and their involvement in disease.

  8. Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer.

    Science.gov (United States)

    Çelen, İrem; Ross, Karen E; Arighi, Cecilia N; Wu, Cathy H

    2015-01-01

    Given the wealth of bioinformatics resources and the growing complexity of biological information, it is valuable to integrate data from disparate sources to gain insight into the role of genes/proteins in health and disease. We have developed a bioinformatics framework that combines literature mining with information from biomedical ontologies and curated databases to create knowledge "maps" of genes/proteins of interest. We applied this approach to the study of beta-catenin, a cell adhesion molecule and transcriptional regulator implicated in cancer. The knowledge map includes post-translational modifications (PTMs), protein-protein interactions, disease-associated mutations, and transcription factors co-activated by beta-catenin and their targets and captures the major processes in which beta-catenin is known to participate. Using the map, we generated testable hypotheses about beta-catenin biology in normal and cancer cells. By focusing on proteins participating in multiple relation types, we identified proteins that may participate in feedback loops regulating beta-catenin transcriptional activity. By combining multiple network relations with PTM proteoform-specific functional information, we proposed a mechanism to explain the observation that the cyclin dependent kinase CDK5 positively regulates beta-catenin co-activator activity. Finally, by overlaying cancer-associated mutation data with sequence features, we observed mutation patterns in several beta-catenin PTM sites and PTM enzyme binding sites that varied by tissue type, suggesting multiple mechanisms by which beta-catenin mutations can contribute to cancer. The approach described, which captures rich information for molecular species from genes and proteins to PTM proteoforms, is extensible to other proteins and their involvement in disease. PMID:26509276

  9. Research on R & D Centers' Resource Demand Position Embedding in Science Parks%嵌入科技园的研发中心资源需求定位研究

    Institute of Scientific and Technical Information of China (English)

    杨震宁; 李德辉; 张皓博

    2015-01-01

    The high-tech enterprises' R&D center location of strategic decision making has a system change, in the international Science Parks setting 'R&D center' has become a Chinese high-tech enterprises' the significant movement of independent innovation, development of new technologies and to chase the market. In this paper, through literature review, to establish the research hypothesis, according to the theory and practice to design re-search scale, based on the 15 Science Parks high-tech enterprises' 'R&D center' management and Science Parks' Managers' Questionnaire (457 samples), to set up research model. The research found that: Science Parks should be of high-tech enterprises' 'R&D center' offers four major innovation resources. Namely, R&D technology re-source support, cluster system support, R&D innovation culture support and technical R&D of hardware support. Science Parks for high-tech enterprises' 'R&D center' of the 'R&D technology resource support' is the most impor-tant resource supply. Science Parks should be to the enterprises' 'R&D center' classified management. Different si-zes, different industry segments and the nature of the high-tech enterprises, embedded in the different types of Sci-ence Parks, the resource demand position is different. According to the research results, this paper also as high-tech enterprises and Science Parks' Managers offers valuable management policy suggestions.%高技术企业对研发中心的选址战略决策发生了一系列变化,在国际化的科技园内建立“研发中心”已经成为跨国公司和中国本土高技术企业自主创新、开发新技术以及追赶市场的重要举措。通过文献回顾,建立研究假设,根据理论和实践研究设计量表,通过对国内15个科技园的高技术企业“研发中心”管理人员和科技园管理者的问卷调查(457个有效样本),建立研究模型,研究发现:科技园应为高技术企业“研发中心”提供四种主

  10. Composable languages for bioinformatics: the NYoSh experiment

    Directory of Open Access Journals (Sweden)

    Manuele Simi

    2014-01-01

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

  11. Composable languages for bioinformatics: the NYoSh experiment.

    Science.gov (United States)

    Simi, Manuele; Campagne, Fabien

    2014-01-01

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

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

    Science.gov (United States)

    Djordjevic, Marko

    2005-11-01

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

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

    Science.gov (United States)

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

    2008-01-01

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

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

    International Nuclear Information System (INIS)

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

  15. Bioinformatics pipeline for functional identification and characterization of proteins

    Science.gov (United States)

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

    2015-09-01

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

  16. WU-Blast2 server at the European Bioinformatics Institute

    OpenAIRE

    Lopez, Rodrigo; Silventoinen, Ville; Robinson, Stephen; Kibria, Asif; Gish, Warren

    2003-01-01

    Since 1995, the WU-BLAST programs (http://blast.wustl.edu) have provided a fast, flexible and reliable method for similarity searching of biological sequence databases. The software is in use at many locales and web sites. The European Bioinformatics Institute's WU-Blast2 (http://www.ebi.ac.uk/blast2/) server has been providing free access to these search services since 1997 and today supports many features that both enhance the usability and expand on the scope of the software.

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

    OpenAIRE

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

    2003-01-01

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

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

    OpenAIRE

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

    2016-01-01

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

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

    OpenAIRE

    Machanick, Philip; Bishop, Ozlem Tastan

    2014-01-01

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

  20. 多技能呼叫中心的I型与V型路由策略人力需求仿真分析%Simulation on Human Resource Requirement of "I" and "V" Design in Multi-skill Call Center

    Institute of Scientific and Technical Information of China (English)

    张星玥; 张艳霞; 霍佳震

    2012-01-01

    Implementing an appropriate Skill-Based Routing is significant to call centers, which concerns the most expensive resource: human resource. We consider three Skill-Based Routing strategies based on "I" design and "V" design. Two types of calls input, measured by service level and utility of call center agents and simulation model developed and implemented, we find "V" design with priority needs the least agents under the same service level, which has the same agent utility as other Skill-Based Routing strategies.%呼叫中心路由策略的选择对多技能呼叫中心至关重要,它影响到呼叫中心最昂贵资源:人力资源的支出.本文针对拓扑结构中的Ⅰ型、V型设计三种路由策略,研究这三种路由策略在两种呼叫类型下人力资源需求的情况.通过仿真模型的建立与运行,发现V型有优先级的路由策略在同样的服务水平和座席占用率下,所需的人力资源最少.

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

    Institute of Scientific and Technical Information of China (English)

    卢蓉; 姜润生; 黄丽; 徐正英; 沈海文; 张杪

    2013-01-01

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

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

    Science.gov (United States)

    Symeonidis, Iphigenia Sofia

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

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

    Science.gov (United States)

    USGS Alaska Science Center

    2007-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Chen C

    2016-03-01

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

  9. Building the Medical Imaging Resource Center Based on PACS to Improve the Teaching Medical Imaging%构建基于PACS的医学影像教学资源中心提升教学质量

    Institute of Scientific and Technical Information of China (English)

    王世威; 姜慧萍; 韩浙; 许茂盛

    2013-01-01

    [目的]构建基于图像存档与传输系统(picture archiving and communication system,PACS)的数字化医学影像教学资源中心,提升医学影像学教学质量。[方法]设计电子教案(electronic teaching file,ETF)生成模块,并把它整合在PACS系统报告工作站,配置电子教案服务器,建立电子教案数据库,并通过与PACS系统交互的接口模块,实现影像电子教案的制作,然后利用医院PACS系统中海量的数字化医学影像资料,建立数字化医学影像教学资源中心。[结果]通过整合在PACS系统报告工作站中的电子教案生成模块,选择典型病例、感兴趣病例,并经过简单的处理后自动快速地生成电子教案,成功构建数字化医学影像教学资源中心。[结论]基于PACS系统成功构建数字化医学影像教学资源中心,最大限度实现医学影像教学资源共享,将改变医学影像学教学模式,极大地提升医学影像学教学质量。%[Purpose] To build the digital Medical Imaging Resource Center based on the picture archiving and communication system(PACS) to improve the teaching medical imaging. [Methods] The generating module of the electronic teaching file(ETF) was developed and integrated into the report work-station of PACS. The ETF server was configurated. The ETF database was created. The ETF was created through the interface module with PACS, and then the medical imaging electronic teaching resources center was built. [Result] Using the generation module of the ETF integrated in report workstation of PACS, the ETF can be automatical y created quickly through simply processing after selecting typical cases or the cases of interest. The medical imaging electronic teaching resources center has been built successful y by using the great number of medical image data in the hospital PACS. [Conclusion]The medical imaging electronic teaching resources center can be built successful y based on PACS

  10. Bioinformatics in the secondary science classroom: A study of state content standards and students' perceptions of, and performance in, bioinformatics lessons

    Science.gov (United States)

    Wefer, Stephen H.

    The proliferation of bioinformatics in modern Biology marks a new revolution in science, which promises to influence science education at all levels. This thesis examined state standards for content that articulated bioinformatics, and explored secondary students' affective and cognitive perceptions of, and performance in, a bioinformatics mini-unit. The results are presented as three studies. The first study analyzed secondary science standards of 49 U.S States (Iowa has no science framework) and the District of Columbia for content related to bioinformatics at the introductory high school biology level. The bionformatics content of each state's Biology standards were categorized into nine areas and the prevalence of each area documented. The nine areas were: The Human Genome Project, Forensics, Evolution, Classification, Nucleotide Variations, Medicine, Computer Use, Agriculture/Food Technology, and Science Technology and Society/Socioscientific Issues (STS/SSI). Findings indicated a generally low representation of bioinformatics related content, which varied substantially across the different areas. Recommendations are made for reworking existing standards to incorporate bioinformatics and to facilitate the goal of promoting science literacy in this emerging new field among secondary school students. The second study examined thirty-two students' affective responses to, and content mastery of, a two-week bioinformatics mini-unit. The findings indicate that the students generally were positive relative to their interest level, the usefulness of the lessons, the difficulty level of the lessons, likeliness to engage in additional bioinformatics, and were overall successful on the assessments. A discussion of the results and significance is followed by suggestions for future research and implementation for transferability. The third study presents a case study of individual differences among ten secondary school students, whose cognitive and affective percepts were

  11. 全国疾病预防控制中心人力资源现状分析%Analysis of human resources current situation in nationwide centers for disease control and prevention

    Institute of Scientific and Technical Information of China (English)

    杨洋; 王松旺; 张英杰; 傅罡

    2013-01-01

    Objective:To analyze the current status of human resources in the centers for disease control and prevention in the whole country,so as to provide foundation for making scientific human resource plans.Methods:The data,such as the number,age,years of working,education background,title of technical post,and profession of personnel in the centers for disease control and prevention at the levels of province,city and county,were collect-ed from the basic information system of China centers for disease control and prevention and analyzed with Excel.Results:Those at the age from 35 to 44 accounted for the largest proportion in the personnel of centers for disease control and prevention.Their years of working were mainly between 20 and 29 years with the education background of technical secondary school,just second to junior college and university.Their titles of posts are mainly at middle and primary level and their scope of practice is mainly in five health items,communicable disease control,planned immunization and health inspection.Conclusion:The governments at all levels should strengthen the personnel construction of centers for disease control and prevention,improve the quality of professional personnel and make appropriate human resource plans for centers for disease control and prevention.%目的:分析全国各级疾病预防控制中心人力资源现状,为今后制定科学的人力资源规划提供依据.方法:通过中国疾病预防控制基本信息系统收集各省、市、县(区)疾病预防控制中心的人员数、年龄、工作年限、学历、职称、从事的专业等数据,用Excel软件进行统计分析.结果:全国疾病预防控制机构人员年龄在35岁~44岁组这个年龄段所占比例最高;工作年限主要集中在20年-29年;学历以大专、大学为主,中专学历次之;职称集中在中级、初级水平;执业范围主要分布在五大卫生、传染病控制、计划免疫和卫生检验这四个范围.结论:

  12. 全国疾病预防控制中心人力资源现状分析%Analysis of Human Resources of Chinese Center for Disease Control And Prevention

    Institute of Scientific and Technical Information of China (English)

    杨洋; 王松旺; 张英杰; 傅罡

    2013-01-01

    Objective:to analyze the status of human resources in the centers for disease control and prevention to provide foundation for making scientific human resource plans. Methods:To collecting such data as the number, age, years of working, education background, title of technical post, and profession of personnel in the centers for disease control and prevention at the level of province, city and county through the basic information system of Chinese centers for disease control and prevention;to analyze the data with Excel. Results:Those at the age from 35 to 44 account for the largest proportion in the personnel of centers for disease control and prevention. Their years of working are mainly from 20 to 29 with the education background of technical secondary school just second to junior college and university. Their titles of posts are mainly at middle and primary level and their scope of practice is mainly in five health, communicable disease control, planned immunization and health inspection. Conclusion:The governments at all levels should strengthen the personnel construction of centers for disease control and prevention, improve the quality of professional personnel and make appropriate human resource plans for centers for disease control and prevention.%目的:分析全国各级疾病预防控制中心人力资源现状,为今后制定科学的人力资源规划提供依据。方法:通过中国疾病预防控制基本信息系统收集各省、市、县(区)疾病预防控制中心的人员数、年龄、工作年限、学历、职称、从事的专业等数据,用Excel软件进行统计分析。结果:全国疾病预防控制机构人员年龄在35-44岁组这个年龄段所占比例最高;工作年限主要集中在20-29年;学历以大专、大学为主,中专学历次之;职称集中在中级、初级水平;执业范围主要分布在五大卫生、传染病控制、计划免疫和卫生检验这四个范围。结论:各级政府应

  13. 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

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

    Institute of Scientific and Technical Information of China (English)

    孟君; 张延生; 狄广义

    2014-01-01

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

  15. VectorBase

    Data.gov (United States)

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

  16. 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…

  17. 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...

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

    NARCIS (Netherlands)

    Wanders, B.

    2012-01-01

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

  19. 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…

  20. 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…