| Accepted Posters |
| Category 'E'- Databases' |
| Poster E01 |
| Information resources linking biology and chemistry |
| Jie Chen- National Center for Biotechnology Information |
| Steve Bryant (National Center for Biotechnology Information, Computational Biology Branch); |
| Short Abstract: This poster will describe how to use MMDB, a database of macromolecular 3D structures as well as tools for their visualization and comparative analysis, and PubChem, a information system providing biological properties and activities of chemical substances, to predict protein strcuture and function. |
| Long Abstract: Click Here |
| Poster E02 |
| DataFATE: A prototypic SIMS (Scientific Information Management System) for Ontology Construction and Mining |
| David Carr- University North Carolina Charlotte |
| No additional authors |
| Short Abstract: DataFATE (Data Feature Analyze Transform Extract) supplies the scientific research community with a relational database model and associated tools designed to handle diverse data arising from interdisciplinary studies. DataFATE achieves this through guided scientific ontology building, which permits the user to define and control the sets used to construct the database. |
| Long Abstract: Click Here |
| Poster E03 |
| Graph-theory meets evolutionary biology: reticulate classification of prokaryotic mobile genetic elements |
| Gipsi Lima-Mendez- Université Libre de Bruxelles |
| Jacques van Helden (Université Libre de Bruxelles, Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe)); Ariane Toussaint (Université Libre de Bruxelles, Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe)); Raphael Leplae (Université Libre de Bruxelles, Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe)); |
| Short Abstract: None On File |
| Long Abstract: Click Here |
| Poster E04 |
| Literature browsing with CiteXplore |
| Mark Rijnbeek- EMBL EBI |
| Stoehr Peter (EMBL EBI, Literature services); |
| Short Abstract: CiteXplore is available at www.ebi.ac.uk/citexplore as a tool for querying PubMed, Agricola, biological patent abstracts and more. Links are provided from citations to relevant biological database entries, such as UniProt proteins. Text-mining methods from the research community like ‘Whatizit’ provide filters for enrichment of text with annotation. |
| Long Abstract: Click Here |
| Poster E05 |
| STRING and STITCH: known and predicted interactions between proteins and chemicals |
| Lars Jensen- European Molecular Biology Laboratory |
| Michael Kuhn (European Molecular Biology Laboratory, Structural and Computational Biology); Christian von Mering (University of Zurich, Molecular Biology); Peer Bork (European Molecular Biology Laboratory, Structural and Computational Biology); |
| Short Abstract: Information on protein-protein and protein-chemical interactions is essential for understanding cellular functions. The STRING and STITCH web resources integrate interaction evidence derived from pathways, automatic literature mining, primary experimental data, and genomic context. The resulting interaction networks cover 1.5 million proteins from 373 organisms and 68,000 chemicals. |
| Long Abstract: Click Here |
| Poster E06 |
| GMOD: Managing genomic data from emerging model organisms |
| Dave Clements- National Evolutionary Synthesis Center (NESCent) |
| Brian Osborne (BioTeam, PI); Hilmar Lapp (National Evolutionary Synthesis Center, (NESCent)); Todd Vision (National Evolutionary Synthesis Center, (NESCent)); |
| Short Abstract: GMOD is a collection of interoperable open-source software components for managing, visualizing and annotating genomic data. In the past year NESCent has joined GMOD to promote and support adoption of GMOD tools, particularly in emerging model organisms. A Help Desk and wiki-based project web site have also been launched. |
| Long Abstract: Click Here |
| Poster E07 |
| RiceRBP: A rice RNA-binding protein database and analysis platform |
| Robert Morris- Washington State University |
| No additional authors |
| Short Abstract: RiceRBP is a new database and web interface dedicated to the study of rice RNA-binding proteins (RBP). The database includes sequence, localization, annotation, ortholog and expression information for each RBP. The proteins included in this database are not identified by in silico prediction methods but rely on empirical evidence. |
| Long Abstract: Click Here |
| Poster E08 |
| Arabidopsis Reactome: a Foundation Knowledgebase for Systems Biology in Plants |
| Nicolas Tsesmetzis- John Innes Centre |
| Matthew Couchman (John Innes Centre, Computational and Systems Biology); Janet Higgins (John Innes Centre, Computational and Systems Biology); Sean Walsh (John Innes Centre, Computational and Systems Biology); |
| Short Abstract: Arabidopsis Reactome is an online knowledgebase of biological processes from Arabidopsis thaliana. Its pathways cover approximately 8% of the Arabidopsis proteome. Arabidopsis Reactome events have been electronically projected onto 5 sequenced plants. Such a system allows the visualization and interpretation of high-throughput data, hypothesis formulation, and as a learning resource. |
| Long Abstract: Click Here |
| Poster E09 |
| The Universal Protein Resource (UniProt) |
| Anastasia Nikolskaya- Protein Information Resource |
| No additional authors |
| Short Abstract: The Universal Protein Resource (UniProt)—the product of collaboration between EBI, PIR and SIB—comprises four components: UniProt Knowledgebase, UniProt Reference Clusters, UniProt Archive and UniProt Metagenomic and Environmental Sequence database. UniProt (http://www.uniprot.org; new website: http://beta.uniprot.org) is updated every three weeks. User feedback is greatly appreciated. |
| Long Abstract: Click Here |
| Poster E10 |
| A community portal for a better PDB |
| Vince Grolmusz- Eotvos University and Uratim Ltd. |
| Rafael Ordog (Eotvos University, PIT); Zoltan Szabadka (Eotvos University, PIT); |
| Short Abstract: The PDB contains experimental information on protein- and nucleic-acid structures, but automated processing of these data is difficult, due to a number of inconsistencies. We provide a web interface for discussion and modification of the databank files by the community. Wikipdb.org automatically detects syntax errors and keeps track of versions. |
| Long Abstract: Click Here |
| Poster E11 |
| Xperanto-SNP: A web-based integrated system for SNP data management and analysis |
| Do Kyoon Kim- Seoul National University Biomedical Informatics (SNUBI) |
| Chan Hee Park (Seoul National University Biomedical Informatics (SNUBI) , Seoul National University College of Medicine); Young Ji Na (Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine); Hee Joon Chung (Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine); Ju Han Kim (Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine); |
| Short Abstract: High-throughput approaches using SNP genotyping chip are being developed to meet the demands of pharmacogenomics, where numerous individuals are studied with thousands of SNP markers. we developed Xperanto-SNP for integrated data management and analysis using user-friendly web-based interface. |
| Long Abstract: Click Here |
| Poster E12 |
| MouseBook: Online integrated mouse information system |
| John Hancock- MRC Mammalian Genetics Unit |
| Andrew Blake (MRC Harwell, Bioinformatics Group); Ann-Marie Mallon (MRC Harwell, Bioinformatics Group); Simon Greenaway (MRC Harwell, Bioinformatics Group); |
| Short Abstract: MouseBook makes a contribution to the understanding of the genetic basis of disease by allowing access to a range of MRC mouse primary data. This single interface facilitates querying of the MRC Frozen Embryo and Sperm Archive, ENU DNA Archive, Mutants from the ENU mutagenesis programme, EMPReSS and EuroPhenome. |
| Long Abstract: Click Here |
| Poster E13 |
| The Comprehensive Phytopathogen Genomics Resource |
| John Hamilton- Michigan State University |
| Jillian Lang (Colorado State University, Bioagricultural Sciences and Pest Management); Jan Leach (Colorado State University, Bioagricultural Sciences and Pest Management); C. Andre Levesque ( Agriculture and Agri-Food Canada, Biodiversity (Mycology and Botany)); Tom Powers (University of Nebraska-Lincoln, Department of Plant Pathology); Ned Tisserat (Colorado State University, Bioagricultural Sciences and Pest Management); C. Robin Buell (Michigan State University, Plant Biology); |
| Short Abstract: The Comprehensive Phytopathogen Genomics Resource (CPGR; http://cpgr.plantbiology.msu.edu) provides a web based portal for plant pathologists and diagnosticians to access genomic data for plant pathogens and to provide tools to rapidly create candidate diagnostic markers. The CPGR features the Genome Warehouse, Genome Browser, rDNA database, and Transcript Assembly Database. |
| Long Abstract: Click Here |
| Poster E14 |
| Analysis of the Mycobacterium tuberculosis interactome |
| Vince Grolmusz- Eotvos University and Uratim Ltd. |
| Gabor Ivan (Eotvos University, Computer Science); Zoltan Szabadka (Eotvos University, Computer Science); |
| Short Abstract: Analysis of protein-protein interaction (PPI) networks in Mycobacterium tuberculosis is presented. We created the metabolic and (physical) interaction PPI networks of the Mycobacterium tuberculosis, then on both networks we ran several graph-algorithms to determine important nodes and node-sets that can serve as a target for drug design. |
| Long Abstract: Click Here |
| Poster E15 |
| EuroPhenome: A Mouse Phenotyping Resource |
| Tim Beck- MRC Harwell |
| Hugh Morgan (MRC Harwell, Mammalian Genetics Unit); Ann-Marie Mallon (MRC Harwell, Mammalian Genetics Unit); Andrew Blake (MRC Harwell, Mammalian Genetics Unit); John Hancock (MRC Harwell, Mammalian Genetics Unit); |
| Short Abstract: EuroPhenome is an online mouse phenotyping resource which has been developed to store phenome data derived from mice using the standardised tests contained in EMPReSS. EuroPhenome is the repository for phenotype data generated by the EUMODIC project, which will phenotype up to 500 knock-out lines generated by the EUCOMM project. |
| Long Abstract: Click Here |
| Poster E16 |
| SNPfun: correlating variation and function |
| Yana Bromberg- Columbia University |
| No additional authors |
| Short Abstract: Evaluation of effects of non-synonymous SNPs on protein function is important for understanding of molecular mechanisms behind complex phenotypes. Here we present a database correlating dbSNP nsSNPs to their functional effects. The database contains SNAP (Screening for Non-Acceptable Polymorphisms) computational predictions and will be supplemented by submitted experimental annotations. |
| Long Abstract: Click Here |
| Poster E17 |
| Periscope/SQ: Fast Interactive Querying on Biological Sequence Datasets |
| Willis Lang- University of Michigan |
| Satwik Reddy (University of Michigan, Computer Science and Engineering); Sandeep Tata (IBM Research, Almaden); Jignesh Patel (University of Michigan, Computer Science and Engineering); |
| Short Abstract: Life science laboratories today must store and manage large sequence datasets. We present a system, Periscope/SQ, that allows us to quickly express complex queries within a declarative framework using database-style query optimization. Our system allows rapid exploration of genomic sequence databases orders of magnitude faster than procedural implementations. |
| Long Abstract: Click Here |
| Poster E18 |
| MeaNS – WHO-European Regional Database on Measles Nucleotide Surveillance |
| Saravanamuttu Gnaneshan- Health Protection Agency |
| Kevin Brown (Health Protection Agency, Virus Reference Department, Centre for Infections); Jonathan Green (Health Protection Agency, Bioinformatics Unit, Centre for Infections); David Brown (Health Protection Agency, Virus Reference Department, Centre for Infections); |
| Short Abstract: A web-based, quality-controlled, public health database (MeaNS) consisting of sequence and epidemiological data of measles infection in the WHO-Euro region was recently developed. Bioinformatics tools in MeaNS allow one to find identical or similar sequences, assign a genotype, display phylogenetic trees, and to temporally and spatially track measles infection. |
| Long Abstract: Click Here |
| Poster E19 |
| An Interactive Plant Metabolomics Database for Exploring the Arabidopsis Metabolome |
| Preeti Bais- Iowa State University |
| Julie Dickerson (Iowa State University, ELECTRICAL AND COMPUTER ENGINEERING); |
| Short Abstract: PlantMetabolomics.org is a web-enabled database for metabolomics data from an NSF-funded Arabidopsis 2010 project to develop metabolomics as a new functional genomics tool for elucidating functions of genes without visible phenotypes. The portal features analysis tools, annotation, and metadata from a range of platforms for different mutants and environmental conditions. |
| Long Abstract: Click Here |
| Poster E20 |
| Eco-informatics: leveraging bioinformatics skills to maximize agility in non-computational environments |
| John Van Hemert- Iowa State University |
| Yves Sucaet (Co-consultant, Genetics, Development, and Organismal Biology); |
| Short Abstract: Ecological survey-projects and associated collections of static data suggest the construction of a centralized platform for eco-informatics. A software development pipeline and platform for eco-informatics was developed in which data management principles are applied to ecological information, achieving consistency and automation. Implemented systems are available at http://eco.bcb.iastate.edu |
| Long Abstract: Click Here |
| Poster E21 |
| Enrichment of COG Database with 905355 sequences from 3414 genomes. |
| Gabriel Fernandes- Universidade Federal de Minas Gerais |
| Daniela Barbosa (UFMG, Biochemistry and Immunology); Francisco Prosdocimi (UFMG, Biochemistry and Immunology); Izabella Pena (UFMG, Biochemistry and Immunology); Lucas Santos (UFMG, Biochemistry and Immunology); Oto Junior (UFMG, Biochemistry and Immunology); Adriano Barbosa-Silva (UFMG, Biochemistry and Immunology); Henrique Velloso (UFMG, Biochemistry and Immunology); Mauricio Mudado (FUNED, Bioinformatics); Darren Natale (Protein Information Resource, Georgetown University Medical Center); Sergio Aguiar (UFMG, ICEX); J Miguel Ortega (UFMG, Biochemistry and Immunology); |
| Short Abstract: We developed a procedure to enrich the COG database. The procedure uses Uniprot UniRef50 clusters. Each COG entry that is a member of a UniRef50 cluster recruits the additional members of the UniRef50 cluster to compose the enriched cluster. To validate the method we tested the clusters with different procedures. |
| Long Abstract: Click Here |
| Poster E22 |
| MSU Solanaceae Comparative Genomics Resource: Tools and resources for cross-species translational genomics |
| Brett Whitty- Michigan State University |
| C. Robin Buell (Michigan State University, Plant Biology); |
| Short Abstract: The MSU Solanaceae Comparative Genomics Resource (http://solanaceae.plantbiology.msu.edu) is a USDA CSREES IRA funded web portal that provides the Solanaceae community with a suite of comparative databases and tools to enable functional genomics study in this large agriculturally important and morphologically diverse family. |
| Long Abstract: Click Here |
| Poster E23 |
| cneViewer: A Database of Conserved Noncoding Elements for Studies of Tissue-Specific Gene Regulation |
| Jeffrey Chuang- Boston College |
| Jason Persampieri (Boston College, Biology); Deborah Ritter (Boston College, Biology); Su Guo (UCSF, Biopharmaceutical Sciences); Qiang Li (UCSF, Biopharmaceutical Sciences); Jessica Lehoczky (Harvard Medical School, Genetics); Daniel Lees (Boston College, Biology); |
| Short Abstract: There are thousands of strongly conserved noncoding elements (CNEs) in vertebrate genomes, and their functions remain largely unknown. These data are in urgent need of biological organization. We present cneViewer, a webtool that enhances CNE studies by systematizing information on CNEs, based on the tissue-specific expression of nearby genes. |
| Long Abstract: Click Here |
| Poster E24 |
| Automated Literature Based Genome Annotation Using MeSH |
| David States- University of Michigan |
| Alex Ade (University of Michigan, National Center for Integrative Biomedical Informatics); Zachary Wright (University of Michigan, National Center for Integrative Biomedical Informatics); Aaron Bookvich (University of Michigan, National Center for Integrative Biomedical Informatics); Barbara Mirel (University of Michigan, National Center for Integrative Biomedical Informatics); James Cavaoloci (University of Michigan, National Center for Integrative Biomedical Informatics); Brian Athey (University of Michigan, National Center for Integrative Biomedical Informatics); |
| Short Abstract: We describe a statistical approach to reliably and automatically annotate genes with the concepts defined in MeSH, the National Library of Medicine’s controlled vocabulary for biomedical concepts. These annotations provide links from genes to the biomedical research literature and complement existing resources including the Gene Ontology and OMIM. |
| Long Abstract: Click Here |
| Poster E25 |
| Automated Literature Based Metabolome Annotation Using MeSH |
| David States- University of Michigan |
| Zachary Wright (University of Michigan, National Center for Integrative Biomedical Informatics); Aaron Bookvich (University of Michigan, National Center for Integrative Biomedical Informatics); Alex Ade (University of Michigan, National Center for Integrative Biomedical Informatics); Barbara Mirel (University of Michigan, National Center for Integrative Biomedical Informatics); Jame Cavalcoli (University of Michigan, National Center for Integrative Biomedical Informatics); Brian Athey (University of Michigan, National Center for Integrative Biomedical Informatics); |
| Short Abstract: We describe a statistical approach to reliably and automatically annotate metabolites with MeSH, the National Library of Medicine’s controlled vocabulary for biomedical concepts. These annotations provide links from chemical substances to the biomedical research literature and complement existing resources including PubChem and the Human Metabolome Database. |
| Long Abstract: Click Here |
| Poster E26 |
| The Pseudomonas Genome Database: A Model for Facilitating User-Friendly, Comprehensive Comparisons of Microbial Genomes |
| Geoff Winsor- Simon Fraser University |
| Thea Van Rossum (Simon Fraser University, Molecular Biology and Biochemistry); Khaira Bhav (Simon Fraser University, Molecular Biology and Biochemistry); Raymond Lo (Simon Fraser University, Molecular Biology and Biochemistry); Matthew Whiteside (Simon Fraser University, Molecular Biology and Biochemistry); Nancy Yu (Simon Fraser University, Molecular Biology and Biochemistry); Martin Ester (Simon Fraser University, School of Computing Science); Robert Hancock (University of British Columbia, Department of Microbiology and Immunology); Fiona Brinkman (Simon Fraser University, Molecular Biology and Biochemistry); James Wagner (Simon Fraser University, School of Computing Science); |
| Short Abstract: The Pseudomonas Genome database is a resource for comparative analyses of the continually-updated Pseudomonas aeruginosa PAO1 genome and closely-related Pseudomonas strains/species. User-friendly search features enable researchers to simultaneously view and compare multiple annotations within or between genomes and perform downstream analyses. Improved ortholog and subcellular localization predictions are provided. |
| Long Abstract: Click Here |
| Poster E27 |
| GRIP: a genome research informatics pipeline with open and closed integration of biological databases |
| Chan Hee Park- Seoul National University Biomedical Informatics (SNUBI) |
| Mingoo Kim (Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine); Hee-Joon Chung (Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine); Young-Ji Na (Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine); Do Kyoon Kim (Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine); Ju Han Kim (Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine); |
| Short Abstract: GRIP is a web-based integrated database for analyzing and accessing biological information of human, mouse and rat. Using tightly-integration and link-based integration approaches, GRIP enables searching navigation and information of each biological objects from id of major databases, visualizes graph profiling, database id version trace and support computational analysis environments. |
| Long Abstract: Click Here |
| Poster E28 |
| Phoenix - A database of heterogenous gene sets |
| Daniel Edsgard- Center for Biological Sequence Analysis, Technical University of Denmark |
| Agnieszka Juncker (Center for Biological Sequence Analysis, Technical University of Denmark, Institute for Systems Biology); Nils Weinhold (Center for Biological Sequence Analysis, Technical University of Denmark, Institute for Systems Biology); Ramneek Gupta (Center for Biological Sequence Analysis, Technical University of Denmark, Institute for Systems Biology); |
| Short Abstract: How are we going to unravel the etiology behind complex diseases? Phoenix is a database that can aid by providing heterogenous collections of gene sets, including contexts such as disease, pathway, genomic position, tissue expression, etc. Coupled to the database is also a tool for automated gene set enrichment analysis. |
| Long Abstract: Click Here |
| Poster E29 |
| IBIDAS: making heterogeneous data sources available through a general data model and scripting language for use in algorithms, visualizations and web services |
| Jan Bot- TU Delft |
| No additional authors |
| Short Abstract: The IBIDAS system provides uniform access to different heterogeneous biological data sources. This data is stored locally. Access is facilitated by an intermediate scripting layer. The ontology based database can be queried using a command-line approach and has a bi-directional link with Cytoscape. An interface module for Taverna is under development. |
| Long Abstract: Click Here |
| Poster E30 |
| EcoliHub: An Information Resource for Experimentalists and Modelers |
| Dawn Whitaker- Purdue University |
| Walid Aref (Purdue University, Computer Science); Kirill Datsenko (Purdue University, Biological Sciences); Sara Ess (Purdue University, Biological Sciences); Michael Gribskov (Purdue University, Biological Sciences); Daisuke Kihara (Purdue University, Biological Sciences); Sangtae Kim (Purdue University, Mechanical Engineering); Ali Roumani (Purdue University, Computer Science); Hirotada Mori (Nara Institute of Science and Technology, Graduate School of Biological Sciences); Barry Wanner (Purdue University, Biological Sciences); |
| Short Abstract: E. coli is the most studied organism, the source for much basic knowledge of cellular processes. EcoliHub is being designed for seamless and transparent bi-directional connections among cooperating E. coli databases through web services, allowing full use of existing knowledge and enabling new discoveries for deeper understanding of life processes. |
| Long Abstract: Click Here |
| Poster E31 |
| Sabio RK - a data warehouse for integrating and analysis of reaction kinetics data |
| Olga Krebs- EML Research |
| Isabel Rojas (EML Research, SDBV); Ulrike Wittig (EML Research, SDBV); Renate Kania (EML Research, SDBV); Marin Golebiewski (EML Research, SDBV); Saqib Mir (EML Research, SDBV); Andreas Wiedemann (EML Research, SDBV); |
| Short Abstract: SABIO-RK is a web-accessible database designed to store information about biochemical reactions and their kinetics manually extracted from published scientific articles and curated by a team of experts. It aims to support modellers in the setting-up of models of biochemical networks. |
| Long Abstract: Click Here |
| Poster E32 |
| KOTIS: The integrated data manipulating system for toxicogenomics |
| Yang-Seok Kim- KyungHee University |
| ChanWhi Uhm (Bioinformatics Division, ISTECH,Inc.); Youngbok Lee (Bioinformatics Division, ISTECH,Inc.); Sungmin Kim (Bioinformatics Division, ISTECH,Inc.); Jinho Yoo (Yonsei University, Cancer Metastasis Research Center); |
| Short Abstract: NITR (National Institute of Toxicological Research) of South Korea and ISTECH has developed database system (KOTIS) for managing every kinds of Toxicogenomics data. KOTIS can deals with expression data from every kinds of array platforms.The KOTIS will be released in this August and support the toxicogenomics research in South Korea. |
| Long Abstract: Click Here |
| Poster E33 |
| The European Genotype Archive |
| Mario Caccamo- EMBL-EBI |
| Ilkka Lappalainen (EMBL-EBI, EGA); Paul Flicek (EMBL-EBI, EGA); |
| Short Abstract: The European Genotype Archive (EGA) database at the EBI provides a permanent archive for all types of genotype data. The EGA contains data subject to consent-agreement limitations, and data approved for public release. The data access decisions are made by the data access-granting organisations. EGA is available at www.ebi.ac.uk/ega. |
| Long Abstract: Click Here |
| Poster E34 |
| InterMine – open source data warehouse and query interface |
| Richard Smith- Cambridge University |
| Xavier Watkins (Cambridge University, Systems Biology Centre); Jakub Kulaviak (Cambridge University, Systems Biology Centre); Gos Micklem (Cambridge University, Systems Biology Centre); Julie Sullivan (Cambridge University, Systems Biology Centre); Matthew Wakeling (Cambridge University, Systems Biology Centre); Hilde Janssens (Cambridge University, Systems Biology Centre); Rachel Lyne (Cambridge University, Systems Biology Centre); Dan Tomlinson (Cambridge University, Systems Biology Centre); Kim Rutherford (Cambridge University, Systems Biology Centre); Sergio Contrino (Cambridge University, Systems Biology Centre); |
| Short Abstract: InterMine is an open-source system for building query-optimised data warehouses. It supports integration from standard biological formats and inclusion of your own data. A web application allows users to create queries, use templates and operate on lists. RESTful web services allow results to be embedded in other sites. |
| Long Abstract: Click Here |
| Poster E35 |
| YeastFunc: A browser for quantitative S. cerevisiae gene function annotations and underlying evidence. |
| John Beaver- Harvard Medical School |
| Weidong Tian (Harvard Medical School, Biological Chemistry and Molecular Pharmacology); Francis D. Gibbons (Harvard Medical School, Biological Chemistry and Molecular Pharmacology); Murat Tasan (Harvard Medical School, Biological Chemistry and Molecular Pharmacology); Joeseph Mellor (Harvard Medical School, Biological Chemistry and Molecular Pharmacology); Gabriel Berriz (Harvard Medical School, Biological Chemistry and Molecular Pharmacology); Timothy R. Hughes (University of Toronto, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research); Frederick P. Roth (Harvard Medical School, Biological Chemistry and Molecular Pharmacology); |
| Short Abstract: Computational predictions allows principled triage to prioritize experimental tasks that would be prohibitive otherwise. YeastFunc allows browsing of quantitative S. cerevisiae gene function annotations produced by integrating diverse genomic data sources and biological relationships. It also displays gene properties and biological relationships that helped form the predictions. |
| Long Abstract: Click Here |
| Poster E36 |
| A Data Transmission Method for Web Services in Bioinformatics Workflows |
| Junya Seo- Osaka University |
| Shigeto Seno (Osaka University, Graduate School of Information Science and Technology); Yoichi Takenaka (Osaka University, Graduate School of Information Science and Technology); Hideo Matsuda (Osaka University, Graduate School of Information Science and Technology); |
| Short Abstract: We propose a way to manage data in bioinformatics workflows efficiently by introducing large data transmission to web services. Our mechanism achieves the efficient transmission of the results of web services by their references in a workflow and decreasing the amount of memory spaces needed in whole workflow execution. |
| Long Abstract: Click Here |
| Poster E37 |
| A Comparison for the Three Protein Representative Selection Methods: PDB-REPRDB, ASTRAL and PISCES |
| Zarrin Minuchehr- National Institute of Genetic Engineering and Biotechnology |
| Mostafa Afshari (1National Institute of Genetic Engineering and Biotechnology, Bioinformatics); Armin Madadkar Sobhani (Institute of Biochemistry & Biophysics, University of Tehran, Bioinformatics); Ali Haghnazari (Zanjan University, Biotechnology); Ahmad Parsian (Faculty of Science, University of Tehran, Mathematics); Bahram Goliaei (Institute of Biochemistry & Biophysics, University of Tehran, Bioinformatics); |
| Short Abstract: Comparison of three most popular protein representative selection methods (PDB-REPRDB, ASTRAL and PISCES) has been reported using a simple and well understood statistical concept. We compiled the representative proteins in various identity intervals for choosing the best method and PISCES, ASTRAL, PDB-REPRDB was suggested respectively. |
| Long Abstract: Click Here |
| Poster E38 |
| EMBRACE – Enabling Data Integration |
| Syed Haider- EMBL-European Bioinformatics Institute |
| Benoit Ballester (EMBL-European Bioinformatics Institute, Hinxton,, ); Richard Holland (EMBL-European Bioinformatics Institute, Hinxton, ); Damian Smedley (EMBL-European Bioinformatics Institute, Hinxton, ); Peter Rice (EMBL-European Bioinformatics Institute, Hinxton, ); Arek Kasprzyk (Ontario Institute for Cancer Research, Toronto, ); |
| Short Abstract: Large quantities of biological data generated by different research centres have been exposed with a variety of programmatic interfaces. The unified presentation and interoperability of these diverse resources is made possible through BioMart web services as an on-going initiative by the EMBRACE project. |
| Long Abstract: Click Here |
| Poster E39 |
| Phenotypes and Models Portal at the Rat Genome Database |
| Melinda Dwinell- Medical College of Wisconsin |
| Mary Shimoyama (Medical College of Wisconsin, Human & Molecular Genetics Center); Rajni Nigam (Medical College of Wisconsin, Human & Molecular Genetics Center); Jeff De Pons (Medical College of Wisconsin, Human & Molecular Genetics Center); Howard Jacob (Medical College of Wisconsin, Physiology/Human & Molecular Genetics Center); |
| Short Abstract: The RGD Phenotypes and Models Portal (http://rgd.mcw.edu) is an entryway to physiological data and disease models for researchers using rat to study physiological function and human disease. This portal provides the data and tools for identifying models, protocols and methodologies, and allows researchers to compare phenotype data across experiments. |
| Long Abstract: Click Here |
| Poster E40 |
| The Synergizer service for database identifier translation |
| Gabriel F. Berriz- Harvard Medical School |
| Frederick P. Roth (Harvard Medical School, Biological Chemistry and Molecular Pharmacology); |
| Short Abstract: Biological databases are an important research tool, but differences in nomenclature get in the way of integrating data from multiple databases. Therefore we developed the Synergizer service, which allows mapping sets of database identifiers via a simple function call. A demonstration client may be found at http://llama.med.harvard.edu/cgi/synergizer/translate. |
| Long Abstract: Click Here |
| Poster E41 |
| CAPIS: A Comprehensive Database for Structural Studies of Protein-DNA Interactions |
| RyangGuk Kim- University of North Carolina at Charlotte |
| No additional authors |
| Short Abstract: CAPIS (for Comprehensive Database for DNA-Protein Interaction Study), a database of protein-DNA complex structures, was developed to study the interactions between protein and DNA. CAPIS provides the most comprehensive information about protein-DNA complex structures compared to other similar databases. |
| Long Abstract: Click Here |
| Poster E42 |
| Automated Data Pipelines for Loading, Integrating, Annotating and Quality Control of Data at the Rat Genome Database |
| Burcu Bakir-Gungor- Medical College of Wisconsin |
| Mary Shimoyama (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Andrew Patzer (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Alexander Stoddard (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Jeff De Pons (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Jennifer Smith (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Victoria Petri (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Stan Laulederkind (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Rajni Nigam (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Timothy Lowry (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Elizabeth Worthey (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Melinda Dwinell (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Simon Twigger (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); Howard Jacob (Medical College of Wisconsin, Human and Molecular Genetics Center, Rat Genome Database); |
| Short Abstract: The Rat Genome Database (RGD, http://rgd.mcw.edu) provides comprehensive rat genetic, genomic and biological data. Automated pipeline mechanisms, quality control measures, and the methods to synchronize multiple pipelines will be presented along with the data types acquired and integrated and the process for resolving data errors and conflicts. |
| Long Abstract: Click Here |
| Poster E43 |
| The Subcellular Location Image Finder: A Publicly-available Database of Annotated Fluorescence Micrographs from Pubmed Central Articles |
| Luis Pedro Coelho- Carnegie Mellon University |
| Andrew Arnold (Carnegie Mellon University, Machine Learning); Saboor Sheikh (Carnegie Mellon University, Center for Bioimage Informatics); Amr Ahmed (Carnegie Mellon University, Computer Science); Eric Xing (Carnegie Mellon University, Machine Learning, Computer Science); William Cohen (Carnegie Mellon University, Machine Learning, Computer Science); Robert F. Murphy (Carnegie Mellon University, Biological Sciences, Machine Learning, Biomedical Engineering); |
| Short Abstract: The Subcellular Location Image Finder (SLIF) uses a combination of text-mining and image analysis techniques to extract assertions from figures and their associated captions. The result is a publicly-available, searchable database (http://slif.cbi.cmu.edu) of over 30,000 fluorescence micrographs from Pubmed Central annotated with the depicted protein, cell type, or pixel resolution. |
| Long Abstract: Click Here |
| Poster E44 |
| The CAMERA Project: Building a “Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis” |
| John Wooley- University of California San Diego |
| Kayo Arima (UCSD, CALIT2); Iddo Friedberg (UCSD, CALIT2); Weizhong Li (UCSD, CALIT2); Paul Gilna (UCSD, CALIT2); |
| Short Abstract: Significant opportunities exist for computational biologists in metagenomics. CAMERA (Community Cyberinfrastructure for Marine Microbial Ecology Research and Analysis) provides access to environmental metagenomic data, and will become a tool for all metagenomics analyses, with functional annotation tools on top of extant fast BLAST and fragment recruitment viewer. |
| Long Abstract: Click Here |
| Poster E45 |
| Integration and Analysis of an EST Database |
| Lan Li- GLFC, Natural Resources Canada |
| Daniel Doucet (co-worker, Biotech); Basil Arif (co-worker, Biotech); Qili Feng (co-worker, Biology); Peter Krell (co-worker, Biology); |
| Short Abstract: An 80,000 Expressed Sequence Tag dataset from the pest insect Choristoneura fumiferana has been generated from 8 different cDNA libraries. More than 16000 putative transcripts were functionally identified by performing a search of Gene Ontology (GO) database and KEGG Orthology (KO) databases. The annotated EST database can be queried at www.pestgenomics.org. |
| Long Abstract: Click Here |
| Poster E46 |
| CGDSNP: A High Quality Integrated Mouse SNP Database |
| Lucie Hutchins- The Jackson Laboratory |
| Gary Churchil (The Jackson Laboratory, Computational Sciences and System Biology); Joel Graber (The Jackson Laboratory, Computational Sciences and System Biology); |
| Short Abstract: SNPs are an important tool to study genetic variations. We present CGDSNP, a database with more than 8M SNPs from 74 laboratory mouse strains. The SNPs have been curated and integrated with various data including functional implications of each SNP. CGDSNP is accessible via a web query interface. |
| Long Abstract: Click Here |
| Poster E47 |
| A Knowledge-based Bioinformatics Workflow Automation System |
| Xin (James) Li- Georgetown University Medical Center |
| No additional authors |
| Short Abstract: This work proposes a bioinformatics workflow automation system which automates the bioinformatics data processing driven by the knowledge extracted from previous data processing records. Machine learning, knowledge base, object-relational database and Web technologies are utilized. |
| Long Abstract: Click Here |
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