Accepted Posters

Category 'E'- Databases'
Poster E01
The Roche Cancer Genome Database
Jan Küntzer- Roche Diagnostics GmbH
Daniela Eggle (Roche Diagnostics GmbH, Translational Research Sciences); Stefan Klostermann (Roche Diagnostics GmbH, pRED Informatics); Helmut Burtscher (Roche Diagnostics GmbH, Oncology Discovery);
Short Abstract: We present a new version of the integrative Roche Cancer Genome Database (RCGDB) for human mutation data. The current version of RCGDB contains an advanced query interface using various filter criteria to search for putative biomarker. Furthermore, we added custom search interfaces for different questions.
Long Abstract:Click Here

Poster E02
An Advanced Web Query Interface for Biological Databases
Peter Karp- SRI International, AE206
Mario Latendresse (SRI International, Bioinformatics Research Group);
Short Abstract: Motivation: Although some biological databases (DBs) offer a Web-based
form to allow users to author DB queries, these query forms are quite
restricted in the complexity of DB queries that they can
formulate. Writing precise queries against biological DBs is usually
left to a programmer skillful enough in query languages like SQL.
Results: We present a Web interface for building precise queries for
biological DBs that can construct much more precise queries than most
Web-based query forms, yet that is user friendly enough to be used by
biologists. It supports queries containing multiple conditions, and
connecting multiple object types without using the join concept, which
is unintuitive to biologists. Users can interactively build a wide
range of queries. Interactive documentation describes the schema of
the queried DBs. Availability: This tool is part of the Pathway Tools
software and is available as part of several bioinformatics Web sites.
Long Abstract:Click Here

Poster E03
Soybean Knowledge Base (SoyKB) : A Web Resource for Soybean Translational Genomics
Trupti Joshi- University of Missouri
Qiuming Yao (University of Missouri, Computer Science ); Levi D. Franklin (University of Missouri, Computer Science ); Gary Stacey (University of Missouri, Division of Plant Sciences); Henry Nguyen (University of Missouri, Division of Plant Sciences); Dong Xu (University of Missouri, Computer Science);
Short Abstract: Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean. SoyKB is designed to handle the storage and integration of soybean genomics, microarray, transcriptomics, proteomics and metabolomics data along with the pathway information. SoyKB can be accessed at http://soykb.org/
Long Abstract:Click Here

Poster E04
BioPAX – A Community Standard for Pathway Data Sharing
Nadia Anwar- Memorial Sloan-Kettering Cancer Center
Emek Demir (Memorial Sloan-Kettering Cancer Center, Computational Biology); Gary Bader (University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research); Igor Rodchenkov (University of Toronto, errence Donnelly Centre for Cellular and Biomolecular Research);
Short Abstract: BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways and processes at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). The standard is defined using the Web Ontology Labguage OWL.
Long Abstract:Click Here

Poster E05
The computer system SitEx for analyzing the protein functional sites distribution in exon structure of corresponding genes.
Irina Medvedeva- Institute of Cytology and Genetics SB RAS
Pavel Demenkov (Institute of Cytology and Genetics SB RAS, Department of Systems Biology ); Vladimir Ivanisenko (Institute of Cytology and Genetics SB RAS, Department of Systems Biology );
Short Abstract: Continue analyzing structural and functional organization of the protein mapped to the exon structure of encoding gene we constructed the database of mapped protein functional sites gene and applied the BLAST search and 3D similar structure search for the polypeptide encoded by one exon, participating in organizing the functional site.
Long Abstract:Click Here

Poster E06
DDBJ Read Annotation Pipeline: A web-based analytical tool for next-generation sequencing data
Eli Kaminuma- National Institute of Genetics
Takako Mochizuki (NIG, CIB-DDBJ); Yuichi Kodama (NIG, CIB-DDBJ); Satoshi Saruhashi (NIG, CIB-DDBJ); Hideaki Sugawara (NIG, CIB-DDBJ); Kousaku Okubo (NIG, CIB-DDBJ); Toshihisa Takagi (NIG, CIB-DDBJ); Yasukazu Nakamura (NIG, CIB-DDBJ);
Short Abstract: We developed 'DDBJ Read Annotation Pipeline', a web-based analytical tool of next-generation sequencing data. The proposed pipeline consists of two processes: basic analysis for genome mapping and de novo assembly, and high-level analysis for structural and functional annotations such as single nucleotide polymorphism (SNP) detection and expression tag counts.
Long Abstract:Click Here

Poster E07
Heterogeneous data integration in context of bioinformatics cloud computing
Hoan Nguyen- IGBMC
Luc Moulinier (IGBMC, Bioinformatics); Olivier Poch (IGBMC, Bioinformatics);
Short Abstract: The BIRD System (Biological Integration and Retrieval of Data) has been designed to automatically ensure the interconnection, the data versioning management and update of the datasets in the Decrypthon grid. The biological query language allows searching and sharing data without replication of the unnecessary data on all the grid nodes.
Long Abstract:Click Here

Poster E08
Frequently appearing spherically aligned substructers in proteins
Rafael Ördög- Eotvos University, Budapest
Vince Grolmusz (Eotvos University, Budapest, Department of Computer Science);
Short Abstract: The Protein Data Bank contains the three-dimensional description of more than 45000 structures today. In one our previous works we used delaunay decompositions to study protein structures. For proper handling of co-spherical atoms (i.e., five atoms on one sphere) we implemented an algorithm capable of fitting spheres on point sets.
Long Abstract:Click Here

Poster E09
ISA infrastructure: supporting standards-compliant experimental reporting and enabling curation at community level
Philippe Rocca-Serra- EBI
Marco Brandizi (EMBL, EBI); Eamonn Maguire (EMBL, EBI); Nataliya Sklyar (EMBL, EBI); Chris Taylor (EMBL, EBI); Susanna-Assunta Sansone (EMBL, EBI);
Short Abstract: The ISA infrastructure (http://isatab.sf.net) is the first freely available software suite that; (i) assists in the reporting and local management of experimental metadata, (ii) empowers researchers to use community-defined minimum information checklists (http://mibbi.org) and ontologies (http://www.obofoundry.org), and (iii) facilitates submission to international public repositories, including ArrayExpress, Pride, ENA and SRA.
Long Abstract:Click Here

Poster E10
G-language Bookmarklet: a gateway for Semantic Web, Linked Data, and Web Services
Kazuharu Arakawa- Institute for Advanced Biosciences, Keio University
Nobuhiro Kido (Institute for Advanced Biosciences, Keio University, ); Kazuki Oshita (Institute for Advanced Biosciences, Keio University, ); Masaru Tomita (Institute for Advanced Biosciences, Keio University, );
Short Abstract: G-language Bookmarklet provides an intuitive gateway interface for Semantic Web (Bio2RDF), Linked Data (NCBI Entrez, EB-eye, KEGG), and web services for biology (BLAST, G-language), which works on any browsers without the requirements for installation or specialized plugins. Freely available at: http://www.g-language.org/wiki/bookmarklet.
Long Abstract:Click Here

Poster E11
Phenotypes and Models Portal at the Rat Genome Database: Identification of disease models for physiological studies
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 DePons (Medical College of Wisconsin, Human & Molecular Genetics Center); Diane Munzenmaier (Medical College of Wisconsin, Human & Molecular Genetics Center); Simon Twigger (Medical College of Wisconsin, Physiology/Human & Molecular Genetics Center); Howard Jacob (Medical College of Wisconsin, Physiology/Human & Molecular Genetics Center);
Short Abstract: The Phenotypes and Models Portal at the Rat Genome Database (http://rgd.mcw.edu) combines existing genomic data with phenotype data to allow physiologists to visualize data, query the strain database, mine phenotype data, and compare strains through the strain medical records to identify appropriate model strains for studying disease.
Long Abstract:Click Here

Poster E12
SAHG: Structural Atlas of Human Genome
Chie Motono- National Institute of Advanced Industrial Science and technology (AIST)
Junichi Nakata (National Institute of Advanced Industrial Science and technology (AIST), Computational Biology Research Center (CBRC)); Kentaro Tomii (National Institute of Advanced Industrial Science and technology (AIST) , Computational Biology Research Center (CBRC)); Kana Shimizu (National Institute of Advanced Industrial Science and technology (AIST), Computational Biology Research Center (CBRC)); Nozomi Nagano (National Institute of Advanced Industrial Science and technology (AIST), Computational Biology Research Center (CBRC)); Tamotsu Noguchi (National Institute of Advanced Industrial Science and technology (AIST), Computational Biology Research Center (CBRC)); Hidekazu Hiroaki (Kobe University, Graduate School of Medicine); Tsuyoshi Shirai (Nagahama Institute of Bioscience and Technology, Department of Bioscience); Matsuyuki Shirota (Tohoku University, Graduate School of Information Science); Ryotaro Koike (Nagoya University, Graduate School of Information Sciences); Kengo Kinoshita (Tohoku University, Graduate School of Information Sciences); Motonori Ota (Nagoya University, Graduate School of Information Sciences);
Short Abstract: SAHG is a comprehensive database, which exhibits protein structures encoded in the human genome. SAHG (http://bird.cbrc.jp/sahg/) has been developed to present the predicted information that is useful for understanding the protein molecular function from its sequence and 3D structure.
Long Abstract:Click Here

Poster E13
Working towards a Target Landscape Knowledge base
Markella Skempri- Pfizer Ltd
Stephen Campbell (Pfizer Ltd, Information Engineering Group); Lee Harland (Pfizer Ltd, Information Engineering Group); Kevin McConnell (Pfizer Ltd, Computational Sciences Centre of Emphasis); Eric Gifford (Pfizer Ltd, Computational Sciences Centre of Emphasis);
Short Abstract: Drug target landscape data are integral in modern drug design. Correct leveraging of both biology and chemistry data will provide high quality information and prediction on polypharmacology, druggability, disease connectivity, toxicological effects and drug safety. We describe an approach to gather the appropriate information and make use of the increasing amount of data.
Long Abstract:Click Here

Poster E14
UniProt: The Universal Protein Resource
Raja Mazumder- Georgetown University
No additional authors
Short Abstract: UniProt is a comprehensive resource on protein sequences and functional annotation, produced by EBI, PIR and SIB. It provides an expertly curated database (UniProt Knowledgebase), a comprehensive sequence repository (UniProt Archive), non redundant data sets (UniProt Reference Clusters) and a metagenomics resource (UniMes). It is freely accessible at: http://www.uniprot.org
Long Abstract:Click Here

Poster E15
Generating a data platform for microarray gene expression experiments using MOLGENIS and MAGE-TAB
Alexandros Kanterakis- University Medical Center Groningen
Tomasz Adamusiak (European Bioinformatics Institute, EMBL-EBI); Juha Muilu (University of Helsinki, Institute for Molecular Medicine Finland); Helen Parkinson (European Bioinformatics Institute, EMBL-EBI); Morris A. Swertz (University of Groningen, Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute);
Short Abstract: Here we present an adaptation of the MAGE-TAB object model to the MOLGENIS environment. The result is a web application management suite that includes programmatic interfaces (R, java, web services) and import/export tools. As a repository, it contains the complete set of microarray experiment data from the ArrayExpress database.
Long Abstract:Click Here

Poster E16
PRIDB: A Protein-RNA Interaction Database
Benjamin Lewis- Iowa State University
Michael Terribilini (Elon University)Rasna Walia (Iowa State University)Jeff Ferguson (University of California, San Diego)Vasant Honavar (Iowa State University)Drena Dobbs (Iowa State University)
Short Abstract: The Protein-RNA Interaction Database (PRIDB) provides researchers with in-depth information about existing PDB structures of protein-RNA complexes and their interfaces, including an up-to-date list of all protein-RNA complexes, atomic and residue level contact information, and interaction propensity statistics for both pre-defined benchmark datasets and user-defined datasets.
Long Abstract:Click Here

Poster E17
The Reactome Reloaded
Robin Haw- Ontario Institute for Cancer Research
Michael Caudy (OICR, Informatics and Bio-computing); David Croft (EBI, Proteomics Services); Phani Garapati (EBI, Proteomics Services); Marc Gillespie (St John's University, Pharmaceutical Sciences); Bijay Jassal (EBI-, Proteomics Services); Steven Jupe (EBI-, Proteomics Services); Shahana Mahajan (NYU School of Medicine, Biochemistry); Lisa Matthews (NYU School of Medicine, Biochemistry); Bruce May (OICR, Informatics and Bio-computing); Gavin O'Kelly (EBI, Proteomics Services); Esther Schmidt (EBI, Proteomics Services); Veronica Shamovsky (NYU School of Medicine, Biochemistry); Guanming Wu (OICR, Informatics and Bio-computing); Ewan Birney (EBI, Panda Group); Henning Hermjakob (EBI, Proteomics Services); Peter D'Eustachio (NYU School of Medicine, Biochemistry); Lincoln Stein (OICR, Informatics and Bio-computing);
Short Abstract: The Reactome project is a collaboration between Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Medical Center and The European Bioinformatics Institute to develop an open-source, curated, peer-reviewed bioinformatics database of pathways and reactions in human biology.
Long Abstract:Click Here

Poster E18
ZFNGenome: A gBrowse-based tool for identifying Zinc Finger Nuclease target sites in model organisms.
Deepak Reyon- Iowa State University
Deepak Reyon (Bioinformatics and Computational Biology, Genetics, Developmental, and Cell Biology); Jessica Kirkpatrick (Iowa State University, Genetics, Developmental and Cell Biology);
Short Abstract: Zinc Finger Nucleases (ZFNs) have tremendous potential as tools to facilitate genomic modifications, such as gene knockouts or replacement by homologous recombination, and to advance both basic research and clinical applications, including gene therapy. ZFNGenome is a comprehensive resource for locating ZFN target sites in the genomes of model organisms
Long Abstract:Click Here

Poster E19
MOLGENIS: rapid generation of flexible software platforms for any genotype and phenotype experiment
Morris Swertz- University Medical Center Groningen/European Bioinformatics Institute
Joeri van der Velde (University of Groningen, Groningen Bioinformatics Center); Juha Muilu (Institute for Molecular Medicine Finland, FIMM); Tomasz Adamusiak (European Bioinformatics Institute, EMBL, Microarray Group); Martijn Dijkstra (University of Groningen, Center for Medical Biomics); Gudmundur Thorisson (University of Leicester, Department of Genetics); Danny Arends (University of Groningen, Groningen Bioinformatics Center); Anthony Brookes (University of Leicester, Department of Genetics); Ritsert Jansen (University of Groningen, Groningen Bioinformatics Center); Helen Parkinson (European Bioinformatics Institute, EMBL, Microarray Group);
Short Abstract: MOLGENIS provides bioinformaticians with a simple model to - on the push of a button – auto generate an intelligent software system for their genotypic, molecular and phenotypic data, including biologist friendly user interfaces, analysis interfaces to R and web services, a text-file exchange format and end-user documentation.
Long Abstract:Click Here

Poster E20
Web Tool OriginS
Claudio Ferreira Junior- Escola Superior de Agricultura Luís de Queiroz - Universidade de São Paulo
Marcelo Mendes Bransão (Escola Superior de Agricultura Luís de Queiroz - Universidade de São Paulo, Genetic); Marcio de Castro Silva Filho (Escola Superior de Agricultura Luís de Queiroz - Universidade de São Paulo, Genetic);
Short Abstract: Development of web search engine based on PHP architecture, which uses the standard adopted by the GENBANK / NCBI BLAST, from local databases to provide the characters and TaxID GI of various organisms and their cladistics, from its Scientific classification or TaxID.
Long Abstract:Click Here

Poster E21
locDB: Experimental annotations of localization for Homo sapiens and Arabidopsis Thaliana
Shruti Rastogi- Columbia University
No additional authors
Short Abstract: LocDB is a curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens(HS) and Arabidopsis thaliana(AT). Currently, it contains entries for 18,764 UniProt proteins (HS:13,349; AT:5,415). Each database entry gives experimentally derived information about localization using the terminology from Gene Ontology (GO) along with prediction annotations.
Long Abstract:Click Here

Poster E22
PhenoDB: A web-based database management system for storage, retrieval, visualization, and analysis of OmniLog phenotypic microarray data
Wenling Chang- The MITRE Corporation
Keri Sarver (The MITRE Corporation, Innovative Information Engineering and Biometrics); Brandon Higgs (The MITRE Corporation, Emerging Technologies Office); Timothy Read (Emory University, Human Genetics); Nichole Nolan (Naval Medical Research Center, Biological Defense Research Directorate); Kimberly Bishop-Lilly (Naval Medical Research Center, Biological Defense Research Directorate); Shanmuga Sozhamannan (Naval Medical Research Center, Biological Defense Research Directorate);
Short Abstract: PhenoDB is a web-based relational database for storage and analysis of phenotypes for multiple organisms and conditions. This open source system is standardized for OmniLog phenotypic microarray (PM) data and allows investigators to better manage and interpret the PM data.
Long Abstract:Click Here

Poster E23
Diseasome: an integrated database of genes, genetic variation, and diseases
JIN OK YANG- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
Sohyun Hwang (Korea Research Institute of Bioscience and Biotechnology (KRIBB), KOBIC);
Short Abstract: Diseasome is an integrated database of genes, genetic variation and diseases. It provides a disease thesaurus with a tree view to show the number of genes that are associated with diseases, and a browser for looking up potentially deleterious SNPs among the genes associated with specific diseases and phenotypes.
Long Abstract:Click Here

Poster E24
PRIDE, the PRoteomics IDEntifications database
Florian Reisinger- EMBL-EBI
Juan-Antonio Vizcaino (EMBL-EBI, Proteomics Services Team); Henning Hermjakob (EMBL-EBI, Proteomics Services Team); Richard Cote (EMBL-EBI, Proteomics Services Team); Rui Wang (EMBL-EBI, Proteomics Services Team); Daniel Rios (EMBL-EBI, Proteomics Services Team); Andreas Schoenegger (EMBL-EBI, Proteomics Services Team); Attila Csordas (EMBL-EBI, Proteomics Services Team);
Short Abstract: The PRoteomics IDEntifications database (PRIDE, http://www.ebi.ac.uk/pride) is a public data repository for mass spectrometry (MS) derived proteomics data. A major aim for PRIDE is the support of the peer-review process. However, PRIDE will evolve into a resource that will provide added value to the data that it contains.
Long Abstract:Click Here

Poster E25
Meeting the computational challenges of Metagenomics
Naveen Kumar- RIKEN Advanced Science Institute
Vineet Sharma (RIKEN Advanced Science Institute, Metasystems Research Team); Tulika Prakash (RIKEN Advanced Science Institute, Metasystems Research Team); Todd Taylor (RIKEN Advanced Science Institute, Metasystems Research Team);
Short Abstract: Metagenomics is the study of metagenomes recovered directly from environmental samples, generating huge amounts of sequence data for computational analysis. For this, we are developing computational resources, i) 'iMetaSys' for comprehensive automated analysis of metagenomic and single-bacterial genomic data and, ii) 'MetaBioME', for exploring 510 commercially useful enzymes in metagenomes.
Long Abstract:Click Here

Poster E26
Inferring protein-protein interactions based on conservation of interfaces in structural homologs
Manoj Tyagi- National Institutes of Health
Ratna R. Thangudu (National Institutes of Health, CBB/National Center for Biotechnology Information (NCBI)); Benjamin A. Shoemaker (National Institutes of Health, CBB/National Center for Biotechnology Information (NCBI)); Stephen H. Bryant (National Institutes of Health, CBB/National Center for Biotechnology Information (NCBI)); Thomas Madej (National Institutes of Health, CBB/National Center for Biotechnology Information (NCBI)); Anna R. Panchenko (National Institutes of Health, CBB/National Center for Biotechnology Information (NCBI));
Short Abstract: A newly developed method, Inferred Biomolecular Interaction Server (IBIS), predicts and annotates protein-protein interactions partners and binding sites by inference from structural homologs. Our method clusters similar binding sites from homologs based on their sequence and structure conservation. Binding site alignment based PSSMs along with other measures are used to rank interaction sites.
Long Abstract:Click Here

Poster E27
GeneCards Version 3: the human gene integrator
Arye Harel- Weizmann Institute of Science
Gil Stelzer (Weizmann Institute of Science, Departments of Molecular Genetics); Irina Dalah (Weizmann Institute of Science, Departments of Molecular Genetics); Naomi Rosen (Weizmann Institute of Science, Departments of Molecular Genetics); Tsippi Iny Stein (Weizmann Institute of Science, Departments of Molecular Genetics); Noam Nativ (Weizmann Institute of Science, Departments of Molecular Genetics); Iris Bahir (Weizmann Institute of Science, Departments of Molecular Genetics); Tirza Doniger (Weizmann Institute of Science, Departments of Molecular Genetics); Hagit Krug (Weizmann Institute of Science, Departments of Molecular Genetics); Alexandra Sirota-Madi (Weizmann Institute of Science, Departments of Molecular Genetics); Tsviya Olender (Weizmann Institute of Science, Departments of Molecular Genetics); Michael Shmoish (Technion - Israel Institute of Technology and Weizmann Institute of Science, Bioinformatics Knowledge Unit, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering and Departments of Molecular Genetics); Marilyn Safran (Weizmann Institute of Science, Departments of Molecular Genetics and Biological Services); Doron Lancet (Weizmann Institute of Science, Departments of Molecular Genetics );
Short Abstract: GeneCards V3, a major upgrade of the authoritative human gene compendium, has multi-faceted, much speedier search, relational database architecture and expanded annotation landscape. Its gene-set capacities, including the GeneALaCart batch query and the GeneDecks functional paralogy tool-set, leverage GeneCards' unique wealth of combinatorial annotations, and allow robust biomedical inference.
Long Abstract:Click Here

Poster E28
Source of annotations in the UniProt Knowledgebase.
Benoit BELY- EBI - European Bioinformatics Institut
No additional authors
Short Abstract: UniProt is a comprehensive resource of protein sequences and functional annotation, produced by the UniProt Consortium. UniProtKB utilises a diversity of sequence and annotation sources to ensure complete coverage of sequence space and annotated information. Computational annotation systems are essential for annotating a growing number of uncharacterised proteins.
Long Abstract:Click Here

Poster E29
ArrayExpress: Archive of Experiments and Gene Expression Atlas
Anna Farne- EBI
Helen Parkinson (EBI, Functional Genomics Group); Misha Kapushesky (EBI, Functional Genomics Group); Ugis Sarkans (EBI, Functional Genomics Group); Niran Abeygunawardena (EBI, Functional Genomics Group); Tony Burdett (EBI, Functional Genomics Group); Miroslaw Dylag (EBI, Functional Genomics Group); Ibrahim Emam (EBI, Functional Genomics Group); Emma Hastings (EBI, Functional Genomics Group); Ele Holloway (EBI, Functional Genomics Group); Nikolay Kolesnikov (EBI, Functional Genomics Group); Natalja Kurbatova (EBI, Functional Genomics Group); Margus Lukk (EBI, Functional Genomics Group); James Malone (EBI, Functional Genomics Group); Roby Mani (EBI, Functional Genomics Group); Ekaterina Pilicheva (EBI, Functional Genomics Group); Anjan Sharma (EBI, Functional Genomics Group); Eleanor Williams (EBI, Functional Genomics Group); Alvis Brazma (EBI, Functional Genomics Group);
Short Abstract: The ArrayExpress Archive is a database of more than 10,000 functional genomics experiments including gene expression, chromatin immunoprecipitation, comparative genomic hybridization and high throughput sequencing experiments. The Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of the ArrayExpress Archive.
Long Abstract:Click Here

Poster E30
Choosing a Genome Browser for a Model Organism Database: Surveying the Maize Community
Taner Sen- USDA-ARS / Iowa State University
Lisa Harper (USDA-ARS, Plant Gene Expression Center); Mary Schaeffer (USDA-ARS, Plant Genetics); Carson Andorf (USDA-ARS, Corn Insects and Crop Genomics Unit); Trent Seigfried (USDA-ARS, Corn Insects and Crop Genomics Unit); Darwin Campbell (USDA-ARS, Corn Insects and Crop Genomics Unit); Carolyn Lawrence (USDA-ARS, Corn Insects and Crop Genomic Unit);
Short Abstract: The model organism database for maize, MaizeGDB, surveyed the maize research community for their genome browser needs to prepare for displaying the maize genome. Based on their input, GBrowse was selected because of its intuitive interface and tools. Here we present survey results and our rationale of choosing GBrowse.
Long Abstract:Click Here

Poster E31
REDIdb: an upgraded bioinformatics resource for organellar RNA editing
Ernesto Picardi- University of Bari
Teresa Maria Rosaria Regina (University of Calabria, Dipartimento di Biologia Cellulare); Daniil Verbitskiy (University of Ulm, Molekulare Botanik); Axel Brennicke (University of Ulm, Molekulare Botanik); Carla Quagliariello (University of Calabria, Dipartimento di Biologia Cellulare);
Short Abstract: Editing sites annotated in primary databases such as GenBank are indicated under the "misc_feature" filed and important details such as the editing type or the nucleotide positions affected are currently omitted. REDIdb is a specialized database to store RNA editing events in their biological context. REDIdb is available at http://biologia.unical.it/py_script/REDIdb/.
Long Abstract:Click Here

Poster E32
COSMIC: Annotating whole-genome resequencing experiments in the Catalogue Of Somatic Mutations In Cancer.
Simon Forbes- Wellcome Trust Sanger Institute
Nidhi Bindal (Wellcome Trust Sanger Institute, CGP); David Beare (Wellcome Trust Sanger Institute, CGP); Andrew Menzies (Wellcome Trust Sanger Institute, CGP); Sally Bamford (Wellcome Trust Sanger Institute, CGP); Elisabeth Dawson (Wellcome Trust Sanger Institute, CGP); Rebecca Shepherd (Wellcome Trust Sanger Institute, CGP); Mingming Jia (Wellcome Trust Sanger Institute, CGP); Joyce Kok (Wellcome Trust Sanger Institute, CGP); Kenrik Leung (Wellcome Trust Sanger Institute, CGP); Charlotte Cole (Wellcome Trust Sanger Institute, CGP); Anthony Webb (Wellcome Trust Sanger Institute, CGP); Jon Teague (Wellcome Trust Sanger Institute, CGP); Peter Campbell (Wellcome Trust Sanger Institute, CGP); Michael R Stratton (Wellcome Trust Sanger Institute, CGP); P Andrew Futreal (Wellcome Trust Sanger Institute, CGP);
Short Abstract: COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://www.sanger.ac.uk/cosmic), is one of the most comprehensive systems describing somatic mutations in human cancer. The latest release includes 112,256 mutations in 452,000 cancer samples, 28 of which have undergone Illumina UHTS. COSMIC is available online and for free download in multiple formats.
Long Abstract:Click Here

Poster E33
BioXSD: the canonical XML-Schema data model for bioinformatics Web services
Matus Kalas- Bergen Center for Computational Science & University of Bergen
Pål Puntervoll (Bergen Center for Computational Science, Uni Research, 5008 Bergen, Computational Biology Unit); Alexandre Joseph (Université Lyon 1; CNRS, UMR 5086; IBCP, Institut de Biologie et Chimie des Protéines, 69367 Lyon Cedex 07, IBCP); Edita Bartaseviciute (Technical University of Denmark, 2800 Kongens Lyngby, Center for Biological Sequence Analysis, Department of Systems Biology); Armin Töpfer (Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Institute for Bioinformatics); Jon Ison (EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, European Bioinformatics Institute); Christophe Blanchet (Université Lyon 1; CNRS, UMR 5086; IBCP, Institut de Biologie et Chimie des Protéines, 69367 Lyon Cedex 07, IBCP); Kristoffer Rapacki (Technical University of Denmark, 2800 Kongens Lyngby, Center for Biological Sequence Analysis, Department of Systems Biology); Inge Jonassen (Bergen Center for Computational Science, Uni Research & University of Bergen, 5008 Bergen, Computational Biology Unit & Department of Informatics);
Short Abstract: BioXSD has been developed by the EMBRACE project partners in order to enable smooth interoperability of the world-wide bioinformatics Web services.
BioXSD aims to serve as the standard exchange formats of the basic, 'everyday' bionformatics data types: sequences, sequence annotations, alignments, references to resources (data, databases, and ontologies).
Long Abstract:Click Here

Poster E34
BioClock: a web server and database aimed for interpreting circadian rhythm
Zhen Su- China Agricultural University
Daofeng Li (State Key Laboratory of Agrobiotechnology, College of Biological Sciences); Rendong Yang (State Key Laboratory of Plant Physiology and Biochemisty, College of Biological Sciences);
Short Abstract: We established a web platform named BioClock which implemented an algorithm named ARSER for users to analysis their time-course microarray data through its web interface. In addition, we collected published time-course expression data and made BioClock as a database for circadian rhythm related data.
Long Abstract:Click Here

Poster E35
Semantic Integration of Data on Transcriptional Regulation
Julia Ponomarenko- University of California, San Diego
Michael Baitaluk (University of California, San Diego, San Diego Supercomputer Center );
Short Abstract: IntegromeDB is a semantic graph based 'deep web' data integration system that automatically captures, integrates, and manages publicly available data concerning transcriptional regulation, as well as other relevant biological information. It is accessible through the web page www.integromedb.org and the integrated research environment BiologicalNetworks at http://www.BiologicalNetworks.org.
Long Abstract:Click Here

Poster E36
An Integrated Data Explorer for Genomic Studies on Mental Disorders
Chun-Nan Hsu- University of Southern California
Jose Luis Ambite (University of Southern California, Information Sciences Institute); Shefali Sharma (University of Southern California, Information Sciences Institute); Yigal Arens (University of Southern California, Information Sciences Institute);
Short Abstract: A web-based query interface service is established to allow integrated access to heterogeneous data sources from the NIH Center for Collaborative Genetic Studies of Mental Disorders (CGSMD). These data sources are collected from decades of large-scale, high density psychiatric genetic studies for autism, bipolar disorder, schizophrenia, depression and Alzheimer's disease.
Long Abstract:Click Here

Poster E37
The Annotation Clearinghouse – Displaying many third party annotations for proteins
Andreas Wilke- University of Chicago
Elizabeth M. Glass (Argonne National Laboratory, Mathematics and Computer Science Division); Ross Overbeek (Fellowship for the Interpretation of Genomes, ); Folker Meyer (Argonne National Laboratory, Mathematics and Computer Science Division);
Short Abstract: Comparative analysis is the key approach to bioinformatics analysis. Data used to perform such analyses against are housed in various bioinformatics databases, most of which use different identifiers. We will present a resource that integrates these databases, allowing for comprehensive sequence analysis. Metagenomic samples will be presented as an example.
Long Abstract:Click Here

Poster E38
TreeBASE2: Sharing Alignments, Trees, And the Analyses That Generated Them
Hilmar Lapp- National Evolutionary Synthesis Center (NESCent)
Jon Auman (National Evolutionary Synthesis Center (NESCent), Informatics); Lucie Chan (San Diego Supercomputer Center, ); Mark Dominus (University of Pennsylvania, ); Vladimir Gapeyev (National Evolutionary Synthesis Center (NESCent), Informatics); Youjun Guo (Yale University, Peabody Museum); William Piel (Yale University, Peabody Museum); Jin Ruan (San Diego Supercomputer Center, ); Rutger Vos (University of Reading, ); Val Tannen (University of Pennsylvania, );
Short Abstract: TreeBASE (http://treebase.org) is a digital repository of phylogenetic data and trees. A completely re-engineered version, released in March 2010, features major improvements of the user interface and the data and metadata it can manage. It also exposes its holdings to the semantic web and to programmatic access.
Long Abstract:Click Here

Poster E39
Gene annotation data in a “schema-free” paradise
Chunlei Wu- Genomics Institute of the Novartis Research Foundation
No additional authors
Short Abstract: We recently migrated our gene annotation database (~300K genes) from Oracle to "schema-free" CouchDB. The entire annotation of each gene is stored as a document with gene ID (Entrez/Ensembl gene ID) as the key. This migration greatly simplifies data loading and data queries, and gains impressive query performance.
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Poster E40
Soybean Knowledge Base (SoyKB) : A Web Resource for Soybean Translational Genomics
Trupti Joshi- University of Missouri
Qiuming Yao (University of Missouri, Computer Science); Levi D. Franklin (University of Missouri, Computer Science ); Gary Stacey (University of Missouri, Division of Plant Sciences ); Henry Nguyen (University of Missouri, Division of Plant Sciences ); Dong Xu (University of Missouri, Computer Science);
Short Abstract: A hallmark of modern biology is that most experiments are now done on a whole genome scale generating tremendous amounts of omics data. These data are massive and often very complex in nature, thereby generating the need for extensive storage, detailed computational analyses, fast retrieval and efficient integration, for a better understanding and hypothesis generation.

Towards this, we have developed Soybean Knowledge Base (SoyKB), a comprehensive all-inclusive web resource for soybean. SoyKB is designed to handle the storage and integration of the genomics, microarray, transcriptomics, proteomics and metabolomics data along with the pathway information. It has four modules including the main mySQL database module at the back end that incorporates and integrates all the soybean genomics and omics data from various experiments. It is designed to contain information on 4 different entities namely genes, miRNAs, metabolites and SNPs. The other three front-end modules are web interface, genome browser and pathway integration.

SoyKB has four tiers of registration options which control the different levels of access to the public and private data. Users can also utilize the website by submitting their data prior to publication and provide links for the reviewers to access. The data will be kept confidential and the user will have control to make it publicly available upon publication. It allows users of certain levels to share their expertise by adding comments to the data, which are visible to all members of the community.

Soybean Knowledge Base (SoyKB) can be accessed at http://soykb.org/
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Poster E41
BISSAP, Biological Sequence Submission Application for Patents
Stephane Nauche- European Patent Office
Bartosz Kondratowicz (EPO, IQ Life sciences); Ana Richart de la Torre (EPO, IQ Life sciences); Hélène Courrier (EPO, IQ Life sciences); wojciech Tomanik (EPO, IQ Life sciences); Menaka Narayasamy (EBI, Text mining);
Short Abstract: The Biological Sequence Submission Application for Patents (BiSSAP) is a tool developed by the European Patent Office in collaboration with the European Bioinformatics Institute. BiSSAP handles preparation of biological sequences sequences and their verification for submission as a part of a patent application. Conversion between supported formats is an additional functionality
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Poster E42
Adaptable Data Management for the Research Enterprise
Sarah Killcoyne- Institute for Systems Biology
John Boyle (Sr Research Scientist, Shmulevich Lab, Computational Biology); Sarah Killcoyne (Project Manager/Sr Software Engineer, Shmulevich Lab, Computational Biology);
Short Abstract: The life sciences are continually evolving. Due to the uncertainties of research, changes occur rapidly, making the development and adoption of generic integration and data management software frameworks challenging. The Addama service architecture has been designed to: provide a flexible means to integrate a variety of high and low throughput data; process it using standard tools and applications as well as ad-hoc analysis tools; share data and tools to enable simpler collaboration through standard web tools. This talk will show how we've used Addama to support three major "big science" research projects with important implications human health, including: characterization of the human proteome; a large collaborative investigation into the innate immune system to understand and fight (re)emerging infectious diseases; identifying genomic dysregulations in more than 20 cancers.
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