Technology Track Presentation ScheduleTechnology Track: TT01 Sunday, July 11: 10:45 a.m. - 11:10 a.m. DASS-GUI – a new data mining toolRoom: 306 Presenting author: Thomas Wilhelm, Institute of Food Research, United Kingdom Abstract: Biological research will benefit from sophisticated mining of large 'omics' data. We demonstrate the data mining tool DASS-GUI (www.ifr.ac.uk/dass/gui), using the case study 'Identification and validation of protein complexes'. DASS-GUI allows pattern identification and additional analyses. It has two unique features, handling of multi-sets and calculation of statistical significances. Presentation PDF: http://www.iscb.org/uploaded/css/56/16831.pdf TOP Technology Track: TT02 Sunday, July 11: 10:45 a.m. - 11:10 a.m. Detection of functionally related proteins with Transitivity ClusteringRoom: 309 Presenting author: Jan Baumbach, Max Planck Institute for Informatics, Germany Abstract: Partitioning biomedical data objects into groups, such that objects in each cluster share common traits, is a long-standing challenge. Here, we introduce Transitivity Clustering. We demonstrate its value exemplarily for protein sequence clustering tasks, i.e. we illustrate how our approach aids at each point in a typical data analysis workflow. Presentation PDF: http://www.iscb.org/uploaded/css/56/18442.pdf TOP Technology Track: TT03 Sunday, July 11: 11:15 a.m. - 11:40 a.m. GenAMap: An integrated analytic and visualization software platform for structured GWA and eQTL analysisRoom: 306 Presenting author: Ross Curtis, Carnegie Mellon University, United States Abstract: GenAMap supports efficient mapping of genome-wide markers to traits structured as a network, time series, or hierarchy. Novel structured sparse regression techniques such as GFLasso, as well as other classical methods, are supported. GenAMap processes large datasets using parallel computing. Natural visualization schemes facilitate interpretation of the results. Presentation PDF: http://www.iscb.org/uploaded/css/56/18465.pdf TOP Technology Track: TT04 Sunday, July 11: 11:15 a.m. - 11:40 a.m. Divining Systems Biology Knowledge from High-throughput Experiments Using EGANRoom: 309 Presenting author: Jesse Paquette, University of California, San Francisco, United States Abstract: EGAN is a software tool that allows a biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships and meta-data. EGAN provides comprehensive, automated calculation of meta-data enrichment statistics for experimentally-derived gene lists and direct links to web resources and literature. Presentation PDF: http://www.iscb.org/uploaded/css/56/18452.pdf TOP Technology Track: TT05 Sunday, July 11: 11:45 a.m. - 12:40 p.m. Computational Biology at PfizerRoom: 306 Presenting author: Enoch Huang, Pfizer, United States Abstract: An overview of the computational biology discipline within Pfizer, including examples of how it positively influences drug discovery efforts. Presentation PDF: http://www.iscb.org/uploaded/css/56/18894.pdf TOP Technology Track: TT06 Sunday, July 11: 11:45 a.m. - 12:10 p.m. The Universal Protein Resource (UniProt)Room: 309 Presenting author: Samuel Patient, EMBL-EBI, United Kingdom Abstract: UniProt is the central resource for storing and interconnecting information from large and disparate sources, and the most comprehensive catalog of protein sequence and functional annotation. The demonstration will cover a brief description of the UniProt databases and methods for accessing UniProt data via our website. Presentation PDF: http://www.iscb.org/uploaded/css/56/18454.pdf TOP Technology Track: TT07 Sunday, July 11: 12:15 p.m. - 12:40 p.m. Novel Ligand Classification Algorithm and Application on Modeling Functionality for 5HT1A GPCR LigandsRoom: 309 Presenting author: Chao Ma, University of Pittsburgh, United States Abstract: We have developed a novel algorithm, Ligand Classifier of Adaptively Boosting Ensemble Decision Stump (LiCABEDS), and validated through ligand functionality predictions, showing average 90% accuracy in classifying agonists/antagonists of 5HT1A GPCR ligands. Implemented in user-friendly interface, LiCABEDS also demonstrates its robustness, flexibility and interpretability in modeling quantitative structure-property relationship. Presentation PDF: http://www.iscb.org/uploaded/css/56/18457.pdf TOP Technology Track: TT08 Sunday, July 11: 2:30 p.m. - 3:25 p.m. InterPro protein sequence analysis and classificationRoom: 306 Presenting author: Sarah Hunter, European Bioinformatics Institute, United Kingdom Abstract: InterPro is an integrated database of predictive protein "signatures" used for the classification and annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains and sites. This session explains the best ways to interpret functional data using InterPro. Presentation PDF: http://www.iscb.org/uploaded/css/56/18892.pdf TOP Technology Track: TT09 Sunday, July 11: 2:30 p.m. - 2:55 p.m. Sequence clustering program CD-HIT and its applications in next-generation sequencesRoom: 309 Presenting author: Weizhong Li, University of California San Diego, United States Abstract: CD-HIT (http://cd-hit.org) is a widely used sequence clustering program. We will show advanced usage of CD-HIT and newly implemented web server. We will demonstrate applications including removal of redundant sequences, family analysis, metagenomic data clustering, rRNA analysis, identification of pyrosequencing artifacts, and improving next-generation sequence assembly by clustering analysis. Presentation PDF: http://www.iscb.org/uploaded/css/56/18460.pdf TOP Technology Track: TT10 Sunday, July 11: 3:00 p.m. - 3:25 p.m. Demonstration of The Pathway Tools Software and BioCyc DatabasesRoom: 309 Presenting author: Peter Karp, Harvard Medical School, United States Abstract: Pathway Tools provides an array of capabilities for storing and analyzing integrated collections of genomic and metabolic information. It supports development of organism-specific databases (DBs) that integrate many bioinformatics datatypes. It supports querying, scientific visualization, web publishing and dissemination of those organism-specific DBs. It performs multiple computational inferences on annotated genomes. Presentation PDF: http://www.iscb.org/uploaded/css/56/18632.pdf TOP Technology Track: TT11 Sunday, July 11: 3:30 p.m. - 4:25 p.m. BIOBASE Knowledge Libraryª and ExPlainª Analysis System: A data analysis platform for life science researchers.Room: 306 Presenting author: Raymond DiDonato, BIOBASE Corporation, Abstract: The BIOBASE Knowledge Libraryª is a database and analysis platform for biomarker and drug target discovery, as well as yeast and plant research. It includes the award-winning ExPlainª Analysis system, which uses TRANSFAC¨ DNA binding data to help researchers find upstream signaling events leading to differential gene expression. Presentation PDF: http://www.iscb.org/uploaded/css/56/18541.pdf TOP Technology Track: TT12 Sunday, July 11: 3:30 p.m. - 3:55 p.m. BioCatalogue: The curated catalogue of Life Science Web ServicesRoom: 309 Presenting author: Jiten Bhagat, University of Manchester, United Kingdom Abstract: By providing an open platform for both service providers and service users, the BioCatalogue has become an essential tool in the area of biological web services. We will present the BioCatalogue and its latest APIs, currently used by several project such as Taverna (http://www.taverna.org.uk/) and the NCRI (http://www.ncri-onix.org.uk/). Presentation PDF: http://www.iscb.org/uploaded/css/56/18479.pdf TOP Technology Track: TT13 Sunday, July 11: 4:00 p.m. - 4:25 p.m. Cytoscape 2.7Room: 309 Presenting author: Scooter Morris, UCSF, United States Abstract: We will demo some of the features of the latest version of Cytoscape, 2.7 along with new and recently enhanced plugins Presentation PDF: http://www.iscb.org/uploaded/css/56/18503.pdf TOP Technology Track: TT14 Monday, July 12: 10:45 a.m. - 11:10 a.m. Challenging algorithms and comprehensive databases in protein structure and functionRoom: 306 Presenting author: Michael Gromiha, CBRC, AIST, Japan Abstract: We have developed comprehensive databases and competitive algorithms for understanding the structure and function of proteins. Our methods include (i) prediction protein subcellular localization, transmembrane proteins/segments, disordered proteins/regions, and protein tertiary structures. Major databases are enzyme catalytic mechanisms, membrane protein function and structural atlas of human genome. Availability: http://www.cbrc.jp/eng/result/database.eng.html. Presentation PDF: http://www.iscb.org/uploaded/css/56/18506.pdf TOP Technology Track: TT15 Monday, July 12: 10:45 a.m. - 11:10 a.m. Jalview: Past, Present and Future.Room: 309 Presenting author: James Procter, University of Dundee, United Kingdom Abstract: In this technology track presentation, we will demonstrate the capabilities of the Jalview alignment visualization, editing and analysis system, and describe how our new programme of development will enable Jalview's users to do more with Jalview in the future. Presentation PDF: http://www.iscb.org/uploaded/css/56/18507.pdf TOP Technology Track: TT16 Monday, July 12: 11:15 a.m. - 11:40 a.m. Software for RNA and Next-gen Sequencer AnalysisRoom: 306 Presenting author: Paul Horton, Computational Biology Research Center, AIST, Japan Abstract: We introduce several new computational methods for the next-gen sequencer age. RECOUNT corrects tag abundance. LAST is a faster replacement for BLAST. CentroidFold predicts RNA 2' structure, fRNAdb holds information on functional RNA's, and miRRim predicts miRNA foldbacks. More at http://cbrc.jp/. Presentation PDF: http://www.iscb.org/uploaded/css/56/18528.pdf TOP Technology Track: TT17 Monday, July 12: 11:15 a.m. - 11:40 a.m. Musite: Global Prediction of General and Kinase-Specific Phosphorylation SitesRoom: 309 Presenting author: Jianjiong Gao, University of Missouri, United States Abstract: We will demonstrate a novel open-source software tool, Musite, specifically designed for large-scale prediction of both general and kinase-specific phosphorylation sites. Musite significantly outperforms existing tools for predicting general phosphorylation sites and is at least comparable to those for predicting kinase-specific phosphorylation sites. Musite is available at http://musite.sourceforge.net/. Presentation PDF: http://www.iscb.org/uploaded/css/56/18518.pdf TOP Technology Track: TT18 Monday, July 12: 11:45 a.m. - 12:10 p.m. Mobyle: An integrated bioinformatics platform for performing web-based analysesRoom: 306 Presenting author: Herve Menager, Institut Pasteur, France Abstract: This presentation demonstrates the Mobyle platform to perform online bioinformatics analyses, focusing on the various aspects that improve the experience of the user. It outlines the features that enable to quickly access tools and perform analyses, as well as the tools that accelerate the publication, configuration, and maintenance of services. Presentation PDF: http://www.iscb.org/uploaded/css/56/18529.pdf TOP Technology Track: TT19 Monday, July 12: 11:45 a.m. - 12:10 p.m. Chipster: Biologist-friendly analysis software for high-throughput dataRoom: 309 Presenting author: Eija Korpelainen, CSC - IT Centre for Science, Finland Abstract: Chipster (http://chipster.csc.fi/) offers a biologist-friendly access to up-to-date analysis methods and efficient visualizations for microarray and next generation sequencing data. Users can save and share automatic workflows, which provides an easy way for bioinformaticians to collaborate with biologists. Chipster is open source and the server installation packages are freely available. Presentation PDF: http://www.iscb.org/uploaded/css/56/18532.pdf TOP Technology Track: TT20 Monday, July 12: 12:15 p.m. - 12:40 p.m. Taxonomical and functional analysis of metagenome data using MEGAN4Room: 306 Presenting author: Suparna Mitra, University of Tuebingen , Germany Abstract: This presentation demonstrates functional analysis of metagenome-, metatranscriptome- and metaproteome data using MEGAN4. Genes are mapped onto functional roles that are grouped into subsystems, based on the SEED system. All navigation and analysis tools that were previously provided only for taxonomical analysis can now also be used for functional analysis. Presentation PDF: http://www.iscb.org/uploaded/css/56/18534.pdf TOP Technology Track: TT21 Monday, July 12: 12:15 p.m. - 12:40 p.m. Web-based gene function prediction and interactive network visualization with GeneMANIARoom: 309 Presenting author: Gary Bader, University of Toronto, Canada Abstract: GeneMANIA is a webserver that performs gene function predictions on-the-fly (http://www.genemania.org). Users enter a gene list, GeneMANIA extends the list and generates a composite network in seconds. A novel network visualization component, Cytoscape Web, has been incorporated into GeneMANIA to help users interpret the predictions. Presentation PDF: http://www.iscb.org/uploaded/css/56/18538.pdf TOP Technology Track: TT22 Monday, July 12: 2:30 p.m. - 2:55 p.m. SysMO-DB: Sharing and Exchanging Data and Models in Systems BiologyRoom: 306 Presenting author: Katy Wolstencroft, University of Manchester, United Kingdom Abstract: SysMO-DB is a web-based resource for sharing data, models, protocols, expertise and analyses in Systems Biology. It is a pragmatic solution to the sharing and management of data and models in multidisciplinary research projects across distributed locations. Presentation PDF: http://www.iscb.org/uploaded/css/56/18540.pdf TOP Technology Track: TT23 Monday, July 12: 2:30 p.m. - 2:55 p.m. Tools of PRIDERoom: 309 Presenting author: Florian Reisinger, EMBL-EBI, United Kingdom Abstract: In this tech track we focus on the PRoteomics IDEntifications data repository (PRIDE) and its associated tools. We will show how the new PRIDE Converter tool greatly simplifies data submission to PRIDE and demonstrate tools like the semantic XML validator, a new DAS server and its use in DASTY2. Presentation PDF: http://www.iscb.org/uploaded/css/56/18544.pdf TOP Technology Track: TT24 Monday, July 12: 3:00 p.m. - 3:25 p.m. CAMERA: Metagenomic Resources and ToolsRoom: 306 Presenting author: Shulei Sun, University of California, San Diego, United States Abstract: CAMERA provides metagenomic data and metadata, computational resources, bioinformatics tools, and so on freely to all members of the scientific community to allow key scientific questions to be addressed. Presentation PDF: http://www.iscb.org/uploaded/css/56/18546.pdf TOP Technology Track: TT25 Monday, July 12: 3:00 p.m. - 3:25 p.m. Using the NCIBI Suite of Integrated Tools and DataRoom: 309 Presenting author: James Cavalcoli, National Center for Integrative Biomedical Informatics, United States Abstract: NCIBI develops and integrates databases and software applications which help scientists retrieve articles based on relevant interactions and concepts, find conceptually similarly gene sets (enrichment), visually explore protein interaction networks and pathways, and explore metabolomic data using publicly available electronic biological data as well as experimentally derived data. Presentation PDF: http://www.iscb.org/uploaded/css/56/18549.pdf TOP Technology Track: TT26 Monday, July 12: 3:30 p.m. - 3:55 p.m. NGS Analyses with Galaxy on the CloudRoom: 306 Presenting author: Anton Nekrutenko, galaxyproject.org, United States Abstract: In this Technology Track we will highlight newly developed Galaxy on the Cloud functionality for the analysis of NGS data. Presentation PDF: http://www.iscb.org/uploaded/css/56/18552.pdf TOP Technology Track: TT27 Monday, July 12: 3:30 p.m. - 3:55 p.m. The Neuroscience Information Framework (NIF): A Unified Semantic Framework for Discovery and Integration of Biomedical Data and Resources on the WebRoom: 309 Presenting author: Jeffrey Grethe, University of California, San Diego, United States Abstract: The Neuroscience Information Framework (NIF; http://neuinfo.org) enables semantic discovery and access to a large collection of open source research data, contained in databases and structured web resources. We will demonstrate key features of the NIF and how they work together to provide a comprehensive data discovery solution for biomedical researchers. Presentation PDF: http://www.iscb.org/uploaded/css/56/18554.pdf TOP Technology Track: TT28 Monday, July 12: 4:00 p.m. - 4:25 p.m. Sample tracking and automated data processing in Galaxy for NGS facilitiesRoom: 306 Presenting author: Anton Nekrutenko, galaxyproject.org, United States Abstract: In this demonstration we will simulate a NGS Core Facility wit with its sample flow from receiving samples to providing analyzed data to customers. This open source solution was designed to help code facilities to manage overwhelming NGS workflows. Presentation PDF: http://www.iscb.org/uploaded/css/56/18555.pdf TOP Technology Track: TT29 Monday, July 12: 4:00 p.m. - 4:25 p.m. The Genome Analysis Toolkit (GATK)Room: 309 Presenting author: Aaron McKenna, The Broad Institute of Harvard and MIT, United States Abstract: The Genome Analysis Toolkit (GATK) is a powerful framework for working with next-generation sequencing data, enabling scientists to quickly create custom sequencer-based analyses tools. Many tools such as Bayesian genotypers, alignment-correction algorithms, and depth-of-coverage metrics have already been developed using the GATK, and are freely available to the public. Presentation PDF: http://www.iscb.org/uploaded/css/56/18556.pdf TOP Technology Track: TT30 Tuesday, July 13: 10:45 a.m. - 11:10 a.m. The Model SEED pipeline for Genome Scale Metabolic ModelingRoom: 306 Presenting author: Matt DeJongh, Hope College/Argonne National Laboratory, United States Abstract: The Model SEED is a web-based resource for high-throughput generation, optimization, and analysis of genome-scale metabolic models (available at http://www.theseed.org/models/). We will demonstrate how to generate metabolic models from genome sequences, and view, analyze and download the models. Users may load their own genome sequences for model generation. Presentation PDF: http://www.iscb.org/uploaded/css/56/18558.pdf TOP Technology Track: TT31 Tuesday, July 13: 10:45 a.m. - 11:10 a.m. Enabling World Class Research through Innovative Data Management StrategiesRoom: 309 Presenting author: Patrick Osborne, Hewlett Packard, United States Abstract: IT plays a significant role in supporting the vision of personalized medicine where clinicians are able to make treatment and medication decisions based on patient’s genetic profile. Learn how HP works with health and life science customers to build an IT foundation, including the right scalable storage solution, to support their vision of personalized medicine. Presentation PDF: http://www.iscb.org/uploaded/css/56/19642.pdf TOP Technology Track: TT32 Tuesday, July 13: 11:15 a.m. - 11:40 a.m. GMOD Presents GBrowse 2.0 and JBrowseRoom: 306 Presenting author: Scott Cain, Ontario Institute for Cancer Research, Canada Abstract: GBrowse2 and JBrowse are open source, web-based genome browsers produced as part of the GMOD project. Here we present new features to both browsers, including increased speed and ability to work with next generation sequencing data. Presentation PDF: http://www.iscb.org/uploaded/css/56/18565.pdf TOP Technology Track: TT33 Tuesday, July 13: 11:15 a.m. - 11:40 a.m. Ontology-based Web Services for Data Annotation and IntegrationRoom: 309 Presenting author: Patricia Whetzel, Stanford University, United States Abstract: Ontologies provide domain knowledge to drive data integration and information retrieval. We present a set of Web services to suggest ontologies for data annotation using the Ontology Recommender, to annotate data using the NCBO Annotator, and to extract ontology-indexed publicly available data using the NCBO Resource Index. Presentation PDF: http://www.iscb.org/uploaded/css/56/18568.pdf TOP Technology Track: TT34 Tuesday, July 13: 11:45 a.m. - 12:40 p.m. Killer App Award SessionRoom: 306 Presenting author: Anita de Waard, Elsevier, Netherlands Abstract: (1) Thomas Abeel 'GenomeView: Visualizing the next generation of sequencing data' http://genomeview.org; (2) Alberto Roca "Visualizing protein family nanoanatomy using ProfileGrids" http://www.profilegrid.org; (3) Venkata Satagopam "bioCompendium: high-throughput experimental data analysis platform" (http://biocompendium.embl.de) (4) Ikuo Uchiyama "RECOG: Research Environment for Comparative Genomics" http://mbgd.nibb.ac.jp/RECOG. The winner will receive an Apple iPad. Presentation PDF: http://www.iscb.org/uploaded/css/56/16989.pdf TOP Technology Track: TT35 Tuesday, July 13: 11:45 a.m. - 12:10 p.m. EMBRACE, BioXSD, EDAM: How to provide smoothly interoperable bioinformatics tools on the World Wide Web of ServicesRoom: 309 Presenting author: Matus Kalas, CBU, BCCS, Norway Abstract: This technical presentation gives an overview of the proposed standards for achieving smooth interoperability among bioinformatics tools and data sources. These recommendations have been developed within the European EMBRACE project and include common exchange formats (BioXSD) and common ontology for describing bioinformatics Web services and their data (EDAM). Presentation PDF: http://www.iscb.org/uploaded/css/56/18569.pdf TOP Technology Track: TT36 Tuesday, July 13: 12:15 p.m. - 12:40 p.m. MOLGENIS: rapid prototyping of biosoftware at the push of a buttonRoom: 309 Presenting author: Morris Swertz, University of Groningen, Netherlands Abstract: MOLGENIS automatically generates flexible web platforms for all possible genomic, molecular and phenotypic experiments from easy to create models. Each generated MOLGENIS provides biologist friendly user interfaces, semantic interfaces to RDF, SPARQL and ontologies, processing interfaces to R and SOAP/REST web services, a text-file exchange format and full documentation. Presentation PDF: http://www.iscb.org/uploaded/css/56/18574.pdf TOP Technology Track: TT37 Tuesday, July 13: 2:15 p.m. - 2:40 p.m. VisANT: multi-scale network visualization, analysis and inference based on the Gene OntologyRoom: 306 Presenting author: Zhenjun Hu, Boston University, United States Abstract: VisANT performs deep integration of Gene Ontology (GO) for the network analysis: (i) Interactive GO Explorer to navigate the GO hierarchy. (ii) Automatic grouping of genes using GO terms to facilitate the multi-scale visualization and analysis. (iii) Flexible annotation schema. (iv) Finding over-represented GO terms and expression enriched GO modules Presentation PDF: http://www.iscb.org/uploaded/css/56/18599.pdf TOP Technology Track: TT38 Tuesday, July 13: 2:45 p.m. - 3:10 p.m. Tools for Functional Genomics: Synergizer, FuncAssociate and FuncBaseRoom: 306 Presenting author: John Beaver, SRI International, United States Abstract: Three tools developed by the Roth Lab (Harvard Medical School) will be presented: 1) Synergizer, a biological identifier mapping service; 2) FuncAssociate, a functional enrichment analysis tool; and 3) FuncBase, a quantitative gene function prediction interactive repository. Presentation PDF: http://www.iscb.org/uploaded/css/56/18476.pdf TOP Technology Track: TT39 Tuesday, July 13: 3:15 p.m. - 3:40 p.m. Room: 306 Presenting author: Dominic Clark, The EMBL-EBI Industry Programme, Abstract: This presentation will provide an overview and demonstration of some of the means by which EMBL-EBI interacts with industry stakeholders including pre-competitive projects.We will also preview the annual forum for SMEs in Munich, October 2010. Presentation PDF: http://www.iscb.org/uploaded/css/56/18896.pdf TOP |
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Roland Krause: "Presentation of resources at the CBRC, Tokyo."
Roland Krause: "Classification of beta-barrel membrane proteins."
Roland Krause: "Positive/negative test data sets for beta-barrel membrane proteins, comparison of existing methods."
Roland Krause: "Prediction of membrane strands and important functional residues. Discrimination of transporters. http://www.ncbi.nlm.nih.gov/pubmed/20196081. Webserver available."
Roland Krause: "Prediction of subcellular location at wolfpsort.org."
Roland Krause: "Speaker: Motone on Forte: Protein structure prediction using profile-profile comparisons. Ranked 3rd in CASP. Web service."
Roland Krause: "Poodle: Disorder prediction, important to protein function. Flavors for the prediction algorithm for different aspects of disorder."
Roland Krause: "EZCatDB: Hierarchical classification of enzyme reaction based on catalytic site and mechanism"
Roland Krause: "SAHG: Structure prediction for multi-domain proteins including disordered regions"