Technology Track: TT01
The Spanish National Bioinformatics Institute (INB)
Monday, June 29 - 10:45 a.m. - 11:10 a.m.
Room: C8
Presenting author: Allan Orozco, The Spanish National Bioinformatics Institute (INB), Spain
Abstract:
The Spanish National Bioinformatics Institute (INB, www.inab.org) is a platform that supports Spanish genome projects in areas of health and agriculture. At the technical level it maintains a large and controlled collection of Bioinformatics web services, several web- based systems for genome analysis, functional and population genomics, and active training activity.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11836.pdf
Technology Track: TT02
ELIXIR: A sustainable infrastructure for biological information in Europe
Monday, June 29 - 10:45 a.m. - 11:40 a.m.
Room: C7
Presenting author: Janet Thornton, European Bioinformatics Institute, United Kingdom
Abstract:
Professor Janet Thornton, Director of EBI will give a presentation entitled ELIXIR: A sustainable infrastructure forbiological information in Europe. Another senior figure TBA will give a talk entitiled Implications of ELIXIR for World Bioinformatics.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11563.pdf
Planning Project for EU infrastructure for bioinformatics. Goals: Co-ordinated data resources, integration & interoperability of data, links to data in other domains, open access to data, enhance euro competitiveness in bioscience, address need for increased funding and its co-ordination. - Cass JohnstonTechnology Track: TT03
caBIG Molecular Analysis Tools Knowledge Center
Monday, June 29 - 11:15 a.m. - 11:40 a.m.
Room: C8
Presenting author: Zhong Li, caBIG Molecular Analysis Tools Knowledge Center, United States
Abstract:
As part of the Enterprise Support Network of caBIG, the Molecular Analysis Tools Knowledge Center (MATKC) offer expertise, knowledge resources, and tools in molecular data management and analysis to the community. The MATKC has established a vibrant online community for the following four tools: caArray, caIntegrator, geWorkbench, and GenePattern.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11778.pdf
Technology Track: TT04
In silico drug repositioning and combinatorial therapy design
Monday, June 29 - 11:45 a.m. - 12:40 p.m.
Room: C8
Presenting author: Anton Yuryev, Ariadne Genomics, United States
Abstract:
We describe a strategy to find new disease indications for existing drugs and design combinatorial therapies by selecting drugs with synergistic therapeutic profiles and compatible toxicity profiles. As a use case, we find new treatment glioblastoma using exclusively in silico methods.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11827.pdf
Technology Track: TT05
The SSAHA2 software pipeline for the mapping of DNA sequencing reads and genotype calling
Monday, June 29 - 11:45 a.m. - 12:10 p.m.
Room: C7
Presenting author: Hannes Ponstingl, Wellcome Trust Sanger Institute, United Kingdom
Abstract:
The SSAHA2 software pipeline efficiently maps DNA sequencing reads onto a genomic reference sequence. A genotype call of the consensus sequence can be produced taking into account a heuristic score of the mapping quality. Reads from most types of sequencing platforms are supported including paired-end sequencing reads.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11850.pdf
Technology Track: TT06
EMBOSS: European Molecular Biology Open Software Suite
Monday, June 29 - 12:15 p.m. - 12:40 p.m.
Room: C7
Presenting author: Peter Rice, European Bioinformatics Institute, United Kingdom
Abstract:
EMBOSS is a mature package of software tools developed in C for the molecular biology community. It includes a comprehensive set of applications for molecular sequence analysis and other tasks and integrates popular third-party software packages under a consistent set of interfaces.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11851.pdf
Technology Track: TT07
An new bioinformatics analysis tools framework at EMBL-EBI
Monday, June 29 - 2:15 p.m. - 2:40 p.m.
Room: C8
Presenting author: Mickael Goujon, European Bioinformatic Institute, United Kingdom
Abstract:
The European Bioinformatics Institute provides a broad range of analytical services to the public. A new framework has been developed to improve the accessibility of these services and introduce several new features which improve the user experience.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11762.pdf
Technology Track: TT08
PaperMaker: Automatic analysis and quality check for biomedical scientific literature
Monday, June 29 - 2:15 p.m. - 2:40 p.m.
Room: C7
Presenting author: Dietrich Rebholz-Schuhmann, European Bioinformatics Institute, United Kingdom
Abstract:
PaperMaker is a Web based service that analyses biomedical scientific publications to give authors feedback on the appropriate use of terminology and references. At the end of the interactive analysis, the author receives an improved version of his document. PaperMaker accepts Word documents and produces structured digital abstracts.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11860.pdf
Technology Track: TT09
Your large data: query, process, share - in no time
Monday, June 29 - 2:45 p.m. - 3:10 p.m.
Room: C8
Presenting author: Tomasz Mikolajczyk, GridwiseTech, Poland
Abstract:
Efficient management of large data and databases is the key challenge in Bioinformatics today. rnHow to design a performant data management system? Accelerate an existing database? Share in fully controlled yet flexible fashion?rnGridwiseTech is the scalability specialist, helping here with knowledge and software. Our customer accelerated queries 10x.
Presentation PDF: http://www.iscb.org/uploaded/css/36/12728.pdf
Technology Track: TT10
The ISA-infrastructure: a software suite to annotate and manage experimental metadata
Monday, June 29 - 2:45 p.m. - 3:10 p.m.
Room: C7
Presenting author: Philippe Rocca-Serra & Eamonn Maguire, EMBL-EBI, United Kingdom
Abstract:
We present standards-supportive infrastructure for managing multi-domain experimental metadata comprising: (1) a data capture/editing tool (ISAcreator http://isatab.sourceforge.net/isacreator.html) that implements a format (ISA-Tab http://isatab.sf.net), reporting guidelines (http://www.mibbi.org) and ontologies (http://www.obofoundry.org); (2) a validator (ISAvalidator); (3) a database (BioInvestigationIndex); (4) a converter (ISAconverter); and (5) a BioConductor analysis package (R-ISApackage).
Presentation PDF: http://www.iscb.org/uploaded/css/36/11853.pdf
Technology Track: TT11
Concept Web Alliance (CWA)
Monday, June 29 - 3:15 p.m. - 4:10 p.m.
Room: C8
Presenting author: Barend Mons, Netherlands Bioinformatics Centre, Netherlands
Abstract:
NBIC is one of the founding members of the Concept Web Alliance (CWA)
Presentation PDF: http://www.iscb.org/uploaded/css/36/12705.pdf
Technology Track: TT12
SIMBioMS - a suite of software for data collection, harmonisation and analysis in large-scale biomedical genomics projects
Monday, June 29 - 3:15 p.m.- 3:40 p.m.
Room: C7
Presenting author: Maria Krestyaninova, EMBL-EBI, United Kingdom
Abstract:
SIMBioMS (simbioms.org)- a multi-component system for management of biomedical data and metadata from the moment of design to the stage of analysis. While SIMBioMS features some classical LIMS functionality, the main area for its usage and application - fast and efficient biomedical data exchange in multi-partner research projects.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11856.pdf
Technology Track: TT13
Reflect: Augmented Browsing for the Life Scientist
Monday, June 29 - 3:45 p.m. - 4:10 p.m.
Room: C7
Presenting author: Sean O'Donoghue, EMBL, Germany
Abstract:
Reflect (http://reflect.ws) is a new, free service that highlights protein and chemical names in any web page, giving access to more detailed information (Pafilis et al., Nature Biotechnology, in press). We demonstrate how Reflect can be used by end-users, and also via API-access to enhance the value of biochemically-related web-content.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11870.pdf
Technology Track: TT14
Color Space Analysis in the SOLiDª System: the Theory, Advantages and Solutions
Tuesday, June 30 - 10:45 a.m. - 11:40 a.m.
Room: C8
Presenting author: Jonathan Mangion, Applied Biosystems, Sweden
Abstract:
SOLiDª System provides significant advantages for system accuracy and downstream data analysis. This session will include an explanation of the properties and advantages of 2 base encoding and tools available for analysis of color space data across a range of applications such as resequencing, transcriptomics, epigenomics and de novo assembly.
Presentation PDF: http://www.iscb.org/uploaded/css/36/12104.pdf
Technology Track: TT15
WikiPDB – A community for enhancing the PDB
Tuesday, June 30 - 10:45 a.m. - 11:10 a.m.
Room: C7
Presenting author: Vince Grolmusz, Eotvos University, Hungary
Abstract:
We provide a Wikipedia like interface(an extension of the Mediawiki software) for modification of the data bank files, and discussionbetween scientists doing research on the same structures. Our system detects syntax errors, provides anAPI for semantic error checking plug-ins, and keeps track of different versions.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11855.pdf
Technology Track: TT16
Ontology Services for Semantic Applications in Healthcare and Life Sciences
Tuesday, June 30 - 11:15 a.m. - 11:40 a.m.
Room: C7
Presenting author: Patricia Whetzel, The National Center for Biomedical Ontology, United States
Abstract:
BioPortal (http://bioportal.bioontology.org) is a repository of biomedical ontologies accessible via Web browsers and Web services. Ontology Web services include search and visualization, the Open Biomedical Annotator Web service ‰Û÷tags‰Ûª user-submitted text with ontology terms, and the Open Biomedical Resources Web services provides access to search ontology-indexed public repositories.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11766.pdf
Technology Track: TT17
Advances in Protein and Antibody Structure Modelling, and Structural Information Sharing
Tuesday, June 30 - 11:45 a.m. - 12:40 p.m.
Room: C8
Presenting author: Stephen Maginn, Chemical Computing Group, United Kingdom
Abstract:
Recent advances in CCG\'s MOE system for protein structure modelling will be described, including revisions to the homology modelling procedures, a new sidechain conformer library, and a tailored interface for antibody structure modelling. The PSILO system for protein-ligand structure information will be demonstrated.
Presentation PDF: http://www.iscb.org/uploaded/css/36/10355.pdf
Technology Track: TT18
Analysis of next-generation genome and transcriptome re-sequencing data using integrated bioinformatics approaches and pipelines
Tuesday, June 30 - 11:45 a.m. - 12:40 p.m.
Room: C7
Presenting author: Arif Anwar, Synamatix , Malaysia
Abstract:
The advent of next generation sequencing has led to enormous challenges interms of data management, analysis and mining. Recent advances in humangenomics research have indicated that the level of genetic variation betweenhumans is higher and more complex than previously thought. Hence the identification of diverse types of mutations and chromosomal aberrations iscritical. Synamatix has developed
Presentation PDF: http://www.iscb.org/uploaded/css/36/11832.pdf
Technology Track: TT19
InterPro: functional annotation database
Tuesday, June 30 - 2:15 p.m. - 2:40 p.m.
Room: K1
Presenting author: Jennifer McDowall, EMBL-EBI, United Kingdom
Abstract:
This demonstration explores the wealth of protein annotation data available through the INTERPRO database (http://www.ebi.ac.uk/interpro/). InterPro integrates data from ten signature databases and five structural databases, providing information on protein families, domains, repeats and sites in which identifiable features found in known proteins can be applied to novel protein sequences.
Presentation PDF: http://www.iscb.org/uploaded/css/36/10357.pdf
Technology Track: TT20
Putting it All Together: Informatics Across Pharmacuetical Discovery
Tuesday, June 30 - 2:15 p.m. - 3:10 p.m.
Room: C8
Presenting author: Jonathan Usuka, Accelrys, United States
Abstract:
The Kinome Viewer: Phylogenetic Navigation of the Target Space – An open access collaboration. rnrnKnowledge Management for Biological Workflows – A three year special interest group for best practices in IT for bench biologists.rnrnBiology in Pipeline Pilot – Flexible data management & text analytics for DNA, gene expression, and proteomics.
Presentation PDF: http://www.iscb.org/uploaded/css/36/12729.pdf
Technology Track: TT21
Galaxy Library System for Management of Next Generation Sequencing Data
Tuesday, June 30 - 2:15 p.m. - 2:40 p.m.
Room: C7
Presenting author: Anton Nekrutenko, anton@bx.psu.edu , United States
Abstract:
In this demonstration we will highlight the latest features of Galaxy system (http://galaxyproject.org) for efficiently storing, organizing, managing, and analyzing of datasets produced by the next-generation sequencing technologies.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11868.pdf
Technology Track: TT22
PSODA: Open Source Phylogenetic Search and DNA Analysis
Tuesday, June 30 - 2:45 p.m. - 3:10 p.m.
Room: K1
Presenting author: Quinn Snell, Brigham Young University, United States
Abstract:
PSODA (s -dĻ) is an open source sequence analysis package that implements sequence alignment using biochemical properties, phylogeny search with parsimony or maximum likelihood criteria and selection detection using biochemical properties (TreeSAAP ). PSODA is compatible with PAUP* and the search algorithms are competitive with those in PAUP*.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11750.pdf
Technology Track: TT23
Utopia Documents: The Digital Meta-Library
Tuesday, June 30 - 2:45 p.m. - 3:10 p.m.
Room: C7
Presenting author: Steve Pettifer, University of Manchester, United Kingdom
Abstract:
An introduction to, and demonstration of Utopia Documents: a new member of the Utopia suite that integrates functions otherwise carried out by separate software: management of one‰Ûªs personal library, document display and literature interpretation.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11843.pdf
Technology Track: TT24
ERIC-BRC – A Free Internet Resource to Mine Salmonella, E. coli, Shigella and Yersinia Genome Annotations
Tuesday, June 30 - 3:15 p.m.- 3:40 p.m.
Room: K1
Presenting author: David Pot, SRA International, Inc., United States
Abstract:
We will demonstrate workflows to access and mine enteropathogen annotation data using: simple queries, combining queries for advanced data-mining (‰ÛÏQuery Intersections‰Û ), whole multiple genome alignments with Mauve, and text mining of literature abstracts using advanced Natural Language Processing with the extraction of facts describing molecular mechanisms of bacterial pathogensisis.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11779.pdf
Technology Track: TT25
The Enzyme Information System BRENDA
Tuesday, June 30 - 3:15 p.m.- 3:40 p.m.
Room: C8
Presenting author: Maurice Scheer, Technische Universitat Braunschweig, Germany
Abstract:
The BRENDA enzyme information system provides a database containing manually curated data on biochemical and molecular information on all classified enzymes, their catalyzed reactions and the metabolites. Furthermore, software tools are provided for querying, visualizing and performing computations on these data.The presentation will explain the system and latest updates.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11818.pdf
Technology Track: TT26
BioModels Database, a database of curated and annotated quantitative models with Web Services and analysis tools
Tuesday, June 30 - 3:15 p.m - 3:40 p.m.
Room: C7
Presenting author: Nicolas Le Noväre, EMBL-EBI, United Kingdom
Abstract:
BioModels Database (www.ebi.ac.uk/biomodels) is a freely available resource storing curated and annotated versions of peer-reviewed quantitative models of biological interests. Models can be searched and retrieved in diverse formats (SBML, CellML, BioPAX, XPP-Aut, SciLab etc.) from the web interface or using Web Services.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11826.pdf
Technology Track: TT27
Creating Computational Workflows through the BioExtract Server
Tuesday, June 30 - 3:45 p.m. - 4:10 p.m.
Room: K1
Presenting author: Carol Lushbough, University of South Dakota, United States
Abstract:
The BioExtract Server (http://bioextract.org) is a Web-based data integration application designed to aid researchers in the development of computational workflows. It allows users, via a Web browser, to query multiple data sources, save query results as searchable data sets, execute local and Web-accessible analytic tools, and create computational workflows.
Presentation PDF: http://www.iscb.org/uploaded/css/36/10255.pdf
Technology Track: TT28
Extending Ensembl beyond Vertebrate Genomes
Tuesday, June 30 - 3:45 p.m. - 4:10 p.m.
Room: C8
Presenting author: Michael Schuster, EMBL - European Bioinformatics Institute, United Kingdom
Abstract:
In this demonstration we would like to introduce the new Ensembl web site and the new Ensembl Genomes project, which will provide a portal for access to genome-scale data from across the taxonomic space. Ensembl Genomes will be working in partnership with the scientific community.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11838.pdf
Technology Track: TT29
The Universal Protein Resource (UniProt)
Tuesday, June 30 - 3:45 p.m. - 4:10 p.m.
Room: C7
Presenting author: Samuel Patient, EMBL - European Bioinformatics Institute, United Kingdom
Abstract:
UniProt (http://www.uniprot.org/) is a comprehensive and freely accessible resource on protein sequences and functional annotation. This demonstration will present how to best access, browse and analyze the protein information stored in our various databases via a tour through the UniProt web site and examples for programmatic access.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11849.pdf
Technology Track: TT30
Demonstration of the SuDS Genome Browser
Wednesday, July 1 - 10:45 a.m. - 11:10 a.m.
Room: C8
Presenting author: Riku Katainen, Department of Computer Science, Finland
Abstract:
The presentation introduces a user interface created to perform queries (e.g. DNA sequences and Position-Specific Scoring Matrices) to compressed suffix tree, that has been computed for the human genome. The demonstration consist of queries, such as longest common substring, k-mismatches and PSSM.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11839.pdf
Technology Track: TT31
GeneMANIA: Gene Function Prediction using a Multiple Association Network Integration Algorithm
Wednesday, July 1 - 10:45 a.m. - 11:10 a.m.
Room: C7
Presenting author: Sylva Donaldson, University of Toronto, Canada
Abstract:
GeneMANIA (www.genemania.org) is an integrated interaction network browser where users analyze gene lists to predict function and identify high-throughput data sources in which the user‰Ûªs query genes are highly associated. GeneMANIA collects large public datasets (interactions, co-expression, protein domains), providing fast and highly accurate gene function predictions using guilt-by-association.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11847.pdf
Technology Track: TT32
Chipster – user-friendly software for reproducible microarray data analysis
Wednesday, July 1 - 11:15 a.m. - 11:40 a.m.
Room: C8
Presenting author: Eija Korpelainen, CSC - IT Centre for Science, Finland
Abstract:
Chipster (http://chipster.csc.fi/) brings a comprehensive collection of up-to-date microarray data analysis methods within the reach of experimental biologists. The workflow functionality of Chipster enables users to perform their analysis in a reproducible and collaborative manner. Chipster is open source and available for local server installations
Presentation PDF: http://www.iscb.org/uploaded/css/36/11842.pdf
Technology Track: TT33
NASCENT: An Automatic Protein Interaction Network
Wednesday, July 1 - 11:15 a.m. - 11:40 a.m.
Room: C7
Presenting author: Vince Grolmusz, Eotvos University, Hungary
Abstract:
We present the functionality of the new protein interaction network generation tool NASCENT.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11837.pdf
Technology Track: TT34
GNUMAP: Unbiased Probabilistic Mapping of Next-Generation Sequencing Reads
Wednesday, July 1 - 11:45 a.m. - 12:10 p.m.
Room: C8
Presenting author: Mark Clement, Brigham, United States
Abstract:
GNUMAP addresses the analyses problems presented by an increase in the quantity of sequence data from next-generation sequencing technologies. The probabilistic nature of the mapping algorithm implemented in GNUMAP provides an accurate and efficient method for mapping large numbers of short sequences to a genome.
Presentation
Presentation PDF: http://www.iscb.org/uploaded/css/36/11864.pdf
Technology Track: TT35
Decomp – A PDB decomposition Tool
Wednesday, July 1 - 11:45 a.m. - 12:10 p.m.
Room: C7
Presenting author: Vince Grolmusz, Eotvos University, Hungary
Abstract:
In our presentation we would like to demonstrate the web server version of decomp (http://decomp.pitgroup.org/) that decomposes any structure deposited in the Protein Data Bank.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11852.pdf
Technology Track: TT36
MONET: A Cytoscape plugin for genome-scale network inference from expression profiles using modularization and parallel processing techniques with supercomputing resources
Wednesday, July 1 - 12:15 p.m. - 12:40 p.m.
Room: C8
Presenting author: Younghoon Kim, KAIST, Korea, Rep
Abstract:
MONET is a Cytoscape plugin to infer genome-scale networks from gene expression profiles. It alleviates the shortage of information by incorporating pre-existing annotations. Currently, MONET utilizes thousands of parallel computational cores in the supercomputing center in KISTI, Korea, to cope with the computational requirement for large scale genetic network inference.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11871.pdf
Technology Track: TT37
Scoring and aligning profile HMMs with Profile Comparer (PRC)
Wednesday, July 1 - 12:15 p.m. - 12:40 p.m.
Room: C7
Presenting author: Martin Madera, University of Bristol, United Kingdom
Abstract:
Profile Comparer (PRC) is a stand-alone program for scoring and alignining profile hidden Markov models (profile HMMs) of protein families. According to independent benchmarks, PRC is the most sensitive method for detecting remote homologies among protein families. We describe recent improvements and show how to use PRC in practice.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11857.pdf
Technology Track: TT38
EMBL-EBI Industry Programme
Wednesday, July 1 - 2:15 p.m. - 2:40 p.m.
Room: C8
Presenting author: Dominic Clark, EMBL-EBI, United Kingdom
Abstract:
This presentation will provide an overview and demonstration of some of the means by which EMBL-EBI interacts with industry stakeholders. We welcome further enquiries about any of the activities described. In the first instance, please email: industry@ebi.ac.uk.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11825.pdf
Technology Track: TT39
OptFlux: a software for metabolic engineering
Wednesday, July 1 - 2:15 p.m. - 2:40 p.m.
Room: C7
Presenting author: Isabel Rocha, IBB - Institute for Biotechnology and Bioengineering - Center of Biological Engineering, Portugal
Abstract:
OptFlux is an open-source, user-friendly and modular software aimed at being the reference computational tool for metabolic engineering applications. It allows the use of stoichiometric models of microbial metabolism for simulation and optimization purposes.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11861.pdf
Technology Track: TT40
BioCatalogue: A Curated Web Service Registry for the Life Science Community
Wednesday, July 1 - 2:45 p.m. - 3:10 p.m.
Room: C8
Presenting author: Franck Tanoh, University of Manchester, United Kingdom
Abstract:
BioCatalogue is a central registry of curated biological web services. A place where providers, users and curators can register, annotate and search for web services. BioCatalogue is a place where the community can meet the maintainers of these services. It is co-developed by the University of Manchester and the EMBL-EBI.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11627.pdf
Technology Track: TT41
Visual PredictProtein and jBio: a JavaScript library for bioinformatics
Wednesday, July 1 - 2:45 p.m. - 3:10 p.m.
Room: C7
Presenting author: Laszlo Kajan, Columbia University, Rost Lab, United States
Abstract:
jBio is our new JavaScript library at the heart of VisualPredictProtein, the on-line PredictProtein results explorer. jBio represents a new solution to on-line bioinformatics knowledge presentation. It offers the same sophistication that we see in our favourite on-line services: straightforward and familiar controls, rich user interactions and themable look.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11863.pdf
Technology Track: TT42
Computational Biology in the cloud, towards a federative and collaborative R-based platform
Wednesday, July 1 - 3:15 p.m.- 3:40 p.m.
Room: C8
Presenting author: Karim Chine, Cloud Era Ltd, United Kingdom
Abstract:
The demo will be an overview of, Biocep, a universal platform for computational sciences based on R. The demo show how Grids and Cloud Computing infrastructures can be used for distributed computing with R,collaborative data analysis of large data sets, rapid creation and delivery of analytical User Interfaces and more.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11824.pdf
Technology Track: TT43
Protein Subcellular Location Image Database, Release 5
Wednesday, July 1 - 3:15 p.m.- 3:40 p.m.
Room: C7
Presenting author: Robert Murphy, Carnegie Mellon University, United States
Abstract:
The Protein Subcellular Location Image Database, the original publicly available database of subcellular patterns, provides public access to images and tools for automated analysis. A major release of PSLID will occur at ISMB/ECCB 2009, including live cell images for 2,000 GFP-tagged cell lines and generative models for their distributions.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11866.pdf
Technology Track: TT44
Protein homology searches and structure prediction with HHpred and the MPI/LMU Bioinformatics Toolkit
Wednesday, July 1 - 3:45 p.m. - 4:10 p.m.
Room: C8
Presenting author: Andreas Biegert, Gene Center (LMU), Germany
Abstract:
We will show how to use the web-based Bioinformatics Toolkit for protein sequence analysis and how to apply our HHpred server to build 3D protein models. We will also demonstrate the new context-specific BLAST, which has twice the sensitivity of BLAST at the same speed.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11873.pdf
Technology Track: TT45
Using the NCIBI Suite of Integrated Tools and Data
Wednesday, July 1 - 3:45 p.m. - 4:10 p.m.
Room: C7
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/36/11828.pdf
Technology Track: TT46
InterMine – open source data warehouse and query interface
Thursday, July 2 - 10:45 a.m. - 11:10 a.m.
Room: K2
Presenting author: Richard Smith, University of Cambridge, United Kingdom
Abstract:
InterMine is an open-source system for building query-optimised data warehouses. It supports data integration from standard biological formats and makes it easy to add your own data. A sophisticated web application provides flexible access for users to create custom queries, use templates and operate on lists.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11841.pdf
Technology Track: TT47
Semantic Data Integration for Systems Biology Research
Thursday, July 2 - 11:15 a.m. - 11:40 a.m.
Room: K2
Presenting author: Chris Rawlings, Rothamsted Research, United Kingdom
Abstract:
A novel combination of a data integration software platform (Ondex) system and the Taverna workbench will demonstrate how bioinformatics services and data integration can be combined to create a powerful data analysis platform for systems biology research.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11846.pdf
Technology Track: TT48
Reactome tools for expression data and pathway visualization
Thursday, July 2 - 11:45 a.m. - 12:10 p.m
Room: K2
Presenting author: David Croft, Wellcome Trust Genome Campus, United Kingdom
Abstract:
Reactome is a curated database of cellular processes in human biology. We will demonstrate existing functionality for importing expression data and projecting it onto pathways. We will also preview a new web-based entity-level pathway view, which provides significantly enhanced visual interaction with our data.
Presentation PDF: http://www.iscb.org/uploaded/css/36/12726.pdf
Technology Track: TT49
BALLView: a molecular viewer and modelling tool with real-time raytracing capabilities
Thursday, July 2 - 12:15 p.m - 12:40 p.m.
Room: K2
Presenting author: Lukas Marsalek, Saarland University, Germany
Abstract:
We will demonstrate our open-source molecular viewer and modelling tool BALLView. The highlight of the presentation is integration of real-time ray tracing capabilities. We will show real-time usage of BALLView\'s visualization models through high-quality ray tracing and demonstrate new ways of graphically exploring molecules arising naturally when using such techniques.
Presentation PDF: http://www.iscb.org/uploaded/css/36/11874.pdf