ISMB 2008 ISCB

16th Annual
International Conference
Intelligent Systems
for Molecular Biology


Metro Toronto Convention Centre (South Building)
Toronto, Canada


 



ISMB 2008 Technology Track Presentations

(as of June 17, 2008)


Technology Track: TT01

GenoCAD: Computer Assisted Design of genetic constructs

Sunday, July 20 - 10:45 a.m. - 11:10 a.m.

Room: 701B

Presented by: Jean Peccoud, Virginia Tech, US

Abstract:
We are creating the infrastructure making it possible for non-specialist to design large genetic constructs used in basic biological research or product development programs. The GenoCAD environment (www.genocad.org) provides a structured and rigorous methodology for organizations to design complex genetic constructs that will be presented through a software demonstration.

Presentation PDF: http://www.iscb.org/uploaded/css/25/3222.pdf


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Technology Track: TT02

PredictProtein - Beyond Secondary Structure Prediction

Sunday, July 20 - 11:15 a.m. - 11:40 a.m.

Room: 701B

Presented by: Guy Yachdav, Laszlo Kajan, Columbia University, US

Abstract:
PredictProtein is a comprehensive sequence analysis server that incorporates an increasing number of services and databases that can be used for protein annotation. Join us for a tour through the multitude of tools available in PredictProtein as we show you how to leverage the service in your day-to-day work.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4110.pdf


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Technology Track: TT03

The InterPro Protein Signature Database

Sunday, July 20 - 11:45 a.m. - 12:10 p.m.

Room: 701B

Presented by: Jennifer McDowall, EMBL-EBI, UK

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/25/4075.pdf


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Technology Track: TT04

Reactome  Pathway Database Demo

Sunday, July 20 - 12:15 p.m. - 12:40 p.m.

Room: 701B

Presented by: Gopal Gopinathrao, Cold Spring Harbor Laboratory, US

Abstract:
Reactome is a curated, open source database of human biological processes. Pathways are authored and peer-reviewed by domain experts. Orthology-based inference of reactions is available for 22 species. Tools for high-throughput data analysis and data mining, and data are provided. Fly, chicken and Arabidopsis Reactome databases are under development.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4087.pdf


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Technology Track: TT05

EMBRACE-Enabling Data Integration

Sunday, July 20 - 2:15 p.m. - 2:40 p.m.

Room: 701B

Presented by: Syed Haider, EMBL-EBI, UK

Abstract:
Large quantities of biological data generated by different research centres have been exposed with a variety of programmatic interfaces. The unified presentation and interoperability of these diverse resources is made possible through BioMart web services as an on-going initiative by the EMBRACE project.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4123.pdf


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Technology Track: TT06

PIR Resources for Protein Knowledge Discovery

Sunday, July 20 - 2:45 p.m. - 3:10 p.m.

Room: 701B

Presented by: Zhang-Zhi Hu, Anastasia Nikolskaya, Georgetown University Medical Center, US

Abstract:
PIR (http://pir.georgetown.edu/) provides bioinformatics resources for protein analysis, including databases and tools tailored for proteomics (expression data, unique proteins lists), ID mapping, text mining (information extraction, entity recognition), and protein annotation (protein entries, family classification). We will demonstrate these web-based resources for protein knowledge discovery.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4109.pdf


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Technology Track: TT07

Fiesta: An Interactive Sequence Management and Analysis Framework

Sunday, July 20 - 2:45 p.m. - 3:10 p.m.

Room: 701B

Presented by: Kannan Vijayan and Dustin Cram, Plant Biotechnology Institute, National Research Council of Canada, CA

Abstract:
We demonstrate Fiesta, a genomics web application that provides a comprehensive and extensible framework for implementing and exposing sequence analysis features. Fiesta provides features allowing for data sharing, online job invocation and tracking, a number of useful analysis features, and a friendly web interface.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4113.pdf


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Technology Track: TT08

VisANT: an integrative platform for multiple-scale visualization and
modeling of biological networks/pathways

Sunday, July 20 - 3:45 p.m. - 4:10 p.m.

Room: 701B

Presented by: Zhenjun Hu, Boston University, US

Abstract:
VisANT is an integrative platform for multiple-scale visualization and modeling of biological networks/pathways. It integrates the context (e.g., modular activity) and the hierarchical organization of cellular agents (e.g., molecules and complexes) in addition to their interactions. It also provides optimized performance to handle large-scale networks with millions nodes and edges.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4068.pdf


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Technology Track: TT09

The Subcellular Location Image Finder - Extracting Information from Text and Images in Biological Journal Articles

Monday, July 21 - 10:45 a.m. - 11:10 a.m.

Room: 701B

Presented by: Robert F. Murphy, Carnegie Mellon University, US

Abstract:
SLIF (Subcellular Location Image Finder) extracts information about protein subcellular locations from figure-caption pairs in biological literature. SLIF separates figures into panels, decides which contain fluorescence microscope images, and analyzes image and text content. The results are freely available via web service which contains all papers in Pubmed Central.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4111.pdf


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Technology Track: TT10

Dominating the Next Generation Sequencing Data Analysis Challenge.

Monday, July 21 - 10:45 a.m. - 11:40 a.m.

Room: 714

Presented by: Thomas Knudsen

Abstract:
CLC bio has overcome the challenge to analyze Next Generation Sequencing data faster than it is produced, by implementing a SIMD-accelerated assembly algorithm in their Next Generation Sequencing solution, CLC Genomics Workbench - a cross-platform desktop application with a graphical user interface.

Presentation PDF: http://www.iscb.org/uploaded/css/25/10077.pdf


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Technology Track: TT11

CiteXplore, Whatizit et al: Latest Innovations in EBI's Literature Infrastructure

Monday, July 21 - 11:15 a.m. - 11:40 a.m.

Room: 701B

Presented by: Dietrich Rebholz-Schuhmann, M. Rijnbeek, EMBL-EBI, UK

Abstract:
EBI provides Literature services for Medline abstracts, patent texts and full text documents (CiteXplore, Whatizit, EBIMed, MedEvi). Also, EBI offers scripted access to text mining services (e.g. Http request, SOAP, DAS services) processing any textual data. The presentation will explain (and demonstrate) the latest updates to EBI’s infrastructure.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4105.pdf


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Technology Track: TT13

CAMERA: Tools and Data for Metagenomics

Monday, July 21 - 11:45 a.m. - 12:10 p.m.

Room: 701B

Presented by: Iddo Friedberg, Weizhong Li, University of California San Diego, US

Abstract:
CAMERA is a project that aims to become a central data and software repository for environmental genomic data. CAMERA contains 14 microbial genomic datasets and software tools. This demonstration is aimed at researchers using metagenomic data and developers who wish to join a growing community of a new bioinformatic discipline

Presentation PDF: http://www.iscb.org/uploaded/css/25/4093.pdf


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Technology Track: TT14

BONDplus, BINDplus and GENESEQ

Monday, July 21 - 11:45 a.m. - 12:40 p.m.

Room: 714

Presented by: Eric Andrade and Sam Sgro, Thomson Reuters, US

Abstract:
This talk will discuss the basics of BONDplus - a data warehouse for public and patent sequence and interaction databases, such as BINDplus and GENESEQ. The demonstration will cover the content and technology base for the Web Platform and API access methods and review practical use cases.

Presentation PDF: http://www.iscb.org/uploaded/css/25/10079.pdf


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Technology Track: TT15

InterMine - Open Source Data Warehouse and Query Interface

Monday, July 21 - 12:15 p.m. - 12:40 p.m.

Room: 701B

Presented by: Richard Smith, University of Cambridge, UK

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/25/4107.pdf


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Technology Track: TT16

Multiplierz and the mzAPI: A Common API and DeskTOP Environment for Mass Spectrometry Based Proteomics

Monday, July 21 - 2:15 p.m. - 2:40 p.m.

Room: 701B

Presented by: Manor Askenazi, Dana-Farber Cancer Institute, US

Abstract:
Mass spectrometry based proteomics constitutes an increasingly important datasource for systems biology. In order to analyze this challenging datatype, bioinformatics researchers must familiarize themselves with the underlying technology. The multiplierz software environment provides an easy to use, scriptable API/framework within which to develop novel algorithms and tools for mass informatics.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4094.pdf


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Technology Track: TT17

Working with the NCBC's: Integration Tools and Data, NCIBI Suite of Tools

Monday, July 21 - 2:15 p.m. - 2:40 p.m.

Room: 714

Presented by: James Cavalcoli, The University of Michigan - National Center for Integrative Biomedical Informatics, US

Abstract:
NCIBI Suite of Tools demonstrates integration between NCIBI Tools and Data (MiMI, SAGA, MiSearch, GIN, Gene2Mesh, BioNLP) and popular bioinformatics resources such as Cytoscape, GenePattern, and NCBI EntrezGene and PubMed to form a network of applications linking protein interactions, pathways data and literature based annotation to uncover potential biological relationships.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4117.pdf


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Technology Track: TT18

How to use Bio2RDF with a Virtuoso Server

Monday, July 21 - 2:45 p.m. - 3:10 p.m.

Room: 701B

Presented by: François Belleau, Centre de Recherche du CHUL (CHUQ), CA

Abstract:
Our vision apply semantic web technology to realize data integration in bioinformatics. In this demo we show how to use Virtuoso server to store Bio2RDF linked data. We also demonstrate how millions of triples from 30 different data providers, can be queried with SPARQL to answer question.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4095.pdf


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Technology Track: TT19

MAGNet: Integrating Tools and Data

Monday, July 21 - 2:45 p.m. - 3:10 p.m.

Room: 714

Presented by: Aris Floratos, Columbia University, US

Abstract:
MAGNet, the National Center for the Multiscale Analysis of Genomic and Cellular Networks (http://magnet.c2b2.columbia.edu/), focuses on the development of computational tools for the systems-level analysis of complex cellular process over a wide range of scales. We demonstrate how these tools are made accessible through geWorkbench, the Center's integrative software platform.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4089.pdf


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Technology Track: TT20

Pathway Tools Software: Regulatory Networks and Recent Developments

Monday, July 21 - 3:15 p.m.- 3:40 p.m.

Room: 701B

Presented by: Peter Karp, SRI International, US

Abstract:
Pathway Tools provides many capabilities for storing and analyzing integrated collections of genomic and metabolic information. The software has been applied to the 370 organism-specific Pathway/Genome Databases (PGDBs) in SRI's BioCyc database collection, and to create curated PGDBs for mouse, yeast, and many plants. Pathway Tools contains expanded capabilities for encoding and displaying regulatory data.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4098.pdf


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Technology Track: TT21

Simbios: Fast Molecular Dynamics Calculations on your LapTOP

Monday, July 21 - 3:15 p.m.- 3:40 p.m.

Room: 714

Presented by: Jeanette Schmidt, Stanford University, US

Abstract:
Long Molecular Dynamics calculations have traditionally required powerful hardware. The Simbios Center for Physics-based Simulation of Biological Structures will present demos of two complementary approaches that tackle this problem 1) exploiting GPUs (your computer’s graphic processors) to speed up computation 2) reducing the degrees of freedom of the simulated molecule.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4122.pdf


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Technology Track: TT22

Chipster - User Friendly Analysis Tool for DNA Microarray Data

Monday, July 21 - 3:45 p.m. - 4:10 p.m.

Room: 701B

Presented by: Eija Korpelainen, CSC, the Finnish IT center for science, FI

Abstract:
Chipster - user friendly analysis tool for DNA microarray data. Our demonstration covers workflows and other advanced functionalities of Chipster (http://chipster.csc.fi/). This open source software offers an intuitive GUI to a comprehensive collection of up-to-date analysis methods developed in the R/Bioconductor project. Chipster supports Affymetrix, Illumina, Agilent and cDNA arrays.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4101.pdf


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Technology Track: TT23

i2b2

Monday, July 21 - 3:45 p.m. - 4:10 p.m.

Room: 714

Presented by: Vivian Gainer, Partners, US

Abstract:
The goal of i2b2 is to provide clinical investigators broadly with the software tools necessary to collect and manage project-related clinical research data in the genomics age as a cohesive entity—a software suite to construct and manage the modern clinical research chart.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4124.pdf


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Technology Track: TT24

NMPDR: National Microbial Pathogen Data Resource

Tuesday, July 22 - 10:45 a.m. - 11:10 a.m.

Room: 701B

Presented by: Leslie McNeil, University of Illinois at Urbana-Champaign, US

Abstract:
The National Microbial Pathogen Data Resource, http://www.nmpdr.org, provides curated functional annotations in a structured biological context. NMPDR is both a central repository for a variety of data on microorganisms, and a platform for tools that support investigator-driven data analysis, including the identification of potential targets of vaccines, therapeutics, and diagnostics.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4120.pdf


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Technology Track: TT25

MG-RAST Rapid Meta-genome Annotation Server

Tuesday, July 22 - 11:15 a.m. - 11:40 a.m.

Room: 701B

Presented by: Leslie McNeil, University of Illinois at Urbana-Champaign, US

Abstract:
MG-RAST (Metagenome RAST http://metagenomics.nmpdr.org/) is a fully-automated metagenome analysis server providing annotation, phylogenetic and functional classification of sequence fragments. MG-RAST processes 454 or Sanger sequence data uploaded in FASTA format. Results may be privately viewed in an online environment optimized for in-depth, comparative analysis of community taxonomy and subsystem distribution.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4119.pdf


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Technology Track: TT26

RAST Rapid Microbial Genome Annotation server

Tuesday, July 22 - 11:45 a.m. - 12:10 p.m.

Room: 701B

Presented by: Leslie McNeil, University of Illinois at Urbana-Champaign, US

Abstract:
RAST (Rapid Annotation using Subsystem Technology; http://rast.nmpdr.org/) is a fully-automated service providing superior annotation of bacterial and archael genomes within 12-24 hours. Computed annotations are based on FIGfams and Subsystems from SEED. Results may be privately viewed in an online environment optimized for comparative analysis, subsystems mapping, and metabolic reconstruction.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4118.pdf


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Technology Track: TT27

A database of Chemical Entities of Biological Interest

Tuesday, July 22 - 12:15 p.m. - 12:40 p.m.

Room: 701B

Presented by: Ana Paula de Matos, European Bioinformatics Institute, UK

Abstract:
Accounting for an increasing importance of chemical information in the life sciences, the European Bioinformatics Institute has created ChEBI, a free, manually curated database and ontology of Chemical Entities of Biological Interest. Here we demonstrate ChEBI's general functionality and new chemical structure searching facilities based on the Chemistry Development Kit.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4102.pdf


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Technology Track: TT28

Designing, Executing, Reusing and Sharing Workflows: Taverna and myExperiment Supporting the in silico Experiment Life Cycle

Tuesday, July 22 - 2:15 p.m. - 2:40 p.m.

Room: 701B

Presented by: Katy Wolstencroft, University of Manchester / OMII-UK, UK

Abstract:
This demonstration showcases the next generation of the Taverna workbench, Taverna 2, an environment for designing and executing workflows. We also introduce myExperiment, a social networking site for scientists to share experiments and expertise. By combining these components, scientists can design, execute, share, reuse and publish workflows in Life Science.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4103.pdf


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Technology Track: TT29

EBI Web Services APIs for Data-retrieval and Analysis

Tuesday, July 22 - 2:45 p.m. - 3:10 p.m.

Room: 701B

Presented by: Franck Valentin, EMBL - EBI
, UK

Abstract:
This session provides an overview of Web Services APIs from EMBL-EBI and demonstrates how to use these for data-retrieval and analysis. The APIs provide main-stream methods for analysing large data sets and mine the scientific record. Users will be shown how to combine services using scripts and workflows enactors.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4104.pdf


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Technology Track: TT30

Galaxy Workflows: Enabling Complex Computational Analysis For Experimental Biologists

Tuesday, July 22 - 3:15p.m. - 3:40p.m.

Room: 701B

Presented by: James Taylor, New York University, US

Abstract:
Galaxy Workflows allow the intuitive construction of complex reusable multi-step analysis. We will demonstrate the different mechanisms for constructing workflows in Galaxy, as well as workflow execution, interface customization, and sharing.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4106.pdf


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Technology Track: TT31

New GALAXY Tools

Tuesday, July 22 - 3:45 p.m. - 4:10 p.m.

Room: 701B

Presented by: Anton Nekrutenko, Penn State University, US

Abstract:
New GALAXY tools for manipulation of multiple alignments, short read analysis, annotation profiling and whole genome association studies. Highlighting new Galaxy features developed within last 12 months and designed to take advantage of bleeding-edge types of data including alignments, short reads, and human polymorphism data.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4092.pdf


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Technology Track: TT32

Pathway Ontology for Analysis of High-throughput Data

Tuesday at 10:45 a.m - 11:40 a.m.

Room: 714

Presented by: Anton Yuryev, Ariadne Genomics, US

Abstract:
We showcase Pathway Ontology designed for analysis of high-throughput data in Pathway Studio. Ariadnes Pathway Ontology allows identification of the cell processes and signaling blocks affected during the experiment, visualized on one global Systems Biology map, and calculation of gene sets for Gene Set Enrichment and Network Enrichment analysis.

Presentation PDF: http://www.iscb.org/uploaded/css/25/10080.pdf


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Technology Track: TT33

EB-eye - The EMBL-EBI search engine

Tuesday, 11:45 a.m. - 12:10 p.m.

Room: 714

Presented by: Franck Valetin

Abstract:
We will describe the EB-eye, a search engine that provides search and retrieval capabilities for the data resources hosted at the EMBL-EBI. We will describe how users can do simple and advanced searches, navigate cross references and access the original resources, as well as introduce its API.

Presentation PDF: http://www.iscb.org/uploaded/css/25/10081.pdf



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Technology Track: TT34

Chimera

Tuesday, July 22 12:15 p.m. – 12:40 p.m.

Room: 714

Presented by: Scooter Morris

Abstract:
Chimera is a program for interactive molecular graphics and modeling. Chimera provides standard graphics features as well as more unique tools for working with sequence alignments (with information flow to and from associated structures), volume data, docking results, molecular dynamics trajectories,and large molecular assemblies. Chimera can be downloaded from http://www.cgl.ucsf.edu/chimera.

Presentation PDF: http://www.iscb.org/uploaded/css/25/4115.pdf



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