ISMB 2008 ISCB






















Technology Track Presentation Schedule

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

ISMB/ECCB 2009 Blog
TT01: Allan Orozco - The Spanish National Bioinformatics Institute (INB)
↑ TOP

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

ISMB/ECCB 2009 Blog
TT02: Janet Thornton - ELIXIR: A sustainable infrastructure for biological information in Europe
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 Johnston
Reports from initial committee meetings (userbase consultation) due now - will define the scope & remit of ELIXIR. Then work on international agreement for goals, costs then look at how to fund. - Cass Johnston
Will provide: core and specialist data resources, compute centres, infrastructure for tools and services integration, support for Bio ESFRI projects, community support and training. - Cass Johnston
Survey of existing EU database resources. See Poster E41 for details - Cass Johnston
DB size / number of users / cost etc follow power law - many small dbs, few users, low cost. A few massive ones. Notably, 90% have no funding security beyond 3 years. So - ELIXIR needs to co-ordinate, prioritise and stabilise funding for these resources. - Cass Johnston
Databases relatively under control compared to other aspects: Standards and ontologies, Literature, Other domains (medical data, biodiversity data etc), Integration - Cass Johnston
Don't need to centralise standards devel, is fine for them to come out of communities, but do need to encourage and publicise standards. OBO. - Cass Johnston
Timeline. Dec 2010: end of preparatory phase. Dec 2016: end of construction phase. - Gabriele Sales
Literature: integrated, open access text-based literature resource would be good :) - Cass Johnston
Compute resources: Modularise organisation of dataresources. Build network of biocomp resources. Catalyst devel of web services and cloud computing. More program to data rather than other way round. Work with EU supercomputing centres. - Cass Johnston
...more...
↑ TOP

Technology 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

ISMB/ECCB 2009 Blog
TT03: Zhong Li - caBIG Molecular Analysis Tools Knowledge Center
↑ TOP

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

ISMB/ECCB 2009 Blog
TT04: Anton Yuryev - In silico drug repositioning and combinatorial therapy design
↑ TOP

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

ISMB/ECCB 2009 Blog
TT05: Hannes Ponstingl - The SSAHA2 software pipeline for the mapping of DNA sequencing reads and genotype calling
Originally for alignment of capillary sequencing, modified to handle short read data. Uses k-mer hashed genome and Smith-Waterman. Can handle paired end reads. Accurately maps a high percentage of reads on simulated data. Has pipeline for calling SNPs, indels - also tested on simulated data. I/O is all text based. Outputs FASTQ, CIGAR, SAM. Can pre-calculate genome hash and can be tuned to run with relatively limited memory requirements. Free to use. - Cass Johnston
question: parallelization? Yes. - Cass Johnston
question: source code availability? Some of the code is from phrap and is proprietary so no. Binaries free to download though - Cass Johnston
↑ TOP

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

ISMB/ECCB 2009 Blog
TT06: Peter Rice - EMBOSS: European Molecular Biology Open Software Suite
↑ TOP

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

ISMB/ECCB 2009 Blog
TT07: Mickael Goujon - An new bioinformatics analysis tools framework at EMBL-EBI
The new framework provides an homogeneous interface to all EBI services (either via a Web Interface or using Web Services - SOAP/REST) - Gabriele Sales
All tools within a category (for example sequence similatiry searches) share the same data model. - Gabriele Sales
REST: parameter documentation -> /parameters, /parameterdetails/{param} - Gabriele Sales
REST: job submission: POST /run (returns job identifier); GET /status/{jobId} (returns job status) - Gabriele Sales
REST: result types -> /resultypes/{jobId} (list of renderers), /result/{jobId}/{type} (results view) - Gabriele Sales
tools are grouped into categories and results are available as XML with a common data model across the tool category (so, eg the XML you get back from any of the sequence search tools can be parsed the same) - Cass Johnston
Still in beta - Cass Johnston
...more...
↑ TOP

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

ISMB/ECCB 2009 Blog
TT08: Dietrich Rebholz-Schuhmann - PaperMaker: Automatic analysis and quality check for biomedical scientific literature
↑ TOP

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

ISMB/ECCB 2009 Blog
TT09: Tomasz Mikolajczyk - Your large data: query, process, share - in no time
↑ TOP

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

ISMB/ECCB 2009 Blog
TT10: Philippe Rocca-Serra & Eamonn Maguire - The ISA-infrastructure: a software suite to annotate and manage experimental metadata
isacreator - standalone java app to annotate and link data on the basis of defined metadata ontologies - Cass Johnston
various visualisations of studies - Cass Johnston
Ontology lookup tool accessible from all columns within the creator - Oliver Hofmann
Legacy data can be handled by a mapper. Requires somewhat structured data, but should be useful for migration purposes - Oliver Hofmann
interface for mapping legacy data formats - Cass Johnston
Having a bit of a problem reading the slides from the back of the room ;-) - Oliver Hofmann
has isatab validator tool - Cass Johnston
and a loader to to put isatab metadata into DB and data files into an archive - Cass Johnston
Loader with RDBMS backend access - Oliver Hofmann
...more...
↑ TOP

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

ISMB/ECCB 2009 Blog
TT11: Barend Mons - Concept Web Alliance (CWA)
↑ TOP

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

ISMB/ECCB 2009 Blog
TT12: Maria Krestyaninova - SIMBioMS - a suite of software for data collection, harmonisation and analysis in large-scale biomedical genomics projects
↑ TOP

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

ISMB/ECCB 2009 Blog
TT13: Sean O'Donoghue - Reflect: Augmented Browsing for the Life Scientist
Sorry - no FF comments as that part of FF was broken at the time. Blog post: http://themindwobbles.wordpress.com/2009/06/29/tt13-reflect-augmented-browsing-for-the-life-scientist-ismb-2009/ , but it's quite short as I was trying to get FF to work. - Allyson Lister
↑ TOP

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

ISMB/ECCB 2009 Blog
TT14: Jonathan Mangion - Color Space Analysis in the SOLiD(TM) System: the Theory, Advantages and Solutions
↑ TOP

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

ISMB/ECCB 2009 Blog
TT15: Vince Grolmusz - WikiPDB – A community for enhancing the PDB
↑ TOP

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

ISMB/ECCB 2009 Blog
TT16: Patricia Whetzel - Ontology Services for Semantic Applications in Healthcare and Life Sciences
Trish has recorded her talk as a screencast as she wanted to do a demo, and she can't trust the wireless - true enough! - Allyson Lister
RESTful services for BioPortal: http://rest.bioontology.org/bioportal (Note this is the prefix for all services, and if you just go to this URL there isn't anything visible) - Allyson Lister
Can store ontologies in OWL, OBO and Protege frames formats. - Allyson Lister
There are also ontology widgets that you can put on your own site, including jump-to feature and term selection widget. This latter one is especially useful because it allows your web app to use term auto-complete without having to code it yourself! - Allyson Lister
The search function is especially important for ontology re-use. For instance, if you're developing a new domain ontology, then you want to make sure you don't reinvent the wheel - Allyson Lister
As with all of these functions, the search features are available both via the website and programmatically - Allyson Lister
BioPortal also allows you to annotate, or add notes, to ontologies. - Allyson Lister
Nice - a tag / term cloud for annotation - Allyson Lister
You may see duplicates in the tag cloud - designed to be this way to show that more than one ontology has that term. - Allyson Lister
...more...
↑ TOP

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

ISMB/ECCB 2009 Blog
TT17: Stephen Maginn - Advances in Protein and Antibody Structure Modelling, and Structural Information Sharing
↑ TOP

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

ISMB/ECCB 2009 Blog
TT18: Arif Anwar - Analysis of next-generation genome and transcriptome re-sequencing data using integrated bioinformatics approaches and pipelines
Established in 2001 by Robert Hercus - Diego M. Riaño-Pachón
current challenges, managing data: storing and moving around - Diego M. Riaño-Pachón
several steps in the analysis pipeline - Diego M. Riaño-Pachón
open source software integrated into synamatix pipeline:one-stop bioinformatics service - Diego M. Riaño-Pachón
de-novo genome and transcriptome assembly: no use of related genomes in the assembly process! - Diego M. Riaño-Pachón
genome assembly: - Diego M. Riaño-Pachón
Basic pipeline: remove contaminant; remove read artifacts, false PEs, homopolymers; trim poor quality reads - Diego M. Riaño-Pachón
use rule matrix to filter and rank SNPs, indels, and structural variations - Diego M. Riaño-Pachón
optimized algorithms for SNP detection even at low coverage - Diego M. Riaño-Pachón
...more...
↑ TOP

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

ISMB/ECCB 2009 Blog
TT19: Jennifer McDowall - InterPro: functional annotation database
↑ TOP

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

ISMB/ECCB 2009 Blog
TT20: Jonathan Usuka - Putting it All Together: Informatics Across Pharmacuetical Discovery
↑ TOP

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

ISMB/ECCB 2009 Blog
TT21: Anton Nekrutenko - Galaxy Library System for Management of Next Generation Sequencing Data
At least 150-200 people in the audience. Not sure whether this reflects general interest in Galaxy or the focus on NSG/large data sets. - Oliver Hofmann
Once again no network connectivity in the C/T area. Notes at http://www.fiamh.info/articles/17/ismbeccb-2009-day-2 - Oliver Hofmann
Bet Galaxy on beating Gene Pattern. - Kuan-Ting Lin
↑ TOP

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 -dƒª) 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

ISMB/ECCB 2009 Blog
TT22: Quinn Snell - PSODA: Open Source Phylogenetic Search and DNA Analysis
↑ TOP

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

ISMB/ECCB 2009 Blog
TT23: Steve Pettifer - Utopia Documents: The Digital Meta-Library
Good luck with the demo! - Philip McDermott
he says "most computer science papers are rubbish" in that in CS, the thing itself is the result, which makes it a different form of literature to life scientists, where papers are about finding out things that already exist. - Allyson Lister
We all want easy access to paper, the information in the paper, the auxillary data - Allyson Lister
What does the community think of a paper? My friend? - Allyson Lister
pubmed grows at about 2 papers per minute. and that's not all of them! - Allyson Lister
A live demo? Risky with this wireless connection - Allyson Lister
When looking at a paper, it will highlight things/sections it recognizes, such as the title and the references - Allyson Lister
If errata/comments have been added to the original paper, utopia will update your pdf with them too. - Allyson Lister
@Allysson, I really like how you summarize the full microblogging in your blog! - Egon Willighagen
...more...
↑ TOP

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

ISMB/ECCB 2009 Blog
TT24: David Pot - ERIC-BRC – A Free Internet Resource to Mine Salmonella, E. coli, Shigella and Yersinia Genome Annotations
↑ TOP

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

ISMB/ECCB 2009 Blog
TT25: Maurice Scheer - The Enzyme Information System BRENDA
↑ TOP

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

ISMB/ECCB 2009 Blog
TT26: Nicolas Le Noväre - BioModels Database, a database of curated and annotated quantitative models with Web Services and analysis tools
Lots of things are called models. He's NOT going to talk about HMM, Bayesian models, sailboat models, supermodels :) - Allyson Lister
Models and their description/metadata need to be accessible - Allyson Lister
Models have to be encoded in SBML and follow the MIRIAM guidelines - Allyson Lister
There's been a steady increase in the numbers of models in BioModels. There are about 35000 reactions and about 400 models. - Allyson Lister
Standard search functionality available from their website at the EBI (http://www.ebi.ac.uk/biomodels) - Allyson Lister
Can export in CellML, BioPAX and others (though the SBML is the curated, perhaps more "trusted", version). - Allyson Lister
You can also just extract portions of the models: these will end up as valid SBML models in their own right. - Allyson Lister
@Alyson: Sorry to be picky, but the abstract says: "Models are accepted in two common formats, SBML and CellML." :-) - Dagmar
@Dagmar - good point. I thought so as well, but that's what Nicolas said. Can we say it's his fault for saying the wrong thing about his database? ;) (If indeed it is the wrong thing?) - Allyson Lister
↑ TOP

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

ISMB/ECCB 2009 Blog
TT27: Carol Lushbough - Creating Computational Workflows through the BioExtract Server
↑ TOP

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

ISMB/ECCB 2009 Blog
TT28: Michael Schuster - Extending Ensembl beyond Vertebrate Genomes
↑ TOP

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

ISMB/ECCB 2009 Blog
TT29: Samuel Patient - The Universal Protein Resource (UniProt)
↑ TOP

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

ISMB/ECCB 2009 Blog
TT30: Riku Katainen - Demonstration of the SuDS Genome Browser
↑ TOP

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

ISMB/ECCB 2009 Blog
TT31: Sylva Donaldson - GeneMANIA: Gene Function Prediction using a Multiple Association Network Integration Algorithm
↑ TOP

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

ISMB/ECCB 2009 Blog
TT32: Eija Korpelainen - Chipster - user-friendly software for reproducible microarray data analysis
↑ TOP

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

ISMB/ECCB 2009 Blog
TT33: Vince Grolmusz - NASCENT: An Automatic Protein Interaction Network
↑ TOP

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

ISMB/ECCB 2009 Blog
TT34: Mark Clement - GNUMAP: Unbiased Probabilistic Mapping of Next-Generation Sequencing Reads
Workflow: hash the genome into short k-mers. Map reads on the genome using a probabilistic algorithm. - Gabriele Sales
Defaults to 10-mers currently - Oliver Hofmann
GNUMap use 10-mers as seeds. - Gabriele Sales
Alignments: probabilistic Needleman-Wunsch to compensate for the variable quality of base calls. - Gabriele Sales
Takes base call quality into account - Oliver Hofmann
Provides a quick overview of single read variation - Oliver Hofmann
The algorithm uses a PWM. - Gabriele Sales
What happens to reads matching multiple loci in the genome? Options: discard (repeats); map to all; pick one. - Gabriele Sales
Uses probabilistic assignment (proportional) for PWMs matching multiple genomic locations - Oliver Hofmann
Relation to other tools via simulation studies - Oliver Hofmann
...more...
↑ TOP

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

ISMB/ECCB 2009 Blog
TT35: Vince Grolmusz - Decomp - A PDB decomposition Tool
↑ TOP

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

ISMB/ECCB 2009 Blog
TT36: Younghoon Kim - MONET: A Cytoscape plugin for genome-scale network inference from expression profiles using modularization and parallel processing techniques with supercomputing resources
Motivation: insufficient information in gene expression data alone for the efficient analysis of thousands of genes - Oliver Hofmann
Improving the sample to gene ratio by modularization - Oliver Hofmann
GO annotation for the functional description. Divide/conquer approach, identify seed genes in global network, build local networks, parallel bayesian network learning - Oliver Hofmann
Available via the cytoscape plugin manager - Oliver Hofmann
↑ TOP

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

ISMB/ECCB 2009 Blog
TT37: Martin Madera - Scoring and aligning profile HMMs with Profile Comparer (PRC)
↑ TOP

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

ISMB/ECCB 2009 Blog
TT38: Dominic Clark - EMBL-EBI Industry Programme
↑ TOP

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

ISMB/ECCB 2009 Blog
TT39: Isabel Rocha - OptFlux: a software for metabolic engineering
↑ TOP

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

ISMB/ECCB 2009 Blog
TT40: Franck Tanoh - BioCatalogue: A Curated Web Service Registry for the Life Science Community
A catalogue where to register web services. REST API, open source codebase. - Gabriele Sales
Estimate of public web services in Life Science: 3000+ - Gabriele Sales
People who have an interest in such services: users, developers, service providers, and tool developers - Allyson Lister
What BioCatalog adds: free text searches, tags (controlled vocabulary), automatic monitoring and testing. - Gabriele Sales
You can bookmark lots of services, even without signing up - Allyson Lister
Each web service is associated to categories. - Gabriele Sales
An icon captures the state of the service (online, not responding). - Gabriele Sales
Can refine searches (aka "search within results") - Gabriele Sales
lists licensing / costs as well - Allyson Lister
...more...
↑ TOP

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

ISMB/ECCB 2009 Blog
TT41: Laszlo Kajan - Visual PredictProtein and jBio: a JavaScript library for bioinformatics
↑ TOP

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

ISMB/ECCB 2009 Blog
TT42: Karim Chine - Computational Biology in the cloud, towards a federative and collaborative R-based platform
Eamonn Maguire talking on behalf of Karim Chine - Gabriele Sales
Java program (web app or web start app) built on R and Scilab - Gabriele Sales
Biocep-R - Allyson Lister
RESTful API. - Allyson Lister
BIOCEP-R has advanced graphics - more than with regular R - Allyson Lister
Built on top of R and Scilab - Cass Johnston
wow - their software is an "ecosystem" :) - Allyson Lister
Computational scripts: R / Python / Groovy - Gabriele Sales
The BIOCEP computational open platform ecosystem: computational data sources, resources, components, GUIs, web services and scripts - Allyson Lister
...more...
↑ TOP

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

ISMB/ECCB 2009 Blog
TT43: Robert Murphy - Protein Subcellular Location Image Database, Release 5
↑ TOP

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

ISMB/ECCB 2009 Blog
TT44: Andreas Biegert - Protein homology searches and structure prediction with HHpred and the MPI/LMU Bioinformatics Toolkit
↑ TOP

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

ISMB/ECCB 2009 Blog
↑ TOP

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

ISMB/ECCB 2009 Blog
TT46: Richard Smith - InterMine – open source data warehouse and query interface
↑ TOP

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

ISMB/ECCB 2009 Blog
TT47: Chris Rawlings - Semantic Data Integration for Systems Biology Research
Also speaking: Catherine Canevet and Paul Fisher - Allyson Lister
Two systems to integrate data. - Gabriele Sales
BBSRC-funded research collaboration in Newcastle, Manchester, and Rothamsted : ONDEX and Taverna - Allyson Lister
Demo on the integration and validation of yeast metabolome models. - Gabriele Sales
Taverna is a workflow workbench to integrate tools (including web services). - Gabriele Sales
Taverna can link ONDEX and external (ex. PubMed) data sources via the web-service interface. - Gabriele Sales
When ONDEX works with Taverna, instead of using the pipeline manager you use the ONDEX web services and access ONDEX from Taverna. This means you can use Taverna to pull in data into ONDEX. - Allyson Lister
Outline of the demo: starting from Janboree Network SMBL, parse it into Ondex, remove currency metabolites and annotate using network analusis results. - Gabriele Sales
Then switch to Taverna. Identify orphans, retrive related enzymes, assemble a PubMed query and link results to the graph. - Gabriele Sales
...more...
↑ TOP

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

ISMB/ECCB 2009 Blog
TT48: David Croft - Reactome tools for expression data and pathway visualization
Reactome collects processes at the cellular level. - Gabriele Sales
Plans for a new visualization for the website. - Gabriele Sales
At the top of the reactome webpage there is a link pointing to the new interface. - Gabriele Sales
The left bar of the interface collect links to single pathways. - Gabriele Sales
Google Map-like buttons: zoom in / out, scroll. - Gabriele Sales
By clicking on a compound, list of other pathways it participates to. - Gabriele Sales
Free text searches: multiple results displayed in a tab. - Gabriele Sales
↑ TOP

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

ISMB/ECCB 2009 Blog
TT49: Lukas Marsalek - BALLView: a molecular viewer and modelling tool with real-time raytracing capabilities
Link to preliminary pictures http://www.ballview.org/raytracing/gallery Definitely looks cool and I hope it will be useful as well. - Pawel Szczesny
Very nice images at Pawel's link. - Neil Saunders
↑ TOP