| Day 1
|
Saturday
|
June 27
|
| 9:00-9:15am
|
Kam Dahlquist
|
[Welcome]
|
| 9:15-10:15
|
Alan Ruttenberg
|
[Keynote] Can we reduce the burden of data integration? Challenge and opportunity in building the web of data
|
| 10:15-10:45
|
Coffee Break
|
| 10:45-11:05
|
Jean-Stéphane Varré
|
[Multicore & GPGPU Computing] Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics ***SLIDES***
|
| 11:05-11:25
|
Josh Buckner
|
[Multicore & GPGPU Computing] Enabling GPU Computing in the R Statistical Environment ***SLIDES***
|
| 11:25-11:40
|
Mikhail Fursov
(cancelled)
|
[Multicore & GPGPU Computing] UGENE – A practical approach for complex computational analysis in molecular biology
|
| 11:40-11:48
|
Oswaldo Trelles
(talk given by Pjotr Prins)
|
[Multicore & GPGPU Computing Lightning Talk] Qnorm: A library of parallel methods for gene-expression Q-normalization ***SLIDES***
|
| 11:48-12:08pm
|
Hajo N. Krabbenhöft
|
[Computational Grids] Taverna workflows across Grids, web services and the command line ***SLIDES***
|
| 12:08-12:23
|
Ann-Kristin Grimm
(talk given by Steffen Moeller)
|
[Computational Grids] Grid-based expression QTL analysis ***SLIDES***
|
| 12:23-12:31
|
Joel Hedlund
|
[Computational Grids Lightning Talk] The Nordic BioGrid project -- Bioinformatics for the grid ***SLIDES***
|
| 12:31-2:00
|
Lunch
|
| 2:00-2:20
|
Allan Kuchinsky
|
[Visualization] Cytoscape Springs Forward: Re-architecture for Version 3.0 ***SLIDES***
|
| 2:20-2:33
|
Frederik Decouttere
|
[Visualization] Bioinformatics simplified with seqpad ***SLIDES***
|
| 2:33-2:46
|
Bernat Gel
|
[Visualization] DASGenExp: an interactive web-based DAS client with client-side rendering ***SLIDES***
|
| 2:46-2:59
|
Kazuharu Arakawa
|
[OS Software] Web Service Interface for G-language Genome Analysis Environment ***SLIDES***
|
| 2:59-3:12
|
Sylvain Brohée
|
[OS Software] Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases ***SLIDES***
|
| 3:12-3:30
|
Bartek Wilczynski
|
[Regulatory Genomics] BNfinder: free software for effective Bayesian Network inference ***SLIDES***
|
| 3:30-4:00
|
Coffee Break
|
| 4:00-4:20
|
Morris Swertz
|
[Data & Analysis Management] MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments
|
| 4:20-4:40
|
Robert Murphy
|
[Data & Analysis Management] PSLID, the Protein Subcellular Location Image Database: Subcellular location assignments, annotated image collections, image analysis tools, and generative models of protein distributions ***SLIDES***
|
| 4:40-5:00
|
Mark Welsh
|
[Data & Analysis Management] BioHDF: Open binary file formats for large-scale data management – Project Update ***SLIDES***
|
| 5:00-5:15
|
Brad Chapman
|
[Data & Analysis Management] Lowering barriers to publishing biological data on the web ***SLIDES***
|
| 5:15-5:30
|
Kam Dahlquist
|
[Data & Analysis Management] XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources ***SLIDES***
|
| 5:30-6:00
|
|
[Lightning Talks]
5:30 Matias Piipari - iMotifs: a motif viewer/editor for the Mac ***SLIDES***
5:38 Kristian Rother - ModeRNA - an Open Source platform for RNA 3D modeling ***SLIDES***
5:46 Tiago Antao - openmalaria - A simulator of malaria epidemology and control ***SLIDES***
Birds of a Feather
|
| 6:15
|
|
O|B|F Board Meeting and No-host Dinner - Rica Talk Hotel Restaurant
|
| Day 2
|
Sunday
|
June 28
|
| 9:00-9:15am
|
Kam Dahlquist
|
[Announcements]
|
| 9:15-10:15
|
Robert Hanmer
|
[Keynote] Software Patterns for Reusable Design ***SLIDES***
|
| 10:15-10:45
|
Coffee Break
|
| 10:45-11:00
|
Peter Rice
|
[Bio* Update] EMBOSS: European Molecular Biology Open Software Suite ***SLIDES***
|
| 11:00-11:15
|
Peter Cock
|
[Bio* Update] Biopython Project Update ***SLIDES***
|
| 11:15-11:30
|
Andreas Prlic
|
[Bio* Update] BioJava 2009: an Open-Source Framework for Bioinformatics ***SLIDES***
|
| 11:30-11:45
|
Jim Procter
|
[Bio* Update] Application of VAMSAS enabled tools for the investigation of protein evolution ***SLIDES***
|
| 11:45-12:00pm
|
Martin Senger
|
[Bio* Update] Soaplab: Open Source Web Services Framework for Bioinformatics Programs ***SLIDES***
|
| 12:00-12:20
|
Pjotr Prins
|
[Bio* Update] BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA
|
| 12:20-12:28
|
Steffen Möller
|
[OS Software Lightning Talk] Debian adopts and disseminates Bioinformatics Open Source Software
|
| 12:30-2:00
|
Lunch
|
| 2:00-2:20
|
Quinn Snell
|
[OS Software] PSODA: Open Source Phylogenetic Search and DNA Analysis ***SLIDES***
|
| 2:20-2:40
|
Finn Drablos
|
[Regulatory Genomics] Computational discovery of composite motifs in DNA ***SLIDES***
|
| 2:40-2:55
|
François Fauteux
|
[Regulatory Genomics] SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY ***SLIDES***
|
| 2:55-3:10
|
Matias Piipari
|
[Regulatory Genomics] Large-scale gene regulatory motif discovery and categorisation with NestedMICA
|
| 3:10-3:30
|
Sophie Schbath
|
[Regulatory Genomics] R'MES
|
| 3:30-4:00
|
Coffee Break
|
| 4:00-4:15
|
Lonnie Welch
|
[Regulatory Genomics] Open Source Implementation of Batch-Extraction for Coding and Non-coding Sequences/An Open Source Framework for Bioinformatics Word Enumeration and Scoring
|
| 4:15-4:50
|
Robert Hanmer (moderator), Lonnie Welch, Aleksi Kallio and Jim Procter.
|
[Panel Discussion] On the Applicability of Design Patterns for the Bioinformatics Open Source Community
|
| 4:50-5:30
|
Birds of a Feather
|
