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Revision as of 17:35, 9 June 2009
- Return to BOSC 2009 main page.
- Click on the talk title to view the individual abstract as a PDF file.
- Click here to download full program in PDF format (2 MB).
- Important Information for Speakers
Schedule
Day 1
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Saturday
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June 27
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9:00-9:15am
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Kam Dahlquist
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[Welcome]
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9:15-10:15
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Alan Ruttenberg
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[Keynote] Can we reduce the burden of data integration? Challenge and opportunity in building the web of data
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10:15-10:45
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Coffee Break
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10:45-11:05
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Jean-Stéphane Varré
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[Multicore & GPGPU Computing] Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics
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11:05-11:25
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Josh Buckner
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[Multicore & GPGPU Computing] Enabling GPU Computing in the R Statistical Environment
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11:25-11:40
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Mikhail Fursov
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[Multicore & GPGPU Computing] UGENE – A practical approach for complex computational analysis in molecular biology
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11:40-11:48
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Oswaldo Trelles
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[Multicore & GPGPU Computing Lightning Talk] Qnorm: A library of parallel methods for gene-expression Q-normalization
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11:48-12:08pm
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Hajo N. Krabbenhöft
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[Computational Grids] Taverna workflows across Grids, web services and the command line
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12:08-12:23
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Ann-Kristin Grimm
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[Computational Grids] Grid-based expression QTL analysis
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12:23-12:31
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Joel Hedlund
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[Computational Grids Lightning Talk] The Nordic BioGrid project -- Bioinformatics for the grid
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12:31-2:00
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Lunch
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2:00-2:20
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Allan Kuchinsky
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[Visualization] Cytoscape Springs Forward: Re-architecture for Version 3.0
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2:20-2:33
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Frederik Decouttere
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[Visualization] Bioinformatics simplified with seqpad
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2:33-2:46
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Bernat Gel
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[Visualization] DASGenExp: an interactive web-based DAS client with client-side rendering
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2:46-2:59
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Kazuharu Arakawa
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[OS Software] Web Service Interface for G-language Genome Analysis Environment
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2:59-3:12
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Sylvain Brohée
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[OS Software] Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases
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3:12-3:30
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Bartek Wilczynski
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[Regulatory Genomics] BNfinder: free software for effective Bayesian Network inference
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3:30-4:00
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Coffee Break
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4:00-4:20
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Morris Swertz
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[Data & Analysis Management] MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments
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4:20-4:40
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Robert Murphy
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[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
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4:40-5:00
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Mark Welsh
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[Data & Analysis Management] BioHDF: Open binary file formats for large-scale data management – Project Update
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5:00-5:15
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Brad Chapman
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[Data & Analysis Management] Lowering barriers to publishing biological data on the web
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5:15-5:30
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Kam Dahlquist
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[Data & Analysis Management] XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources
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5:30-6:00
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Lightning Talks and Birds of a Feather
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7:00
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O|B|F Board Meeting and No-host Dinner (location TBA)
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Day 2
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Sunday
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June 28
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9:00-9:15am
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Kam Dahlquist
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[Announcements]
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9:15-10:15
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Robert Hanmer
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[Keynote] Software Patterns for Reusable Design
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10:15-10:45
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Coffee Break
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10:45-11:00
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Peter Rice
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[Bio* Update] EMBOSS: European Molecular Biology Open Software Suite
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11:00-11:15
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Peter Cock
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[Bio* Update] Biopython Project Update
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11:15-11:30
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Andreas Prlic
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[Bio* Update] BioJava 2009: an Open-Source Framework for Bioinformatics
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11:30-11:45
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Jim Procter
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[Bio* Update] Application of VAMSAS enabled tools for the investigation of protein evolution
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11:45-12:00pm
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Martin Senger
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[Bio* Update] Soaplab: Open Source Web Services Framework for Bioinformatics Programs
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12:00-12:20
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Pjotr Prins
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[Bio* Update] BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA
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12:20-12:28
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Steffen Möller
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[OS Software Lightning Talk] Debian adopts and disseminates Bioinformatics Open Source Software
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12:30-2:00
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Lunch
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2:00-2:20
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Quinn Snell
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[OS Software] PSODA: Open Source Phylogenetic Search and DNA Analysis
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2:20-2:40
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Finn Drablos
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[Regulatory Genomics] Computational discovery of composite motifs in DNA
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2:40-2:55
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François Fauteux
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[Regulatory Genomics] SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY
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2:55-3:10
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Matias Piipari
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[Regulatory Genomics] Large-scale gene regulatory motif discovery and categorisation with NestedMICA
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3:10-3:30
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Sophie Schbath
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[Regulatory Genomics] R'MES
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3:30-4:00
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Coffee Break
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4:00-4:15
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Lonnie Welch
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[Regulatory Genomics] Open Source Implementation of Batch-Extraction for Coding and Non-coding Sequences/An Open Source Framework for Bioinformatics Word Enumeration and Scoring
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4:15-4:50
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Robert Hanmer (moderator), Lonnie Welch, Aleksi Kallio, other panelists TBA
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[Panel Discussion] On the Applicability of Design Patterns for the Bioinformatics Open Source Community
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4:50-5:30
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Lightning Talks and Birds of a Feather
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