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BOSC 2009 Schedule
From Open Bioinformatics Foundation
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- Important Information for Speakers
Schedule
| 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 |
| 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 |
| 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 |
| 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 |
| 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 5:46 Tiago Antao - openmalaria - A simulator of malaria epidemology and control ***SLIDES*** | |
| 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 |
| 10:15-10:45 | Coffee Break | |
| 10:45-11:00 | Peter Rice | [Bio* Update] EMBOSS: European Molecular Biology Open Software Suite |
| 11:00-11:15 | Peter Cock | [Bio* Update] Biopython Project Update |
| 11:15-11:30 | Andreas Prlic | [Bio* Update] BioJava 2009: an Open-Source Framework for Bioinformatics |
| 11:30-11:45 | Jim Procter | [Bio* Update] Application of VAMSAS enabled tools for the investigation of protein evolution |
| 11:45-12:00pm | Martin Senger | [Bio* Update] Soaplab: Open Source Web Services Framework for Bioinformatics Programs |
| 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 |
| 2:20-2:40 | Finn Drablos | [Regulatory Genomics] Computational discovery of composite motifs in DNA |
| 2:40-2:55 | François Fauteux | [Regulatory Genomics] SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY |
| 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 |
