BOSC 2009 Schedule

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Day 1 Saturday June 27
9:00-9:15am Kam Dahlquist [Welcome] ***SLIDES***
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


[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 ***SLIDES***
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   OBF 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 2009 ***SLIDES*** ***PDF***
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 ***SLIDES***
12:20-12:28 Steffen Möller [OS Software Lightning Talk] Debian adopts and disseminates Bioinformatics Open Source Software ***SLIDES***
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 ***SLIDES***
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 ***SLIDES***
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 Panel ***SLIDES******Kallio SLIDES***
4:50-5:30 Birds of a Feather