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
(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 ***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 |
|
