|
|
(6 intermediate revisions by 2 users not shown) |
Line 119: |
Line 119: |
| | 6:15 | | | 6:15 |
| | | | | |
− | | <nowiki>O|B|F</nowiki> Board Meeting and No-host Dinner - Rica Talk Hotel Restaurant | + | | <nowiki>OBF</nowiki> Board Meeting and No-host Dinner - Rica Talk Hotel Restaurant |
| |- | | |- |
| | '''Day 2''' | | | '''Day 2''' |
Line 142: |
Line 142: |
| | 11:00-11:15 | | | 11:00-11:15 |
| | Peter Cock | | | Peter Cock |
− | | [Bio* Update] [[Media:Bosc2009_submission_19.pdf | Biopython Project Update]] [http://www.slideshare.net/bosc/cock-biopython-bosc2009 ***SLIDES***] | + | | [Bio* Update] [[Media:Bosc2009_submission_19.pdf | Biopython Project Update 2009]] [http://www.slideshare.net/bosc/cock-biopython-bosc2009 ***SLIDES***] [http://biopython.org/DIST/docs/presentations/Biopython_BOSC_2009.pdf ***PDF***] |
| |- | | |- |
| | 11:15-11:30 | | | 11:15-11:30 |
Line 158: |
Line 158: |
| | 12:00-12:20 | | | 12:00-12:20 |
| | Pjotr Prins | | | Pjotr Prins |
− | | [Bio* Update] [[Media:Bosc2009_submission_4.pdf | BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA]] | + | | [Bio* Update] [[Media:Bosc2009_submission_4.pdf | BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA]] [http://www.slideshare.net/bosc/prins-bio-lib-bosc-2009 ***SLIDES***] |
| |- | | |- |
| | 12:20-12:28 | | | 12:20-12:28 |
| | Steffen Möller | | | Steffen Möller |
− | | [OS Software Lightning Talk] [[Media:Bosc2009_submission_30.pdf | Debian adopts and disseminates Bioinformatics Open Source Software]] | + | | [OS Software Lightning Talk] [[Media:Bosc2009_submission_30.pdf | Debian adopts and disseminates Bioinformatics Open Source Software]] [http://www.slideshare.net/bosc/moeller-debian-bosc2009 ***SLIDES***] |
| |- | | |- |
| | '''12:30-2:00''' | | | '''12:30-2:00''' |
Line 192: |
Line 192: |
| | 4:00-4:15 | | | 4:00-4:15 |
| | Lonnie Welch | | | Lonnie Welch |
− | | [Regulatory Genomics] [[Media:Bosc2009_submission_7_21.pdf | Open Source Implementation of Batch-Extraction for Coding and Non-coding Sequences/An Open Source Framework for Bioinformatics Word Enumeration and Scoring]] | + | | [Regulatory Genomics] [[Media:Bosc2009_submission_7_21.pdf | Open Source Implementation of Batch-Extraction for Coding and Non-coding Sequences/An Open Source Framework for Bioinformatics Word Enumeration and Scoring]] [http://www.slideshare.net/bosc/welch-wordifier-bosc2009 ***SLIDES***] |
| |- | | |- |
| | 4:15-4:50 | | | 4:15-4:50 |
| | Robert Hanmer (moderator), [[Media:Bosc2009_submission_9.pdf | Lonnie Welch]], [[Media:Bosc2009_submission_17.pdf | Aleksi Kallio]] and Jim Procter. | | | Robert Hanmer (moderator), [[Media:Bosc2009_submission_9.pdf | Lonnie Welch]], [[Media:Bosc2009_submission_17.pdf | Aleksi Kallio]] and Jim Procter. |
− | | [Panel Discussion] On the Applicability of Design Patterns for the Bioinformatics Open Source Community http://www.slideshare.net/bosc/kallio-chipster-bosc2009 ***Kallio SLIDES***] | + | | [Panel Discussion] On the Applicability of Design Patterns for the Bioinformatics Open Source Community [http://www.slideshare.net/bosc/software-patterns-panel-bos2009 Panel ***SLIDES***][http://www.slideshare.net/bosc/kallio-chipster-bosc2009 ***Kallio SLIDES***] |
| |- | | |- |
| |4:50-5:30 | | |4:50-5:30 |
| | [[BOSC_2009/Birds-of-a-Feather | Birds of a Feather]] | | | [[BOSC_2009/Birds-of-a-Feather | Birds of a Feather]] |
| |} | | |} |
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
(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
|