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Difference between revisions of "BOSC 2009 Schedule"

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Return to [[BOSC_2009 | BOSC 2009]] main page.
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* Return to '''[[BOSC_2009 | BOSC 2009]]''' main page.
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* Click on the talk title to view the individual abstract as a PDF file.
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== Keynote Speakers ==
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* Click '''[[Media:BOSC2009_program_20090601.pdf | here]]''' to download full program in PDF format (2 MB).
−
 
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* Important '''[[BOSC_2009#Information_for_Speakers | Information for Speakers]]'''
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The BOSC 2009 Organizing committee is pleased to announce our two Keynote Speakers:
 
−
 
 
−
=== Alan Ruttenberg ===
 
−
 
 
−
[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg] is a Principal Scientist at [http://sciencecommons.org Science Commons].  He works with Semantic Web technologies in computational biology, with an emphasis on the creation and application of structured biological knowledge to interpret experimental results. He is currently involved in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that will form the upper level ontology for the OBO foundry, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), the Information Artifact Ontology (IAO), and BioPAX-OBO for representing molecular and cellular pathways. These interests and efforts come together in my project at Science Commons - the Neurocommons, a large scale Semantic Web knowledge base of biological information aimed at supporting, initially, the neurosciences. He is also an active participant in W3C Semantic Web activities. In 2006 and 2007 he was a member of the Health Care Life Sciences Interest Group, and early work on the Neurocommons became the core of the prototype life sciences knowledge base that the group has documented. He is a chair of the OWL Working Group specifying OWL 2, and a coordinating editor of the OBO Foundry.
 
−
His graduate work was at the MIT Media Lab in the Music and Cognition Group, and he has an undergraduate degree in Physics and Mathematics from Brandeis University.
 
−
 
 
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=== Robert S. Hanmer ===
 
−
 
 
−
Robert S. Hanmer is a Consulting Member of Technical Staff in the Technical Component Management area in Alcatel-Lucent’s Operations area.  He is based in Naperville, Illinois, USA. Current responsibilities include developing software-sourcing strategies for middleware and open source software. Previous positions within Lucent and Bell Laboratories have included development, architecture and evaluation of highly reliable systems focusing especially on the areas of reliability and performance.  He is active in the software patterns community, including serving as program chair at several pattern conferences.  He has authored or co-authored 14 journal articles, several book chapters and the book Patterns for Fault Tolerant Software. He is a member of the IEEE Computer Society,  a Senior Member of the ACM and current President of [http://hillside.net/ The Hillside Group], the organization that sponsors the PLoP conference.  He received his B.S. and M.S. degrees in Computer Science from Northwestern University in Evanston, Illinois.
 
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His talk at BOSC will be entitled "Software Patterns for Reusable Design".
 
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== Multicore & GPGPU Computing ==
 
−
 
 
−
Click on the title to view the abstract.
 
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* Jean-Stéphane Varré - [[Media:Bosc2009_submission_22.pdf | Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics]] (15 min.)
 
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* Josh Buckner - [[Media:Bosc2009_submission_32.pdf | Enabling GPU Computing in the R Statistical Environment]] (15 min.)
 
−
* Mikhail Fursov - [[Media:Bosc2009_submission_18.pdf | UGENE – A practical approach for complex computational analysis  in molecular biology]] (10 min.)
 
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* Oswaldo Trelles - [[Media:Bosc2009_submission_11.pdf | Qnorm: A library of parallel methods for gene-expression Q-normalization]] (5 min. Lightning Talk)
 
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== Computational Grids ==
 
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−
Click on the title to view the abstract.
 
−
 
 
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* Hajo N. Krabbenhöft - [[Media:Bosc2009_submission_31.pdf | Taverna workflows across Grids, web services and the command line]] (15 min.)
 
−
* Ann-Kristin Grimm - [[Media:Bosc2009_submission_12.pdf | Grid-based expression QTL analysis]] (10 min.)
 
−
* Joel Hedlund - [[Media:Bosc2009_submission_28.pdf | The Nordic BioGrid project -- Bioinformatics for the grid]] (5 min. Lightning Talk)
 
−
 
 
−
== Visualization ==
 
−
 
 
−
Click on the title to view the abstract.
 
−
 
 
−
* Allan Kuchinsky - [[Media:Bosc2009_submission_23.pdf | Cytoscape Springs Forward: Re-architecture for Version 3.0]] (15 min.)
 
−
* Frederik Decouttere - [[Media:Bosc2009_submission_8.pdf | Bioinformatics simplified with seqpad]] (10 min.)
 
−
* Bernat Gel - [[Media:Bosc2009_submission_26.pdf | DASGenExp: an interactive web-based DAS client with client-side rendering]] (10 min.)
 
−
 
 
−
== Open Source Software ==
 
−
 
 
−
Click on the title to view the abstract.
 
−
 
 
−
* Kazuharu Arakawa - [[Media:Bosc2009_submission_39.pdf | Web Service Interface for G-language Genome Analysis Environment]] (10 min.)
 
−
* Sylvain Brohée - [[Media:Bosc2009_submission_3.pdf | Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases]] (10 min.)
 
−
* Quinn Snell - [[Media:Bosc2009_submission_33.pdf | PSODA: Open Source Phylogenetic Search and DNA Analysis]] (15 min.)
 
−
 
 
−
== Data & Analysis Management (shared session with D&AM SIG) ==
 
−
 
 
−
Click on the title to view the abstract.
 
−
 
 
−
* Morris Swertz - [[Media:Bosc2009_submission_27.pdf | MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments]] (15 min.)
 
−
* Mark Welsh - [[Media:Bosc2009_submission_10.pdf | BioHDF: Open binary file formats for large-scale data management – Project Update]] (15 min.)
 
−
* Robert Murphy - [[Media:Bosc2009_submission_34.pdf | PSLID, the Protein Subcellular Location Image Database: Subcellular location assignments, annotated image collections, image analysis tools, and generative models of protein distributions]] (15 min.)
 
−
* Kam Dahlquist - [[Media:Bosc2009_submission_35.pdf | XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources]] (10 min.)
 
−
* Brad Chapman - [[Media:Bosc2009_submission_14.pdf | Lowering barriers to publishing biological data on the web]] (10 min.)
 
−
 
 
−
== Bio* Update ==
 
−
 
 
−
Click on the title to view the abstract.
 
−
 
 
−
* Martin Senger - [[Media:Bosc2009_submission_13.pdf | Soaplab: Open Source Web Services Framework for Bioinformatics Programs]] (10 min.)
 
−
* Pjotr Prins - [[Media:Bosc2009_submission_4.pdf | BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA]] (15 min.)
 
−
* Peter Rice - [[Media:Bosc2009_submission_5.pdf | EMBOSS: European Molecular Biology Open Software Suite]] (10 min.)
 
−
* Peter Cock - [[Media:Bosc2009_submission_19.pdf | Biopython Project Update]] (10 min.)
 
−
* Andreas Prlic - [[Media:Bosc2009_submission_15.pdf | BioJava 2009: an Open-Source Framework for Bioinformatics]] (10 min.)
 
−
* Jim Procter - [[Media:Bosc2009_submission_16.pdf | Application of VAMSAS enabled tools for the investigation of protein evolution]] (10 min.)
 
−
* Steffen Möller - [[Media:Bosc2009_submission_30.pdf | Debian adopts and disseminates Bioinformatics Open Source Software]] (5 min. Lightning Talk)
 
−
 
 
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== Regulatory Genomics ==
 
−
 
 
−
Click on the title to view the abstract.
 
−
 
 
−
* Finn Drablos - [[Media:Bosc2009_submission_6.pdf | Computational discovery of composite motifs in DNA]] (15 min.)
 
−
* Sophie Schbath - [[Media:Bosc2009_submission_38.pdf | R'MES]] (15 min.)
 
−
* Matias Piipari - [[Media:Bosc2009_submission_24.pdf | Large-scale gene regulatory motif discovery and categorisation with NestedMICA]] (10 min.)
 
−
* Bartek Wilczynski - [[Media:Bosc2009_submission_29.pdf | BNfinder: free software for effective Bayesian Network inference]] (15 min.)
 
−
* Lonnie Welch - [[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]] (10 min.)
 
−
* François Fauteux - [[Media:Bosc2009_submission_40.pdf | SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY]] (10 min.)
 
−
 
 
−
== Design Patterns Panel Discussion ==
 
−
 
 
−
'''On the Applicability of Design Patterns for the Bioinformatics Open Source Community'''
 
−
 
 
−
Click on the author's name to view the abstract submitted for the panel.
 
−
 
 
−
* Robert Hanmer - Moderator
 
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* [[Media:Bosc2009_submission_9.pdf | Lonnie Welch]]
 
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* [[Media:Bosc2009_submission_17.pdf | Aleksi Kallio]]
 
  
 
== Schedule ==
 
== Schedule ==
Line 101: Line 13:
 
| 9:00-9:15am
 
| 9:00-9:15am
 
| Kam Dahlquist
 
| Kam Dahlquist
−
| [Welcome]
+
| [Welcome] [http://www.slideshare.net/bosc/bosc-intro-20090627 ***SLIDES***]
 
|-
 
|-
 
| 9:15-10:15
 
| 9:15-10:15
−
| Alan Ruttenberg
+
| [[BOSC_2009#Alan_Ruttenberg | Alan Ruttenberg]]
−
| [Keynote] Semantic Web Technologies
+
| [Keynote] Can we reduce the burden of data integration?  Challenge and opportunity in building the web of data
 
|-
 
|-
 
| '''10:15-10:45'''
 
| '''10:15-10:45'''
Line 112: Line 24:
 
| 10:45-11:05
 
| 10:45-11:05
 
| Jean-Stéphane Varré
 
| Jean-Stéphane Varré
−
| [Multicore & GPGPU Computing] Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics
+
| [Multicore & GPGPU Computing] [[Media:Bosc2009_submission_22.pdf | Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics]] [http://www.slideshare.net/bosc/varrebiomanycoresbosc2009 ***SLIDES***]
 
|-
 
|-
−
| 11:25-11:40
+
| 11:05-11:25
 
| Josh Buckner
 
| Josh Buckner
−
| [Multicore & GPGPU Computing] Enabling GPU Computing in the R Statistical Environment
+
| [Multicore & GPGPU Computing] [[Media:Bosc2009_submission_32.pdf | Enabling GPU Computing in the R Statistical Environment]] [http://www.slideshare.net/bosc/bucknergpurbosc2009 ***SLIDES***]
 
|-
 
|-
 
| 11:25-11:40
 
| 11:25-11:40
 
| Mikhail Fursov
 
| Mikhail Fursov
−
| [Multicore & GPGPU Computing] UGENE – A practical approach for complex computational analysis in molecular biology
+
 
 +
(cancelled)
 +
| [Multicore & GPGPU Computing] [[Media:Bosc2009_submission_18.pdf | UGENE – A practical approach for complex computational analysis in molecular biology]]
 
|-
 
|-
 
| 11:40-11:48
 
| 11:40-11:48
 
| Oswaldo Trelles
 
| Oswaldo Trelles
−
| [Multicore & GPGPU Computing Lightning Talk] Qnorm: A library of parallel methods for gene-expression Q-normalization
+
 
 +
(talk given by Pjotr Prins)
 +
| [Multicore & GPGPU Computing Lightning Talk] [[Media:Bosc2009_submission_11.pdf | Qnorm: A library of parallel methods for gene-expression Q-normalization]] [http://www.slideshare.net/bosc/trellesqnormbosc2009 ***SLIDES***]
 
|-
 
|-
 
| 11:48-12:08pm
 
| 11:48-12:08pm
 
| Hajo N. Krabbenhöft
 
| Hajo N. Krabbenhöft
−
| [Computational Grids] Taverna workflows across Grids, web services and the command line
+
| [Computational Grids] [[Media:Bosc2009_submission_31.pdf | Taverna workflows across Grids, web services and the command line]] [http://www.slideshare.net/bosc/krabbenhofttavernaarcbosc2009 ***SLIDES***]
 
|-
 
|-
 
| 12:08-12:23
 
| 12:08-12:23
 
| Ann-Kristin Grimm
 
| Ann-Kristin Grimm
−
| [Computational Grids] Grid-based expression QTL analysis
+
 
 +
(talk given by Steffen Moeller)
 +
| [Computational Grids] [[Media:Bosc2009_submission_12.pdf | Grid-based expression QTL analysis]] [http://www.slideshare.net/bosc/moellergridqtlbosc2009 ***SLIDES***]
 
|-
 
|-
 
| 12:23-12:31
 
| 12:23-12:31
 
| Joel Hedlund
 
| Joel Hedlund
−
| [Computational Grids Lightning Talk] The Nordic BioGrid project -- Bioinformatics for the grid
+
| [Computational Grids Lightning Talk] [[Media:Bosc2009_submission_28.pdf | The Nordic BioGrid project -- Bioinformatics for the grid]] [http://www.slideshare.net/bosc/hedlundbiogridbosc2009 ***SLIDES***]
 
|-  
 
|-  
 
| '''12:31-2:00'''
 
| '''12:31-2:00'''
Line 143: Line 61:
 
| 2:00-2:20
 
| 2:00-2:20
 
| Allan Kuchinsky
 
| Allan Kuchinsky
−
| [Visualization] Cytoscape Springs Forward: Re-architecture for Version 3.0
+
| [Visualization] [[Media:Bosc2009_submission_23.pdf | Cytoscape Springs Forward: Re-architecture for Version 3.0]] [http://www.slideshare.net/bosc/kuchinskycytoscapebosc2009 ***SLIDES***]
 
|-
 
|-
 
| 2:20-2:33
 
| 2:20-2:33
 
| Frederik Decouttere
 
| Frederik Decouttere
−
| [Visualization] Bioinformatics simplified with seqpad
+
| [Visualization] [[Media:Bosc2009_submission_8.pdf | Bioinformatics simplified with seqpad]] [http://www.slideshare.net/bosc/decouttereseqpad-bosc2009 ***SLIDES***]
 
|-
 
|-
 
| 2:33-2:46
 
| 2:33-2:46
 
| Bernat Gel
 
| Bernat Gel
−
| [Visualization] DASGenExp: an interactive web-based DAS client with client-side rendering
+
| [Visualization] [[Media:Bosc2009_submission_26.pdf | DASGenExp: an interactive web-based DAS client with client-side rendering]] [http://www.slideshare.net/bosc/geldasgenexpbosc2009 ***SLIDES***]
 
|-
 
|-
 
| 2:46-2:59
 
| 2:46-2:59
 
| Kazuharu Arakawa
 
| Kazuharu Arakawa
−
| [OS Software] Web Service Interface for G-language Genome Analysis Environment
+
| [OS Software] [[Media:Bosc2009_submission_39.pdf | Web Service Interface for G-language Genome Analysis Environment]] [http://www.slideshare.net/bosc/arakawaglanguagebosc2009 ***SLIDES***]
 
|-
 
|-
 
| 2:59-3:12
 
| 2:59-3:12
 
| Sylvain Brohée
 
| Sylvain Brohée
−
| [OS Software] Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases
+
| [OS Software] [[Media:Bosc2009_submission_3.pdf | Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases]] [http://www.slideshare.net/bosc/broheewikibosc2009 ***SLIDES***]
 
|-  
 
|-  
 
| 3:12-3:30
 
| 3:12-3:30
 
| Bartek Wilczynski
 
| Bartek Wilczynski
−
| [Regulatory Genomics] BNfinder: free software for effective Bayesian Network inference
+
| [Regulatory Genomics] [[Media:Bosc2009_submission_29.pdf | BNfinder: free software for effective Bayesian Network inference]] [http://www.slideshare.net/bosc/wilczynskibnfinderbosc2009 ***SLIDES***]
 
|-
 
|-
 
| '''3:30-4:00'''
 
| '''3:30-4:00'''
Line 170: Line 88:
 
| 4:00-4:20
 
| 4:00-4:20
 
| Morris Swertz
 
| Morris Swertz
−
| [Data & Analysis Management] MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments
+
| [Data & Analysis Management] [[Media:Bosc2009_submission_27.pdf | MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments]] [http://www.slideshare.net/bosc/swertz-molgenis-bosc2009 ***SLIDES***]
 
|-  
 
|-  
 
| 4:20-4:40
 
| 4:20-4:40
 
| Robert Murphy
 
| 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
+
| [Data & Analysis Management] [[Media:Bosc2009_submission_34.pdf | PSLID, the Protein Subcellular Location Image Database: Subcellular location assignments, annotated image collections, image analysis tools, and generative models of protein distributions]] [http://www.slideshare.net/bosc/murphypslidbosc2009 ***SLIDES***]
 
|-
 
|-
 
|4:40-5:00
 
|4:40-5:00
 
| Mark Welsh
 
| Mark Welsh
−
| [Data & Analysis Management] BioHDF: Open binary file formats for large-scale data management – Project Update
+
| [Data & Analysis Management] [[Media:Bosc2009_submission_10.pdf | BioHDF: Open binary file formats for large-scale data management – Project Update]] [http://www.slideshare.net/bosc/welshbiohdfbosc2009 ***SLIDES***]
 
|-
 
|-
 
| 5:00-5:15
 
| 5:00-5:15
 
| Brad Chapman
 
| Brad Chapman
−
| [Data & Analysis Management] Lowering barriers to publishing biological data on the web
+
| [Data & Analysis Management] [[Media:Bosc2009_submission_14.pdf | Lowering barriers to publishing biological data on the web]] [http://www.slideshare.net/bosc/chapmanpublishingwebbosc2009 ***SLIDES***]
 
|-
 
|-
 
| 5:15-5:30
 
| 5:15-5:30
 
| Kam Dahlquist
 
| Kam Dahlquist
−
| [Data & Analysis Management] XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources
+
| [Data & Analysis Management] [[Media:Bosc2009_submission_35.pdf | XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources]] [http://www.slideshare.net/bosc/dahlquistxmlpipedbbosc2009 ***SLIDES***]
 
|-  
 
|-  
 
| 5:30-6:00
 
| 5:30-6:00
 
|  
 
|  
−
| Lightning Talks and Birds of a Feather
+
| [Lightning Talks]
 +
5:30 Matias Piipari - [http://imotifs.pearcomp.com/ iMotifs]: a motif viewer/editor for the Mac [http://www.slideshare.net/bosc/piipariimotifbosc2009 ***SLIDES***]
 +
 
 +
5:38 Kristian Rother - [http://genesilico.pl/moderna/ ModeRNA] - an Open Source platform for RNA 3D modeling [http://www.slideshare.net/bosc/rothermodernabosc2009 ***SLIDES***]
 +
 
 +
5:46 Tiago Antao - [http://code.google.com/p/openmalaria openmalaria] - A simulator of malaria epidemology and control [http://www.slideshare.net/bosc/antaoopenmalariabosc2009 ***SLIDES***]
 +
 
 +
[[BOSC_2009/Birds-of-a-Feather | Birds of a Feather]]
 
|-  
 
|-  
−
| 7:00
+
| 6:15
 
|  
 
|  
−
| <nowiki>O|B|F</nowiki> Board Meeting and No-host Dinner (location TBA)
+
| <nowiki>OBF</nowiki> Board Meeting and No-host Dinner - Rica Talk Hotel Restaurant
 
|-
 
|-
 
| '''Day 2'''
 
| '''Day 2'''
Line 205: Line 130:
 
|-
 
|-
 
| 9:15-10:15
 
| 9:15-10:15
−
| Robert Hanmer
+
| [[BOSC_2009#Robert_S._Hanmer | Robert Hanmer]]
−
| [Keynote] Software Patterns for Reusable Design
+
| [Keynote] Software Patterns for Reusable Design [http://www.slideshare.net/bosc/hanmer-software-patterns-bosc2009 ***SLIDES***]
 
|-
 
|-
 
| '''10:15-10:45'''
 
| '''10:15-10:45'''
Line 213: Line 138:
 
| 10:45-11:00
 
| 10:45-11:00
 
| Peter Rice
 
| Peter Rice
−
| [Bio* Update] EMBOSS: European Molecular Biology Open Software Suite
+
| [Bio* Update] [[Media:Bosc2009_submission_5.pdf | EMBOSS: European Molecular Biology Open Software Suite]] [http://www.slideshare.net/bosc/rice-emboss-bosc2009 ***SLIDES***]
 
|-
 
|-
 
| 11:00-11:15
 
| 11:00-11:15
 
| Peter Cock
 
| Peter Cock
−
| [Bio* Update] Biopython Project Update
+
| [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
−
| Andreas Prlic
+
| [http://biojava.org/wiki/Andreas_Prlic Andreas Prlic]
−
| [Bio* Update] BioJava 2009: an Open-Source Framework for Bioinformatics
+
| [Bio* Update] [[Media:Bosc2009_submission_15.pdf | BioJava 2009: an Open-Source Framework for Bioinformatics]] [http://www.slideshare.net/bosc/prlic-bio-java-bosc2009 ***SLIDES***]
 
|-  
 
|-  
 
| 11:30-11:45
 
| 11:30-11:45
 
| Jim Procter
 
| Jim Procter
−
| [Bio* Update] Application of VAMSAS enabled tools for the investigation of protein evolution
+
| [Bio* Update] [[Media:Bosc2009_submission_16.pdf | Application of VAMSAS enabled tools for the investigation of protein evolution]] [http://www.slideshare.net/bosc/procter-vamsas-bosc2009 ***SLIDES***]
 
|-
 
|-
 
| 11:45-12:00pm
 
| 11:45-12:00pm
 
| Martin Senger
 
| Martin Senger
−
| [Bio* Update] Soaplab: Open Source Web Services Framework for Bioinformatics Programs
+
| [Bio* Update] [[Media:Bosc2009_submission_13.pdf | Soaplab: Open Source Web Services Framework for Bioinformatics Programs]] [http://www.slideshare.net/bosc/senger-soaplab-bosc2009 ***SLIDES***]
 
|-
 
|-
 
| 12:00-12:20
 
| 12:00-12:20
 
| Pjotr Prins
 
| Pjotr Prins
−
| [Bio* Update] 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] 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 244: Line 169:
 
| 2:00-2:20
 
| 2:00-2:20
 
| Quinn Snell
 
| Quinn Snell
−
| [OS Software] PSODA: Open Source Phylogenetic Search and DNA Analysis
+
| [OS Software] [[Media:Bosc2009_submission_33.pdf | PSODA: Open Source Phylogenetic Search and DNA Analysis]] [http://www.slideshare.net/bosc/snell-psoda-bosc2009 ***SLIDES***]
 
|-  
 
|-  
 
| 2:20-2:40
 
| 2:20-2:40
 
| Finn Drablos
 
| Finn Drablos
−
| [Regulatory Genomics] Computational discovery of composite motifs in DNA
+
| [Regulatory Genomics] [[Media:Bosc2009_submission_6.pdf | Computational discovery of composite motifs in DNA]] [http://www.slideshare.net/bosc/drablos-composite-motifs-bosc2009 ***SLIDES***]
 
|-  
 
|-  
 
| 2:40-2:55
 
| 2:40-2:55
 
| François Fauteux
 
| François Fauteux
−
| [Regulatory Genomics] SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY
+
| [Regulatory Genomics] [[Media:Bosc2009_submission_40.pdf | SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY]] [http://www.slideshare.net/bosc/fauteux-seeder-bosc2009 ***SLIDES***]
 
|-
 
|-
 
| 2:55-3:10
 
| 2:55-3:10
 
| Matias Piipari
 
| Matias Piipari
−
| [Regulatory Genomics] Large-scale gene regulatory motif discovery and categorisation with NestedMICA
+
| [Regulatory Genomics] [[Media:Bosc2009_submission_24.pdf | Large-scale gene regulatory motif discovery and categorisation with NestedMICA]]
 
|-
 
|-
 
| 3:10-3:30
 
| 3:10-3:30
 
| Sophie Schbath  
 
| Sophie Schbath  
−
| [Regulatory Genomics] R'MES:
+
| [Regulatory Genomics] [[Media:Bosc2009_submission_38.pdf | R'MES]] [http://www.slideshare.net/bosc/schbath-rmes-bosc2009 ***SLIDES***]
 
|-  
 
|-  
 
| '''3:30-4:00'''
 
| '''3:30-4:00'''
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| 4:00-4:15
 
| 4:00-4:15
 
| Lonnie Welch
 
| 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
+
| [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), Lonnie Welch, Aleksi Kallio, other panelists TBA
+
| 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
+
| [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
−
| Lightning Talks and Birds of a Feather
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| [[BOSC_2009/Birds-of-a-Feather | Birds of a Feather]]
 
|}
 
|}

Latest revision as of 18:11, 7 September 2015

Schedule

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
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