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Difference between revisions of "BOSC 2009 Schedule"

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(link to iMotif slides)
(Change inline use of O|B|F to OBF)
 
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| 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
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| 10:45-11:05
 
| 10:45-11:05
 
| Jean-Stéphane Varré
 
| Jean-Stéphane Varré
−
| [Multicore & GPGPU Computing] [[Media:Bosc2009_submission_22.pdf | 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***]
 
|-
 
|-
 
| 11:05-11:25
 
| 11:05-11:25
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(talk given by Pjotr Prins)
 
(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]]
+
| [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
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| 3:12-3:30
 
| 3:12-3:30
 
| Bartek Wilczynski
 
| Bartek Wilczynski
−
| [Regulatory Genomics] [[Media:Bosc2009_submission_29.pdf | 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'''
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| 4:00-4:20
 
| 4:00-4:20
 
| Morris Swertz
 
| Morris Swertz
−
| [Data & Analysis Management] [[Media:Bosc2009_submission_27.pdf | 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
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|4:40-5:00
 
|4:40-5:00
 
| Mark Welsh
 
| Mark Welsh
−
| [Data & Analysis Management] [[Media:Bosc2009_submission_10.pdf | 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
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5:30 Matias Piipari - [http://imotifs.pearcomp.com/ iMotifs]: a motif viewer/editor for the Mac [http://www.slideshare.net/bosc/piipariimotifbosc2009 ***SLIDES***]
 
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
+
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***]
 
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***]
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| 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'''
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| 9:15-10:15
 
| 9:15-10:15
 
| [[BOSC_2009#Robert_S._Hanmer | 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'''
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| 10:45-11:00
 
| 10:45-11:00
 
| Peter Rice
 
| Peter Rice
−
| [Bio* Update] [[Media:Bosc2009_submission_5.pdf | 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] [[Media:Bosc2009_submission_19.pdf | 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
 
| [http://biojava.org/wiki/Andreas_Prlic Andreas Prlic]
 
| [http://biojava.org/wiki/Andreas_Prlic Andreas Prlic]
−
| [Bio* Update] [[Media:Bosc2009_submission_15.pdf | 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] [[Media:Bosc2009_submission_16.pdf | 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] [[Media:Bosc2009_submission_13.pdf | 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] [[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'''
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| 2:00-2:20
 
| 2:00-2:20
 
| Quinn Snell
 
| Quinn Snell
−
| [OS Software] [[Media:Bosc2009_submission_33.pdf | 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] [[Media:Bosc2009_submission_6.pdf | 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] [[Media:Bosc2009_submission_40.pdf | 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
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| 3:10-3:30
 
| 3:10-3:30
 
| Sophie Schbath  
 
| Sophie Schbath  
−
| [Regulatory Genomics] [[Media:Bosc2009_submission_38.pdf | 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] [[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
+
| [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]]
 
|}
 
|}

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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