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Difference between revisions of "BOSC 2011 Schedule"

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m (→‎Day 1: Friday, July 15 (Austria Center Vienna, Room F2))
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|-
 
|-
 
| 9:15-10:15
 
| 9:15-10:15
−
| [Keynote] The role of openness in knowledge-based systems for biomedicine
+
| [Keynote] The role of openness in knowledge-based systems for biomedicine [http://www.slideshare.net/bosc2011/a01openness-in-knowledgebased-systems ***SLIDES***]
 
| Lawrence Hunter (University of Colorado)
 
| Lawrence Hunter (University of Colorado)
 
|-
 
|-
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|-
 
|-
 
| 10:45-11:05
 
| 10:45-11:05
−
|[Genome Content Management] Unipro UGENE: an open source toolkit for complex genome analysis
+
|[Genome Content Management] Unipro UGENE: an open source toolkit for complex genome analysis [http://www.slideshare.net/bosc2011/unipro-ugene-bosc-2011-update ***SLIDES***]
 
| Konstantin Okonechnikov
 
| Konstantin Okonechnikov
 
|-
 
|-
 
| 11:05-11:25
 
| 11:05-11:25
−
|[Genome Content Management] Exploring the genome with Dalliance
+
|[Genome Content Management] Exploring the genome with Dalliance [http://www.biodalliance.org/people/thomas/dalliance-talk-201107/dalliance.html ***SLIDES webpage***]
 
| Thomas Down
 
| Thomas Down
 
|-
 
|-
 
| 11:25-11:45
 
| 11:25-11:45
−
|[Genome Content Management] InterMine - Using RESTful Webservices for Interoperability
+
|[Genome Content Management] InterMine - Using RESTful Webservices for Interoperability [http://www.slideshare.net/bosc2011/alex-interminebosc-presentation ***SLIDES***]
 
| Alex Kalderimis
 
| Alex Kalderimis
 
|-
 
|-
 
| 11:45-11:55
 
| 11:45-11:55
−
|[Genome Content Management] easyDAS: Automatic creation of DAS servers
+
|[Genome Content Management] easyDAS: Automatic creation of DAS servers [http://www.slideshare.net/bosc2011/easy-das-bosc2011 ***SLIDES***]
 
| Bernat Gel
 
| Bernat Gel
 
|-
 
|-
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|-
 
|-
 
| 12:05-12:15
 
| 12:05-12:15
−
|[Genome Content Management] Mobyle 1.0: new features, new types of services
+
|[Genome Content Management] Mobyle 1.0: new features, new types of services [http://www.slideshare.net/bosc2011/mobyle-1-0newfeaturesnewtypesofservice ***SLIDES***]
 
| Hervé Ménager
 
| Hervé Ménager
 
|-
 
|-
 
| 12:15-12:25
 
| 12:15-12:25
−
|[Genome Content Management] BioMart 0.8 offers new tools, more interfaces, and increased flexibility through plug-ins
+
|[Genome Content Management] BioMart 0.8 offers new tools, more interfaces, and increased flexibility through plug-ins [http://www.slideshare.net/bosc2011/b07genomecontentbiomart ***SLIDES***]
 
| Junjun Zhang
 
| Junjun Zhang
 
|-
 
|-
 
| 12:25-12:32
 
| 12:25-12:32
−
|[Genome Content Management] Running Workflows Through Taverna Server [lightning]
+
|[Genome Content Management] Running Workflows Through Taverna Server [lightning] [http://www.slideshare.net/bosc2011/running-workflows-through-galaxy-bosc-presentation ***SLIDES***]
 
| Donal Fellows
 
| Donal Fellows
 
|-
 
|-
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|-
 
|-
 
| 2:30-2:50
 
| 2:30-2:50
−
|[Visualization] Cytoscape 3.0: Architecture for Extension
+
|[Visualization] Cytoscape 3.0: Architecture for Extension [http://www.slideshare.net/bosc2011/bosc-talk-7152011x ***SLIDES***]
 
| Michael Smoot
 
| Michael Smoot
 
|-
 
|-
 
| 2:50-3:10
 
| 2:50-3:10
−
| [Visualization] Applying Visual Analytics to Extend the Genome Browser from Visualization Tool to Analysis Tool  
+
| [Visualization] Applying Visual Analytics to Extend the Genome Browser from Visualization Tool to Analysis Tool [http://www.slideshare.net/bosc2011/goecks-bosc-2011 ***SLIDES***]
 +
 
 
| Jeremy Goecks
 
| Jeremy Goecks
 
|-
 
|-
 
| 3:10-3:20
 
| 3:10-3:20
−
| [Visualization] WebApollo: A web-based sequence annotation editor for community annotation
+
| [Visualization] WebApollo: A web-based sequence annotation editor for community annotation [http://www.slideshare.net/bosc2011/webapollo-bosc2011 ***SLIDES***]
 
| Nomi Harris
 
| Nomi Harris
 
|-
 
|-
 
| 3:20-3:30
 
| 3:20-3:30
−
| [Visualization] The isobar R package: Analysis of quantitative proteomics data
+
| [Visualization] The isobar R package: Analysis of quantitative proteomics data [http://www.slideshare.net/bosc2011/bosc2011-isobarfbp ***SLIDES***]
 
| Florian Breitwieser
 
| Florian Breitwieser
 
|-
 
|-
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|-
 
|-
 
| 4:20-4:40
 
| 4:20-4:40
−
| [Next-Generation Sequencing] Large scale NGS pipelines using the MOLGENIS platform: processing the Genome of the Netherlands
+
| [Next-Generation Sequencing] Large scale NGS pipelines using the MOLGENIS platform: processing the Genome of the Netherlands [http://www.slideshare.net/bosc2011/d02nextgenseqmolgenis ***SLIDES***]
 
| Morris Swertz
 
| Morris Swertz
 
|-
 
|-
 
| 4:40-4:50
 
| 4:40-4:50
−
| [Next-Generation Sequencing] Bio-NGS: BioRuby plugin to conduct programmable workflows for Next Generation Sequencing data
+
| [Next-Generation Sequencing] Bio-NGS: BioRuby plugin to conduct programmable workflows for Next Generation Sequencing data [http://www.slideshare.net/bosc2011/raoul-bosc2011bio-ngs ***SLIDES***]
 
| Raoul Bonnal
 
| Raoul Bonnal
 
|-
 
|-
 
| 4:50-5:00
 
| 4:50-5:00
−
| [Next-Generation Sequencing] Goby framework: native support in GSNAP, BWA and IGV 2.0
+
| [Next-Generation Sequencing] Goby framework: native support in GSNAP, BWA and IGV 2.0 [http://campagnelab.org/files/campagne-lab-bosc-presentation-2011-final.zip ***SLIDES as PREZI***]
 
| Kevin C. Dorff
 
| Kevin C. Dorff
 
|-
 
|-
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|-
 
|-
 
| 7:00
 
| 7:00
−
| Pay-your-own-way optional dinner at [http://www.ufertaverne.at Ufertaverne], A-1220 Wien, An der Oberen Alten Donau 186. [http://maps.google.com/maps?saddr=Austria+Center+Vienna&daddr=A-1220+Wien,+An+der+Oberen+Alten+Donau+186&hl=en&ll=48.236522,16.421256&spn=0.009904,0.021758&sll=48.23755,16.42124&sspn=0.009904,0.021758&geocode=FYoC4AIdc3T6ACl5Giph7wZtRzFexwA0Boj8xQ%3BFaIY4AIdjKX6AClz0v2A6gZtRzFn2dZ8En5z8w&mra=ltm&dirflg=w&z=16  (map)]
+
| Pay-your-own-way optional dinner
 
|
 
|
 
|-  
 
|-  
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|-
 
|-
 
| 10:45-11:05
 
| 10:45-11:05
−
|[Cloud Computing] Mygene.info: Gene Annotation as a Service - GAaaS
+
|[Cloud Computing] Mygene.info: Gene Annotation as a Service - GAaaS [http://www.slideshare.net/bosc2011/2011-bosc-ismbtalkcwu ***SLIDES***]
 
| Chunlei Wu
 
| Chunlei Wu
 
|-
 
|-
 
| 11:05-11:25
 
| 11:05-11:25
−
|[Cloud Computing] Cloud BioLinux: open source, fully-customizable bioinformatics computing on the cloud for the genomics
+
|[Cloud Computing] Cloud BioLinux: open source, fully-customizable bioinformatics computing on the cloud for the genomics community and beyond [http://www.slideshare.net/bosc2011/bosc2011-ntinokrampisfull ***SLIDES***]
−
community and beyond
 
 
| Konstantinos Krampis
 
| Konstantinos Krampis
 
|-
 
|-
 
| 11:25-11:35
 
| 11:25-11:35
−
|[Cloud Computing] OBIWEE : an open source bioinformatics cloud environment
+
|[Cloud Computing] OBIWEE : an open source bioinformatics cloud environment [http://www.slideshare.net/bosc2011/obiwee-slide-v3 ***SLIDES***]
 
| Olivier Sallou
 
| Olivier Sallou
 
|-
 
|-
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|-
 
|-
 
| 11:45-12:05
 
| 11:45-12:05
−
|[Cloud Computing] Sequencescape - a cloud enabled Laboratory Information Management Systems (LIMS) for second and third generation sequencing
+
|[Cloud Computing] Sequencescape - a cloud enabled Laboratory Information Management Systems (LIMS) for second and third generation sequencing [http://www.slideshare.net/bosc2011/lj3-bosc-2011sequencescape ***SLIDES***]
 
| Lars Jorgensen
 
| Lars Jorgensen
 
|-
 
|-
 
| 12:05-12:15
 
| 12:05-12:15
−
|[Cloud Computing] Enabling NGS Analysis with(out) the Infrastructure
+
|[Cloud Computing] Enabling NGS Analysis with(out) the Infrastructure [http://www.slideshare.net/bosc2011/cloud-man-enisafganbosc2011 ***SLIDES***]
 
| Enis Afgan
 
| Enis Afgan
 
|-
 
|-
 
| 12:15-12:25
 
| 12:15-12:25
−
|[Cloud Computing] Hadoop-BAM: A Library for Genomic Data Processing
+
|[Cloud Computing] Hadoop-BAM: A Library for Genomic Data Processing [http://www.slideshare.net/bosc2011/kallio-bosc2011-hadoopbam ***SLIDES***]
 
| Aleksi Kallio
 
| Aleksi Kallio
 
|-
 
|-
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|-
 
|-
 
| 2:00-2:10
 
| 2:00-2:10
−
|[Semantic Web] SADI for GMOD: Bringing Model Organism Data onto the Semantic Web
+
|[Semantic Web] SADI for GMOD: Bringing Model Organism Data onto the Semantic Web [http://www.slideshare.net/bosc2011/talk1-ben-sadi-forgmodbosc2011 ***SLIDES***]
 
| Ben Vandervalk
 
| Ben Vandervalk
 
|-
 
|-
 
| 2:10-2:20
 
| 2:10-2:20
−
|[Semantic Web] Scufl2: because a workflow is more than its definition
+
|[Semantic Web] Scufl2: because a workflow is more than its definition [http://www.slideshare.net/soilandreyes/2011-0716-scufl2-because-a-workflow-is-more-than-its-definition-bosc-2011 ***SLIDES***]
 
| Stian Soiland-Reyes
 
| Stian Soiland-Reyes
 
|-
 
|-
 
| 2:20-2:30
 
| 2:20-2:30
−
|[Semantic Web] OntoCAT - an integrated programming toolkit for common ontology application tasks
+
|[Semantic Web] OntoCAT - an integrated programming toolkit for common ontology application tasks [http://www.slideshare.net/bosc2011/np-adamusiak-bosc2011ontocat ***SLIDES***]
 
| Tomasz Adamusiak
 
| Tomasz Adamusiak
 
|-
 
|-
 
| 2:30-2:50
 
| 2:30-2:50
−
|[Misc.] Debian Med: individuals' expertize and their sharing of package build instructions
+
|[Misc.] Debian Med: individuals' expertize and their sharing of package build instructions [http://www.slideshare.net/bosc2011/debianmed-bosc-05 ***SLIDES***]
 
| Steffen Möller
 
| Steffen Möller
 
|-
 
|-
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|-
 
|-
 
| 3:10-3:20
 
| 3:10-3:20
−
|[Misc.] Biopython Project Update
+
|[Misc.] Biopython Project Update 2011 [http://www.slideshare.net/bosc2011/talk6-biopython-bosc2011 *** SLIDES***]
 
| Peter Cock
 
| Peter Cock
 
|-
 
|-
 
| 3:20-3:27
 
| 3:20-3:27
−
|[Misc.] What's new with GMOD [lightning]
+
|[Misc.] What's new with GMOD [lightning] [http://www.slideshare.net/bosc2011/gmod-bosc-2011 ***SLIDES***]
 
| Scott Cain
 
| Scott Cain
 
|-
 
|-
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|-
 
|-
 
| 4:00-4:10
 
| 4:00-4:10
−
|[Misc.] EMBOSS: New developments and extended data access
+
|[Misc.] EMBOSS: New developments and extended data access [http://www.slideshare.net/bosc2011/emboss-8619441 ***SLIDES***]
 
| Peter Rice
 
| Peter Rice
 
|-
 
|-
 
| 4:10-4:20
 
| 4:10-4:20
−
|[Misc.] G-language Project: the last 10 years and beyond
+
|[Misc.] G-language Project: the last 10 years and beyond [http://www.slideshare.net/bosc2011/bosc2011-arakawa ***SLIDES***]
 
| Kazuharu Arakawa
 
| Kazuharu Arakawa
 
|-
 
|-
 
| 4:20-4:30
 
| 4:20-4:30
−
|[Misc.] A Framework for Bioinformatics on the Microsoft Platform
+
|[Misc.] A Framework for Bioinformatics on the Microsoft Platform [http://www.slideshare.net/bosc2011/bosc-mercer ***SLIDES***]
 
| Simon Mercer
 
| Simon Mercer
 
|-
 
|-

Latest revision as of 20:18, 10 September 2013

Day 1: Friday, July 15 (Austria Center Vienna, Room F2)

Time Topic Speaker or Moderator
7:30-9:00 Pick up badges for BOSC 2011, Austria Center Vienna

(Early arrival is recommended as there are usually long lines)

Registration
9:00-9:15 Introduction and welcome Nomi Harris (Co-Chair, BOSC)
9:15-10:15 [Keynote] The role of openness in knowledge-based systems for biomedicine ***SLIDES*** Lawrence Hunter (University of Colorado)
10:15-10:45 Coffee Break
10:45-12:30 Session: Genome Content Management Chair: Peter Rice
10:45-11:05 [Genome Content Management] Unipro UGENE: an open source toolkit for complex genome analysis ***SLIDES*** Konstantin Okonechnikov
11:05-11:25 [Genome Content Management] Exploring the genome with Dalliance ***SLIDES webpage*** Thomas Down
11:25-11:45 [Genome Content Management] InterMine - Using RESTful Webservices for Interoperability ***SLIDES*** Alex Kalderimis
11:45-11:55 [Genome Content Management] easyDAS: Automatic creation of DAS servers ***SLIDES*** Bernat Gel
11:55-12:05 [Genome Content Management] Enacting Taverna Workflows through Galaxy Kostas Karasavvas
12:05-12:15 [Genome Content Management] Mobyle 1.0: new features, new types of services ***SLIDES*** Hervé Ménager
12:15-12:25 [Genome Content Management] BioMart 0.8 offers new tools, more interfaces, and increased flexibility through plug-ins ***SLIDES*** Junjun Zhang
12:25-12:32 [Genome Content Management] Running Workflows Through Taverna Server [lightning] ***SLIDES*** Donal Fellows
12:30-2:00 Lunch
1:30-2:30 Poster Session I (Foyer A)
2:30-3:30 Session: Visualization Chair: Jan Aerts
2:30-2:50 [Visualization] Cytoscape 3.0: Architecture for Extension ***SLIDES*** Michael Smoot
2:50-3:10 [Visualization] Applying Visual Analytics to Extend the Genome Browser from Visualization Tool to Analysis Tool ***SLIDES*** Jeremy Goecks
3:10-3:20 [Visualization] WebApollo: A web-based sequence annotation editor for community annotation ***SLIDES*** Nomi Harris
3:20-3:30 [Visualization] The isobar R package: Analysis of quantitative proteomics data ***SLIDES*** Florian Breitwieser
3:30-4:00 Coffee Break
4:00-5:30 Session: Next-Generation Sequencing and Parallel Processing Chair: Thomas Down
4:00-4:20 [Next-Generation Sequencing] Stacks: building and genotyping loci de novo from short-read sequences Julian Catchen
4:20-4:40 [Next-Generation Sequencing] Large scale NGS pipelines using the MOLGENIS platform: processing the Genome of the Netherlands ***SLIDES*** Morris Swertz
4:40-4:50 [Next-Generation Sequencing] Bio-NGS: BioRuby plugin to conduct programmable workflows for Next Generation Sequencing data ***SLIDES*** Raoul Bonnal
4:50-5:00 [Next-Generation Sequencing] Goby framework: native support in GSNAP, BWA and IGV 2.0 ***SLIDES as PREZI*** Kevin C. Dorff
5:00-5:10 [Parallel Processing] A Scalable Multicore Implementation of the TEIRESIAS Algorithm Frank Drews
5:10-5:20 [Parallel Processing] Biomanycores, open-source parallel code for many-core bioinformatics Jean-Frédéric Berthelot
5:20-5:30 [Next-Generation Sequencing] GemSIM: General, Error-Model Based Simulator of next-generation sequencing Kerensa McElroy
5:30-6:30 Poster Session II (Foyer A)
5:30-6:30 BOFs
7:00 Pay-your-own-way optional dinner

Day 2: Saturday, July 16 (Austria Center Vienna, Room F2)

Time Topic Speaker or Moderator
8:45-8:50 Announcements
8:50-9:50 [Keynote] Into the Wonderful Matt Wood (Amazon)
9:50-10:15 [Cloud computing] Securing and sharing bioinformatics in the cloud Richard Holland (Eagle Genomics)
10:15-10:45 Coffee Break
10:45-12:30 Session: Cloud Computing Chair: Brad Chapman
10:45-11:05 [Cloud Computing] Mygene.info: Gene Annotation as a Service - GAaaS ***SLIDES*** Chunlei Wu
11:05-11:25 [Cloud Computing] Cloud BioLinux: open source, fully-customizable bioinformatics computing on the cloud for the genomics community and beyond ***SLIDES*** Konstantinos Krampis
11:25-11:35 [Cloud Computing] OBIWEE : an open source bioinformatics cloud environment ***SLIDES*** Olivier Sallou
11:35-11:45 [Cloud Computing] SeqWare: Analyzing Whole Human Genome Sequence Data on Amazon's Cloud Brian O'Connor
11:45-12:05 [Cloud Computing] Sequencescape - a cloud enabled Laboratory Information Management Systems (LIMS) for second and third generation sequencing ***SLIDES*** Lars Jorgensen
12:05-12:15 [Cloud Computing] Enabling NGS Analysis with(out) the Infrastructure ***SLIDES*** Enis Afgan
12:15-12:25 [Cloud Computing] Hadoop-BAM: A Library for Genomic Data Processing ***SLIDES*** Aleksi Kallio
12:30-2:00 Lunch
1:00-2:00 Poster Session III (Foyer A)
2:00-3:30 Session: Semantic Web and Misc. Open Source Projects Chair: Peter Cock
2:00-2:10 [Semantic Web] SADI for GMOD: Bringing Model Organism Data onto the Semantic Web ***SLIDES*** Ben Vandervalk
2:10-2:20 [Semantic Web] Scufl2: because a workflow is more than its definition ***SLIDES*** Stian Soiland-Reyes
2:20-2:30 [Semantic Web] OntoCAT - an integrated programming toolkit for common ontology application tasks ***SLIDES*** Tomasz Adamusiak
2:30-2:50 [Misc.] Debian Med: individuals' expertize and their sharing of package build instructions ***SLIDES*** Steffen Möller
2:50-3:10 [Misc.] The BALL project: The Biochemical Algorithms Library (BALL) for Rapid Application Development in Structural Bioinformatics and its graphical user interface BALLView Andreas Hildebrandt
3:10-3:20 [Misc.] Biopython Project Update 2011 *** SLIDES*** Peter Cock
3:20-3:27 [Misc.] What's new with GMOD [lightning] ***SLIDES*** Scott Cain
3:27-3:34 [Misc.] Exploring human variation data with Clojure [lightning] Brad Chapman
3:30-4:00 Coffee Break
4:00-4:30 Session: Misc. Open Source Projects Chair: Jim Procter
4:00-4:10 [Misc.] EMBOSS: New developments and extended data access ***SLIDES*** Peter Rice
4:10-4:20 [Misc.] G-language Project: the last 10 years and beyond ***SLIDES*** Kazuharu Arakawa
4:20-4:30 [Misc.] A Framework for Bioinformatics on the Microsoft Platform ***SLIDES*** Simon Mercer
4:30-5:20 Panel: Meeting the challenges of inter-institutional collaboration Moderator: Brad Chapman

Panelists: Richard Holland (Eagle Genomics),

Hilmar Lapp (National Evolutionary Synthesis Center),

Jean Peccoud (Virginia Bioinformatics Institute),

Peter Rice (European Bioinformatics Institute)

5:20-5:30 Presentation of awards Nomi Harris
5:30-6:30 BOFs

Return to BOSC 2011 main page

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