-

Difference between revisions of "BOSC 2011 Schedule"

From Open Bioinformatics Foundation
Jump to: navigation, search
m (Day 1: Friday, July 15 (Austria Center Vienna, Room TBA))
m (Put year in Biopython Update title)
 
(48 intermediate revisions by 3 users not shown)
Line 1: Line 1:
'''NOTE: Schedule is preliminary--subject to change.'''
+
== Day 1: Friday,  July 15  (Austria Center Vienna,  Room F2) ==
 
 
== Day 1: Friday,  July 15  (Austria Center Vienna,  Room TBA) ==
 
  
 
{| border="1" cellspacing="0" cellpadding="10"
 
{| border="1" cellspacing="0" cellpadding="10"
 
! Time
 
! Time
! Session
+
! Topic
 
! Speaker or Moderator
 
! Speaker or Moderator
 
|-  
 
|-  
Line 18: Line 16:
 
|-
 
|-
 
| 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)
 
|-
 
|-
Line 27: Line 25:
 
| 10:45-12:30
 
| 10:45-12:30
 
| Session: Genome Content Management
 
| Session: Genome Content Management
|
+
| Chair: Peter Rice
 +
|-
 +
| 10:45-11:05
 +
|[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
 +
|-
 +
| 11:05-11:25
 +
|[Genome Content Management] Exploring the genome with Dalliance [http://www.biodalliance.org/people/thomas/dalliance-talk-201107/dalliance.html ***SLIDES webpage***]
 +
| Thomas Down
 +
|-
 +
| 11:25-11:45
 +
|[Genome Content Management] InterMine - Using RESTful Webservices for Interoperability [http://www.slideshare.net/bosc2011/alex-interminebosc-presentation ***SLIDES***]
 +
| Alex Kalderimis
 +
|-
 +
| 11:45-11:55
 +
|[Genome Content Management] easyDAS: Automatic creation of DAS servers [http://www.slideshare.net/bosc2011/easy-das-bosc2011 ***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 [http://www.slideshare.net/bosc2011/mobyle-1-0newfeaturesnewtypesofservice ***SLIDES***]
 +
| Hervé Ménager
 +
|-
 +
| 12:15-12:25
 +
|[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
 +
|-
 +
| 12:25-12:32
 +
|[Genome Content Management] Running Workflows Through Taverna Server [lightning] [http://www.slideshare.net/bosc2011/running-workflows-through-galaxy-bosc-presentation ***SLIDES***]
 +
| Donal Fellows
 
|-
 
|-
 
| '''12:30-2:00'''
 
| '''12:30-2:00'''
Line 34: Line 64:
 
|-
 
|-
 
| 1:30-2:30
 
| 1:30-2:30
| Poster Session I
+
| '''Poster Session I''' (Foyer A)
 
|
 
|
 
|-
 
|-
 
| 2:30-3:30
 
| 2:30-3:30
 
| Session: Visualization
 
| Session: Visualization
|
+
| Chair: Jan Aerts
 +
|-
 +
| 2:30-2:50
 +
|[Visualization] Cytoscape 3.0: Architecture for Extension [http://www.slideshare.net/bosc2011/bosc-talk-7152011x ***SLIDES***]
 +
| Michael Smoot
 +
|-
 +
| 2:50-3:10
 +
| [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
 +
|-
 +
| 3:10-3:20
 +
| [Visualization] WebApollo: A web-based sequence annotation editor for community annotation [http://www.slideshare.net/bosc2011/webapollo-bosc2011 ***SLIDES***]
 +
| Nomi Harris
 +
|-
 +
| 3:20-3:30
 +
| [Visualization] The isobar R package: Analysis of quantitative proteomics data [http://www.slideshare.net/bosc2011/bosc2011-isobarfbp ***SLIDES***]
 +
| Florian Breitwieser
 
|-
 
|-
 
| '''3:30-4:00'''
 
| '''3:30-4:00'''
Line 46: Line 93:
 
|-
 
|-
 
| 4:00-5:30
 
| 4:00-5:30
| Session: Next Generation Sequencing
+
| 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 [http://www.slideshare.net/bosc2011/d02nextgenseqmolgenis ***SLIDES***]
 +
| Morris Swertz
 +
|-
 +
| 4:40-4:50
 +
| [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
 +
|-
 +
| 4:50-5:00
 +
| [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
 +
|-
 +
| 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
 
| 5:30-6:30
| Poster Session II
+
| '''Poster Session II''' (Foyer A)
 
|
 
|
 
|-
 
|-
 
| 5:30-6:30
 
| 5:30-6:30
| BOFs
+
| [[BOSC_2011/BOFs|BOFs]]
 
|
 
|
 
|-
 
|-
 
| 7:00
 
| 7:00
| Pay-your-own-way optional dinner at a nearby restaurant
+
| Pay-your-own-way optional dinner
 
|
 
|
|-
+
|-  
 
|}
 
|}
  
== Day 2: Saturday, July 16 (Austria Center Vienna, Room TBA) ==
+
== Day 2: Saturday, July 16 (Austria Center Vienna, Room F2) ==
  
 
{| border="1" cellspacing="0" cellpadding="10"
 
{| border="1" cellspacing="0" cellpadding="10"
 
! Time
 
! Time
! Session
+
! Topic
 
! Speaker or Moderator
 
! Speaker or Moderator
 
|-  
 
|-  
Line 79: Line 154:
 
|-
 
|-
 
| 9:50-10:15
 
| 9:50-10:15
| [Cloud] Securing and sharing bioinformatics in the cloud
+
| [Cloud computing] Securing and sharing bioinformatics in the cloud
| Richard Holland (Eagle Genomics)          
+
| Richard Holland (Eagle Genomics)
 
|-
 
|-
 
| '''10:15-10:45'''
 
| '''10:15-10:45'''
Line 87: Line 162:
 
|-
 
|-
 
| 10:45-12:30
 
| 10:45-12:30
| Session: Cloud Computing and Parallel Processing
+
| Session: Cloud Computing
|
+
| Chair: Brad Chapman
 +
|-
 +
| 10:45-11:05
 +
|[Cloud Computing] Mygene.info: Gene Annotation as a Service - GAaaS [http://www.slideshare.net/bosc2011/2011-bosc-ismbtalkcwu ***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 [http://www.slideshare.net/bosc2011/bosc2011-ntinokrampisfull ***SLIDES***]
 +
| Konstantinos Krampis
 +
|-
 +
| 11:25-11:35
 +
|[Cloud Computing] OBIWEE : an open source bioinformatics cloud environment [http://www.slideshare.net/bosc2011/obiwee-slide-v3 ***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 [http://www.slideshare.net/bosc2011/lj3-bosc-2011sequencescape ***SLIDES***]
 +
| Lars Jorgensen
 +
|-
 +
| 12:05-12:15
 +
|[Cloud Computing] Enabling NGS Analysis with(out) the Infrastructure [http://www.slideshare.net/bosc2011/cloud-man-enisafganbosc2011 ***SLIDES***]
 +
| Enis Afgan
 +
|-
 +
| 12:15-12:25
 +
|[Cloud Computing] Hadoop-BAM: A Library for Genomic Data Processing [http://www.slideshare.net/bosc2011/kallio-bosc2011-hadoopbam ***SLIDES***]
 +
| Aleksi Kallio
 
|-
 
|-
 
| '''12:30-2:00'''
 
| '''12:30-2:00'''
Line 95: Line 198:
 
|-
 
|-
 
| 1:00-2:00
 
| 1:00-2:00
| Poster Session III
+
| '''Poster Session III''' (Foyer A)
 
|
 
|
 
|-
 
|-
 
| 2:00-3:30
 
| 2:00-3:30
| Session: Project Updates, Various Open Source bioinformatics projects        
+
| 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 [http://www.slideshare.net/bosc2011/talk1-ben-sadi-forgmodbosc2011 ***SLIDES***]
 +
| Ben Vandervalk
 +
|-
 +
| 2:10-2:20
 +
|[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
 +
|-
 +
| 2:20-2:30
 +
|[Semantic Web] OntoCAT - an integrated programming toolkit for common ontology application tasks [http://www.slideshare.net/bosc2011/np-adamusiak-bosc2011ontocat ***SLIDES***]
 +
| Tomasz Adamusiak
 +
|-
 +
| 2:30-2:50
 +
|[Misc.] Debian Med: individuals' expertize and their sharing of package build instructions [http://www.slideshare.net/bosc2011/debianmed-bosc-05 ***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 [http://www.slideshare.net/bosc2011/talk6-biopython-bosc2011 *** SLIDES***]
 +
| Peter Cock
 +
|-
 +
| 3:20-3:27
 +
|[Misc.] What's new with GMOD [lightning] [http://www.slideshare.net/bosc2011/gmod-bosc-2011 ***SLIDES***]
 +
| Scott Cain
 +
|-
 +
| 3:27-3:34
 +
| [Misc.] Exploring human variation data with Clojure [lightning]
 +
| Brad Chapman
 
|-
 
|-
 
| '''3:30-4:00'''
 
| '''3:30-4:00'''
Line 106: Line 241:
 
|
 
|
 
|-
 
|-
| 4:00-5:30
+
| 4:00-4:30
| Session: Visualization and Semantic Web
+
| Session: Misc. Open Source Projects
|
+
| Chair: Jim Procter
 
|-
 
|-
 
| 4:00-4:10
 
| 4:00-4:10
| Presentation of Awards
+
|[Misc.] EMBOSS: New developments and extended data access [http://www.slideshare.net/bosc2011/emboss-8619441 ***SLIDES***]
|
+
| Peter Rice
 +
|-
 +
| 4:10-4:20
 +
|[Misc.] G-language Project: the last 10 years and beyond [http://www.slideshare.net/bosc2011/bosc2011-arakawa ***SLIDES***]
 +
| Kazuharu Arakawa
 +
|-
 +
| 4:20-4:30
 +
|[Misc.] A Framework for Bioinformatics on the Microsoft Platform [http://www.slideshare.net/bosc2011/bosc-mercer ***SLIDES***]
 +
| Simon Mercer
 
|-
 
|-
| 4:10-4:30
+
| 4:30-5:20
| Session: Lightning Talks
+
| '''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)
 
|-
 
|-
| 4:30-5:30
+
| 5:20-5:30
| Panel: Meeting the challenges of inter-institutional collaboration
+
| Presentation of awards
|
+
| Nomi Harris
 
|-
 
|-
 
| 5:30-6:30
 
| 5:30-6:30
| BOFs
+
| [[BOSC_2011/BOFs|BOFs]]
 
|
 
|
 
|-
 
|-
 
|}
 
|}
 
'''NOTE: Schedule is preliminary--subject to change.'''
 
  
 
== Return to '''[[BOSC_2011 | BOSC 2011]]''' main page ==
 
== Return to '''[[BOSC_2011 | BOSC 2011]]''' main page ==

Latest revision as of 15:18, 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