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Difference between revisions of "BOSC 2011 Schedule"

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Line 24: Line 24:
 
| '''Coffee Break'''
 
| '''Coffee Break'''
 
|
 
|
 +
|-
 +
| 10:45-12:30
 +
| Session: Genome Content Management
 +
|
 
|-
 
|-
 
| 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
 
| 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
 
| 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
 
| 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
 
| Bernat Gel
 
| Bernat Gel
 
|-
 
|-
 
| 11:55-12:05
 
| 11:55-12:05
−
|[Genome content management] Enacting Taverna Workflows through Galaxy
+
|[Genome Content Management] Enacting Taverna Workflows through Galaxy
 
| Marco Roos
 
| Marco Roos
 
|-
 
|-
 
| 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
 
| 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
 
| Junjun Zhang
 
| Junjun Zhang
 
|-
 
|-
Line 62: Line 66:
 
|-
 
|-
 
| 1:30-2:30
 
| 1:30-2:30
−
| Poster Session I
+
| "Poster Session I"
 
|
 
|
 +
|-
 +
| 2:30-4:00
 +
| Session: Visualization
 +
|
 
|-
 
|-
 
| 2:30-2:50
 
| 2:30-2:50
Line 84: Line 92:
 
| '''Coffee Break'''
 
| '''Coffee Break'''
 
|
 
|
 +
|-
 +
| 4:00-5:30
 +
| Session: Next-Generation Sequencing and Parallel Processing]
 +
|
 
|-
 
|-
 
| 4:00-4:20
 
| 4:00-4:20
−
| [Next-generation Sequencing] Stacks: building and genotyping loci de novo from short-read sequences
+
| [Next-Generation Sequencing] Stacks: building and genotyping loci de novo from short-read sequences
 
| Julian Catchen
 
| Julian Catchen
 
|-
 
|-
 
| 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
 
| 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
 
| 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
 
| Fabien Campagne
 
| Fabien Campagne
 
|-
 
|-
 
| 5:00-5:10
 
| 5:00-5:10
−
| [Parallel processing] A Scalable Multicore Implementation of the TEIRESIAS Algorithm
+
| [Parallel Processing] A Scalable Multicore Implementation of the TEIRESIAS Algorithm
 
| Frank Drews
 
| Frank Drews
 
|-
 
|-
 
| 5:10-5:20
 
| 5:10-5:20
−
| [Parallel processing] Biomanycores, open-source parallel code for many-core bioinformatics
+
| [Parallel Processing] Biomanycores, open-source parallel code for many-core bioinformatics
 
| Mathieu Giraud
 
| Mathieu Giraud
 
|-
 
|-
 
| 5:20-5:30
 
| 5:20-5:30
−
| [Next-generation Sequencing] GemSIM: General, Error-Model Based Simulator of next-generation sequencing
+
| [Next-Generation Sequencing] GemSIM: General, Error-Model Based Simulator of next-generation sequencing
 
| Kerensa McElroy
 
| Kerensa McElroy
 
|-
 
|-
 
| 5:30-6:30
 
| 5:30-6:30
−
| Poster Session II
+
| "Poster Session II"
 
|
 
|
 
|-
 
|-
Line 149: Line 161:
 
| '''Coffee Break'''
 
| '''Coffee Break'''
 
|
 
|
 +
|-
 +
| 10:45-12:30
 +
| Session: Cloud Computing
 +
|
 
|-
 
|-
 
| 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
 
| 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
 
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
 
| Jonathan Piat
 
| Jonathan Piat
 
|-
 
|-
 
| 11:35-11:45
 
| 11:35-11:45
−
|[Cloud computing] SeqWare: Analyzing Whole Human Genome Sequence Data on Amazon's Cloud
+
|[Cloud Computing] SeqWare: Analyzing Whole Human Genome Sequence Data on Amazon's Cloud
 
| Brian O'Connor
 
| Brian O'Connor
 
|-
 
|-
 
| 11:45-12:05
 
| 11:45-12:05
−
|[Cloud computing] Sequencescape - a cloud enabled Laboratory Information Management Systems (LIMS) for second and
+
|[Cloud Computing] Sequencescape - a cloud enabled Laboratory Information Management Systems (LIMS) for second and
 
third generation sequencing
 
third generation sequencing
 
| 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
 
| 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
 
| Aleksi Kallio
 
| Aleksi Kallio
 
|-
 
|-
Line 185: Line 201:
 
|-
 
|-
 
| 1:00-2:00
 
| 1:00-2:00
−
| Poster Session III
+
| "Poster Session III"
 
|
 
|
 +
|-
 +
| 2:00-3:30
 +
| Session: Semantic Web and Misc. Open Source Projects
 +
|
 
|-
 
|-
 
| 2:00-2:10
 
| 2:00-2:10
Line 238: Line 258:
 
|-
 
|-
 
| 4:30-5:20
 
| 4:30-5:20
−
| Panel: Meeting the challenges of inter-institutional collaboration
+
| '''Panel''': Meeting the challenges of inter-institutional collaboration
 
| Panelists: Richard Holland (Eagle Genomics),
 
| Panelists: Richard Holland (Eagle Genomics),
 
Hilmar Lapp (National Evolutionary Synthesis Center),
 
Hilmar Lapp (National Evolutionary Synthesis Center),

Revision as of 17:09, 17 June 2011

NOTE: Schedule is preliminary--subject to change.

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

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 Lawrence Hunter (University of Colorado)
10:15-10:45 Coffee Break
10:45-12:30 Session: Genome Content Management
10:45-11:05 [Genome Content Management] Unipro UGENE: an open source toolkit for complex genome analysis Konstantin Okonechnikov
11:05-11:25 [Genome Content Management] Exploring the genome with Dalliance Thomas Down
11:25-11:45 [Genome Content Management] InterMine - Using RESTful Webservices for Interoperability Alex Kalderimis
11:45-11:55 [Genome Content Management] easyDAS: Automatic creation of DAS servers Bernat Gel
11:55-12:05 [Genome Content Management] Enacting Taverna Workflows through Galaxy Marco Roos
12:05-12:15 [Genome Content Management] Mobyle 1.0: new features, new types of services Hervé Ménager
12:15-12:25 [Genome Content Management] BioMart 0.8 offers new tools, more interfaces, and increased flexibility through plug-ins Junjun Zhang
12:25-12:32 [Genome content management] Running Workflows Through Taverna Server [lightning] Donal Fellows
12:30-2:00 Lunch
1:30-2:30 "Poster Session I"
2:30-4:00 Session: Visualization
2:30-2:50 [Visualization] Cytoscape 3.0: Architecture for Extension Michael Smoot
2:50-3:10 [Visualization] Applying Visual Analytics to Extend the Genome Browser from Visualization Tool to Analysis Tool Jeremy Goecks
3:10-3:20 [Visualization] WebApollo: A web-based sequence annotation editor for community annotation Nomi Harris
3:20-3:30 [Visualization] The isobar R package: Analysis of quantitative proteomics data Florian Breitwieser
3:30-4:00 Coffee Break
4:00-5:30 Session: Next-Generation Sequencing and Parallel Processing]
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 Morris Swertz
4:40-4:50 [Next-Generation Sequencing] Bio-NGS: BioRuby plugin to conduct programmable workflows for Next Generation Sequencing data Raoul Bonnal
4:50-5:00 [Next-Generation Sequencing] Goby framework: native support in GSNAP, BWA and IGV 2.0 Fabien Campagne
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 Mathieu Giraud
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"
5:30-6:30 BOFs
7:00 Pay-your-own-way optional dinner at a nearby restaurant

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

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
10:45-11:05 [Cloud Computing] Mygene.info: Gene Annotation as a Service - GAaaS 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

Konstantinos Krampis
11:25-11:35 [Cloud Computing] OBIWEE : an open source bioinformatics cloud environment Jonathan Piat
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

Lars Jorgensen
12:05-12:15 [Cloud Computing] Enabling NGS Analysis with(out) the Infrastructure Enis Afgan
12:15-12:25 [Cloud Computing] Hadoop-BAM: A Library for Genomic Data Processing Aleksi Kallio
12:30-2:00 Lunch
1:00-2:00 "Poster Session III"
2:00-3:30 Session: Semantic Web and Misc. Open Source Projects
2:00-2:10 [Semantic Web] SADI for GMOD: Bringing Model Organism Data onto the Semantic Web Ben Vandervalk
2:10-2:20 [Semantic Web] Scufl2: because a workflow is more than its definition Stian Soiland-Reyes
2:20-2:30 [Semantic Web] OntoCAT - an integrated programming toolkit for common ontology application tasks Tomasz Adamusiak
2:30-2:50 [Misc.] Debian Med: individuals' expertize and their sharing of package build instructions 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 Peter Cock
3:20-3:27 [Misc.] What's new with GMOD [lightning] Scott Cain
3:27-3:34 Exploring human variation data with Clojure [lightning] Brad Chapman
3:30-4:00 Coffee Break
4:00-4:10 [Misc.] EMBOSS: New developments and extended data access Peter Rice
4:10-4:20 [Misc.] G-language Project: the last 10 years and beyond Kazuharu Arakawa
4:20-4:30 [Misc.] A Framework for Bioinformatics on the Microsoft Platform Simon Mercer
4:30-5:20 Panel: Meeting the challenges of inter-institutional collaboration 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


NOTE: Schedule is preliminary--subject to change.

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