View source for BOSC 2011 Schedule

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

{| border="1" cellspacing="0" cellpadding="10"
! 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 [http://www.slideshare.net/bosc2011/a01openness-in-knowledgebased-systems ***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 [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'''
| '''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 [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'''
| '''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 [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
| '''Poster Session II''' (Foyer A)
|
|-
| 5:30-6:30
| [[BOSC_2011/BOFs|BOFs]]
|
|-
| 7:00
| Pay-your-own-way optional dinner
|
|- 
|}

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

{| border="1" cellspacing="0" cellpadding="10"
! 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 [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'''
| '''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 [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
| 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 [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'''
| '''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 [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
|-
| 4:30-5:20
| '''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
| [[BOSC_2011/BOFs|BOFs]]
|
|-
|}

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