BOSC 2011 Schedule

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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)

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] 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

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