BOSC 2011 Schedule

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