Difference between revisions of "BOSC 2011 Schedule"

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m (Day 2: Saturday, July 16 (Austria Center Vienna, Room TBA))
m (Day 2: Saturday, July 16 (Austria Center Vienna, Room TBA))
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Panelists: Richard Holland (Eagle Genomics),
Panelists: Richard Holland (Eagle Genomics),
Hilmar Lapp (National Evolutionary Synthesis Center),
Hilmar Lapp (National Evolutionary Synthesis Center),
Jean Peccoud (Virginia Bioinformatics Institute),
Jean Peccoud (Virginia Bioinformatics Institute),
Peter Rice (European Bioinformatics Institute)
Peter Rice (European Bioinformatics Institute)

Revision as of 13:12, 30 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)

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
2:30-3:30 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 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 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 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 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 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

NOTE: Schedule is preliminary--subject to change.

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