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 |
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