BOSC 2012 Schedule

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Revision as of 16:04, 28 May 2012 by Nomi (talk) (Day 2: Saturday, July 14 (Preliminary Schedule))

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Day 1: Friday, July 13 (Preliminary Schedule)

Time Topic Speaker or Moderator
7:30-9:00 Registration (Early arrival is recommended as there are usually long lines) Registration
9:00-9:15 Introduction and welcome Nomi Harris (Chair, BOSC 2012)
9:15-10:15 [Keynote] Science Wants to Be Open - If Only We Could Get Out of Its Way Jonathan Eisen (University of California, Davis)
10:15-10:45 Coffee Break
10:45-12:30 Session: Cloud and Parallel Computing Chair:
10:45 [Cloud] Cloudgene - an execution platform for MapReduce programs in public and private clouds Sebastian Schoenherr
11:10 [Cloud] Data reduction and division approaches for assembling short-read data in the cloud C. Titus Brown
11:35 [Cloud] MGTAXA - a toolkit and a Web server for predicting taxonomy of the metagenomic sequences with Galaxy front-end and parallel computational back-end Andrey Tovchigrechko
12:00 [Cloud] Workflows on the Cloud - Scaling for National Service Shoaib Sufi
12:15 [Cloud] How to use BioJava to calculate one billion protein structure alignments at the RCSB PDB website Andreas Prlic
12:30-1:30 Lunch
12:30-2:00 Poster Session I (Room TBA)
2:00-3:30 Session: Genome-scale Data Management Chair:
2:00 [Genome-scale] Using HDF5 to Work With Large Quantities of Biological Data Dana Robinson
2:15 [Genome-scale] Large scale data management in Chipster 2 workflow environment Aleksi Kallio
2:30 [Genome-scale] JBrowse 2012 Ian Holmes
2:45 [Genome-scale] Khmer: A probabilistic approach for efficient counting of k-mers Qingpeng Zhang
3:00 [Genome-scale] AmiGO 2: a document-oriented approach to ontology software and escaping the heartache of an SQL backend Seth Carbon
3:15 [Genome-scale] Discovery of motif-based regulatory signatures in whole genome methylation experiments Jens Lichtenberg
3:30-4:00 Coffee Break
4:00-5:20 Session: Linked Data and Translational Knowledge Discovery Chair: Jan Aerts
4:00 [Linked / Translational] The open source ISA metadata tracking framework: from data curation and management at the source, to the linked data universe Philippe Rocca-Serra
4:25 [Linked / Translational] Automated infrastructure for custom variant comparison and analysis Brad Chapman
4:50 [Linked / Translational] KUPKB: Sharing, Connecting and Exposing Kidney and Urinary Knowledge using RDF and OWL Julie Klein
5:05 [Linked / Translational] eagle-i: development and expansion of a scientific resource discovery network Sophia Cheng
5:20-5:30 Report on Codefest 2012 Brad Chapman
5:30-5:40 Introduction to the Open Bioinformatics Foundation Hilmar Lapp (President, Open Bioinformatics Foundation)
5:40-6:30 Poster Session II (Room TBA)
5:40-6:30 BOFs
7:00 Pay-your-own-way optional dinner (place TBA)

Day 2: Saturday, July 14 (Preliminary Schedule)

Time Topic Speaker or Moderator
8:45-8:50 Announcements Nomi Harris
8:50-9:50 [Keynote] Title TBA Carole Goble (University of Manchester)
9:50-10:15 [Misc.] Pistoia Alliance Sequence Squeeze: Using a competition model to spur development of novel open-source algorithms Richard Holland
10:15-10:45 Coffee Break
10:45-12:30 Session: Software Interoperability Chair:
10:45-11:00 [Interoperability] Take-aways from the Interoperability SIG (BSI-SIG) Michael Reich (Co-Chair, BSI-SIG)
11:00-11:15 [Interoperability] Galaxy Project Update Dannon Baker
11:15-11:30 [Interoperability] Zero to a Bioinformatics Analysis Platform in 4 Minutes Enis Afgan
11:30-11:55 [Interoperability] PyPedia: A python crowdsourcing development environment for bioinformatics and computational biology Alexandros Kanterakis
11:55-12:10 [Interoperability] InterMine - Embeddable Data-Mining Components Alexis Kalderimis
12:10-12:25 [Interoperability] Creating biology pipelines with BioUno Bruno Kinoshi ta
12:30-1:30 Lunch
12:30-1:45 Poster Session III (Room TBA)
1:45-3:30 Session: Bioinformatics Open Source Project Updates Chair:
1:45-2:00 [Project Updates] Mobyle Web Framework: New Features Hervé Ménager
2:00-2:15 [Project Updates] Biopython Project Update Eric Talevich
2:15-2:40 [Project Updates] Biogem,Ruby UCSC API, and BioRuby Hiroyuki Mishima
2:40-2:55 [Project Updates] A Framework for Interactive Visual Analysis of NGS Data using Galaxy Jeremy Goecks
2:55-3:10 [Project Updates] scabio - a framework for bioinformatics algorithms in Scala Markus Gumbel
3:10-3:35 [Project Updates] Why Scientists Should Contribute to Wikipedia Spencer Bliven
3:30-4:00 Coffee Break
4:00-4:30 Session: Lightning Talks (Instructions for submitting a lightning talk abstract) Chair: Kam Dahlquist
4:30-5:30 Panel: Bioinformatics Paper Reviews: Openness of Standards and Standards of Openness Moderator: Brad Chapman

Panelists: C. Titus Brown, Hilmar Lapp, Scott Markel, Ben Temperton

5:30-5:40 Presentation of awards Nomi Harris
5:40-6:30 BOFs

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