BOSC 2012 Schedule

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: Richard Holland
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 (Instructions for submitting last-minute poster abstract)
2:00-3:30	Session: Genome-scale Data Management	Chair: Ronald Taylor
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