BOSC 2012 Schedule

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Please note: hardcopies of this schedule will be distributed at BOSC, but hardcopies of the complete program will not, so attendees should print the program before leaving for BOSC, if they want it on paper. There will not be access to printers at the meeting.

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 Schönherr
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	Katy Wolstencroft
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)
5:40-6:40	BOFs
7:00	Pay-your-own-way BOSC dinner ($25/person): George’s Greek Café, 135 Pine Avenue, Long Beach (near the Convention Center)

Day 2: Saturday, July 14 (Preliminary Schedule)

Time	Topic	Speaker or Moderator
8:45-8:50	Announcements	Nomi Harris
8:50-9:50	[Keynote] If I Build It Will They Come?	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: Hilmar Lapp
10:45-11:00	[Interoperability] GenomeSpace: An open source environment for frictionless bioinformatics	Michael Reich
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: Jeremy Goecks
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] Why Scientists Should Contribute to Wikipedia	Spencer Bliven
3:10-3:25	[Project Updates] scabio - a framework for bioinformatics algorithms in Scala	Markus Gumbel
3:30-4:00	Coffee Break
4:00-4:30	Session: Lightning Talks (Send last-minute lightning talk abstracts to bosc @ open-bio.org!)	Chair: Kam Dahlquist
4:00-4:07	[Lightning] bioKepler: A Comprehensive Bioinformatics Scientific Workflow Module for Distributed Analysis of Large-Scale Biological Data	Jianwu Wang
4:07-4:14	[Lightning] Dao: a novel programming language for bioinformatics	Limin Fu
4:14-4:21	[Lightning]
4:21-4:28	[Lightning] Bioinformatics Testing Consortium: Codebase peer-review to improve robustness of bioinformatic pipelines	Ben Temperton
4:30-5:30	Panel: Bioinformatics Paper Reviews: Openness of Standards and Standards of Openness	Moderator: Brad Chapman Panelists: C. Titus Brown, Iain Hrynaszkiewicz, Hilmar Lapp, Scott Markel, Ben Temperton
5:30-5:40	Presentation of awards	Nomi Harris
5:40-6:40	BOFs