BOSC 2013 Schedule

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Day 1: Friday, July 19

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 2013)
9:15-10:15	[Keynote] Network ready research: The role of open source and open thinking	Cameron Neylon (Public Library of Science)
10:15-10:45	Coffee Break
10:45-12:30	Session: Open Science	Chair: Hilmar Lapp
10:45	[Open Science] Open Science Data Framework: A Cloud enabled system to store, access, and analyze scientific data	Anup Mahurkar
11:00	[Open Science] myExperiment Research Objects: Beyond Workflows and Packs	Stian Soiland-Reyes
11:15	[Open Science] Empowering Cancer Research Through Open Development	Juli Klemm
11:30	[Open Science] DNAdigest - a not-for-profit organisation to promote and enable open-access sharing of genomics data	Fiona Nielsen
11:45	[Open Science] Jug: Reproducible Research in Python	Luis Pedro Coelho
11:50	[Open Science] OpenLabFramework: A Next-Generation Open-Source Laboratory Information Management System for Efficient Sample Tracking	Markus List
11:55	[Open Science] Ten Simple Rules for the Open Development of Scientific Software (followed by discussion)	Andreas Prlic
12:30-1:30	Lunch
1:00-2:00	Poster Session I
2:00-3:30	Session: Visualization	Chair: Jan Aerts
2:00	[Visualization] Refinery Platform - Integrating Visualization and Analysis of Large-Scale Biological Data	Nils Gehlenborg
2:25	[Visualization] MetaSee: An interactive visualization toolbox for metagenomic sample analysis and comparison	Kang Ning
2:40	[Visualization] DGE-Vis: Visualisation of RNA-seq data for Differential Gene Expression analysis	David Powell
2:55	[Visualization] Genomic Visualization Everywhere with Dalliance	Thomas Down
3:10	[Visualization] Robust quality control of Next Generation Sequencing alignment data	Konstantin Okonechnikov
3:25	[Visualization] Visualizing bacterial sequencing data with GenomeView	Thomas Abeel
3:30-4:00	Coffee Break
4:00-5:15	Session: Bioinformatics Open Source Project Updates	Chair: Hans-Rudolf Hotz
4:00	[Project Updates] BioRuby project updates - power of modularity in the community-based open source development model	Toshiaki Katayama
4:15	[Project Updates] Biopython project update	Peter Cock
4:30	[Project Updates] InterMine - Collaborative Data Mining	Alex Kalderimis
4:45	[Project Updates] The GenoCAD 2.2 Grammar Editor	Jean Peccoud
5:00	[Project Updates] Improvements and new features in the 7th major release of the Bio-Linux distro	Timothy Booth
5:15	Announcements	Nomi Harris (Chair, BOSC 2013)
5:20-6:30	Poster Session II
5:20-6:30	BOFs -- suggest a BOF topic here!
7:00	Pay-your-own-way BOSC dinner, Hendrik’s, Straße des 17. Juni 13, 10623 Berlin. (Space limited--you must RSVP to attend.)

Day 2: Saturday, July 20

Time	Topic	Speaker or Moderator
8:45	Announcements	Nomi Harris
8:50	Codefest 2013 Report	Brad Chapman
9:00	Open Bioinformatics Foundation: A Community For, By, and Of You	Hilmar Lapp (President, Open Bioinformatics Foundation)
9:15	[Keynote] Biological sequence analysis in the post-data era	Sean Eddy (Janelia Farm)
10:15-10:45	Coffee Break
10:45-12:30	Session: Software Interoperability	Chair: Jeremy Goecks
10:45	[Interoperability] BioBlend - Enabling Pipeline Dreams	Enis Afgan
11:10	[Interoperability] Taverna Components: Semantically annotated and shareable units of functionality	Alan Williams
11:35	[Interoperability] UGENE Workflow Designer – flexible control and extension of pipelines with scripts	Yuriy Vaskin
11:50	[Interoperability] Reproducible Quantitative Transcriptome Analysis with Oqtans	Vipin T. Sreedharan
12:05	[Interoperability] PhyloCommons: community storage, annotation and reuse of phylogenies	Hilmar Lapp
12:10	[Interoperability] GEMBASSY: an EMBOSS associated package for genome analysis using G-language SOAP/REST web services	Hidetoshi Itaya
12:15	[Interoperability] Rubra - flexible distributed pipelines for bioinformatics	Clare Sloggett
12:30-1:30	Lunch
12:30-1:30	Poster Session III
1:30-3:30	Session: Cloud and Genome-Scale Computing	Chair: Peter Cock
1:30	[Cloud/Genome-Scale] Towards Enabling Big Data and Federated Computing in the Cloud	Enis Afgan
1:45	[Cloud/Genome-Scale] MyGene.info: Making Elastic and Extensible Gene­-centric Web Services	Chunlei Wu
2:00	[Cloud/Genome-Scale] An update on the Seal Hadoop-based sequence processing toolbox	Luca Pireddu
2:15	[Cloud/Genome-Scale] Open Source Configuration of Bioinformatics Infrastructure	John Chilton
2:30	[Cloud/Genome-Scale] An Open Source Framework for Gene Prioritization	Hoan Nguyen
2:55	[Cloud/Genome-Scale] RAMPART: an automated de novo assembly pipeline	Daniel Mapleson
3:10	[Cloud/Genome-Scale] OmicsConnect: flexible multi-omics data capture and integration tools for high-throughput biology	Joeri van der Velde
3:30-4:00	Coffee Break
4:00-4:40	Session: Translational Genomics	Chair: Nomi Harris
4:00	[Translational] Community development of human variant calling and validation pipelines	Brad Chapman
4:25	[Translational] Understanding Cancer Genomes Using Galaxy	Jeremy Goecks
4:40-5:30	Panel: Strategies for Funding and Maintaining Open Source Software	Moderator: Brad Chapman Panelists: Peter Cock, Sean Eddy, Carole Goble, Scott Markel, Jean Peccoud
5:30-5:40	Presentation of Student Travel Awards	Nomi Harris
5:40-6:40	BOFs -- suggest a BOF topic here!

You can also:

- Download schedule as PDF (A4 format).

- Download the complete program

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