BOSC 2013 Schedule

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You can also:

- Download schedule as PDF (A4 format).

- Download the complete program

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 (PDF, YouTube) Nomi Harris (Chair, BOSC 2013)
9:15-10:15 [Keynote] Network ready research: The role of open source and open thinking (SlideShare YouTube) 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 (PDF) Anup Mahurkar
11:00 [Open Science] myExperiment Research Objects: Beyond Workflows and Packs (PDF, SlideShare) Stian Soiland-Reyes
11:15 [Open Science] Empowering Cancer Research Through Open Development: The National Cancer Informatics Program Open Development Initiative (PDF) Juli Klemm
11:30 [Open Science] DNAdigest - a not-for-profit organisation to promote and enable open-access sharing of genomics data (PDF) Fiona Nielsen
11:45 [Open Science] Jug: Reproducible Research in Python (PDF) Luis Pedro Coelho
11:50 [Open Science] OpenLabFramework: A Next-Generation Open-Source Laboratory Information Management System for Efficient Sample Tracking (PDF) Markus List
11:55 [Open Science] Ten Simple Rules for the Open Development of Scientific Software (followed by discussion) (PDF) Andreas Prlic, Jim Procter, Hilmar Lapp
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 (PDF) Nils Gehlenborg
2:25 [Visualization] MetaSee: An interactive visualization toolbox for metagenomic sample analysis and comparison (PDF) Xiaoquan Su (delayed to Day 2)
2:25 [Substitute Talk] Genomics applications in the cloud with the DNAnexus Platform (PDF) Andrey Kislyuk
2:40 [Visualization] DGE-Vis: Visualisation of RNA-seq data for Differential Gene Expression analysis (PDF) David Powell
2:55 [Visualization] Genomic Visualization Everywhere with Dalliance (Slides) Thomas Down
3:10 [Visualization] Robust quality control of Next Generation Sequencing alignment data (PDF) Konstantin Okonechnikov
3:25 [Visualization] Visualizing bacterial sequencing data with GenomeView (PDF) 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 (PDF) Toshiaki Katayama
4:15 [Project Updates] Biopython project update 2013 (PDF, SlideShare) Peter Cock
4:30 [Project Updates] InterMine - Collaborative Data Mining (PDF) Alex Kalderimis
4:45 [Project Updates] The GenoCAD 2.2 Grammar Editor (PDF) Jean Peccoud
5:00 [Project Updates] Improvements and new features in the 7th major release of the Bio-Linux distro (PDF) 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.)


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Day 2: Saturday, July 20

Time Topic Speaker or Moderator
8:45 Announcements Nomi Harris
8:50 Codefest 2013 Report (SlideShare YouTube) Brad Chapman
9:00 Open Bioinformatics Foundation: A Community For, By, and Of You (SlideShare YouTube) Hilmar Lapp (President, Open Bioinformatics Foundation)
9:15 [Keynote] Biological sequence analysis in the post-data era (PDF, YouTube) 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 (PDF) Enis Afgan
11:10 [Interoperability] Taverna Components: Semantically annotated and shareable units of functionality (PDF YouTube) Donal Fellows
11:35 [Interoperability] UGENE Workflow Designer – flexible control and extension of pipelines with scripts (PDF YouTube) Yuriy Vaskin
11:50 [Interoperability] Reproducible Quantitative Transcriptome Analysis with Oqtans (PDF YouTube) Vipin T. Sreedharan
12:05 [Visualization] MetaSee: An interactive visualization toolbox for metagenomic sample analysis and comparison (PDF YouTube) Xiaoquan Su (postponed from day 1)
12:15 [Interoperability] PhyloCommons: community storage, annotation and reuse of phylogenies (PDF, SlideShare YouTube) Hilmar Lapp
12:20 [Interoperability] GEMBASSY: an EMBOSS associated package for genome analysis using G-language SOAP/REST web services (PDF) Hidetoshi Itaya
12:25 [Interoperability] Rubra - flexible distributed pipelines for bioinformatics (PDF, YouTube) 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 (PDF) Enis Afgan
1:45 [Cloud/Genome-Scale] MyGene.info: Making Elastic and Extensible Gene­-centric Web Services (PDF) Chunlei Wu
2:00 [Cloud/Genome-Scale] An update on the Seal Hadoop-based sequence processing toolbox (PDF YouTube) Luca Pireddu
2:15 [Cloud/Genome-Scale] Open Source Configuration of Bioinformatics Infrastructure (PDF YouTube) John Chilton
2:30 [Cloud/Genome-Scale] GEPETTO: An Open Source Framework for Gene Prioritization (PDF YouTube) Vincent Walter
2:55 [Cloud/Genome-Scale] RAMPART: an automated de novo assembly pipeline (PDF YouTube) Daniel Mapleson
3:10 [Cloud/Genome-Scale] OmicsConnect: flexible multi-omics data capture and integration tools for high-throughput biology (PDF) 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 (slides YouTube) Brad Chapman
4:25 [Translational] Understanding Cancer Genomes Using Galaxy (PDF YouTube) Jeremy Goecks
4:40-5:30 Panel: Strategies for Funding and Maintaining Open Source Software (YouTube) Moderator: Brad Chapman

Panelists: Peter Cock, Sean Eddy, Carole Goble, Scott Markel, Jean Peccoud

5:30-5:40 Presentation of Student Travel Awards (PDF) Nomi Harris
5:40-6:40 BOFs -- suggest a BOF topic here!

Posters

This table currently only lists presented posters for which the authors have shared the PDF.

Title Presenter
BIOINFO-C: C-based Bioinformatics Library and Web Application Framework (PDF) Detlef Wolf
Reproducible Quantitative Transcriptome Analysis with ocqtans (PDF) Vipin T. Sreedharan



You can also:

- Download schedule as PDF (A4 format).

- Download the complete program


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