| 7:30-9:00AM |
Registration |
Pick up badges for BOSC 2010, Hynes Convention Center (early arrival is recommended as there are usually long lines) |
| 9:00-9:15AM |
Kam Dahlquist |
[Welcome] Introduction to the OBF and Welcome to BOSC 2010 |
| 9:15-10:15 |
Guy Coates |
[Keynote] Clouds: all fluff and no substance? ***SLIDES*** |
| 10:15-10:45 |
|
Coffee Break |
| 10:45-11:05 |
Ronald Taylor |
[Cloud Computing/HT 'omics Data] An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics ***SLIDES*** |
| 11:05-11:25 |
M. Hanna |
[Cloud Computing/HT 'omics Data] The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data ***SLIDES*** |
| 11:25-11:45 |
Brian D. O'Connor |
[Cloud Computing/HT 'omics Data] SeqWare Query Engine: Storing and Searching Sequence Data in the Cloud ***SLIDES*** |
| 11:45-12:00PM |
Judy Qiu |
[Cloud Computing/HT 'omics Data] Hybrid Cloud and Cluster Computing Paradigms for Life Science Applications ***SLIDES*** |
| 12:00-12:15 |
Ben Langmead |
[Cloud Computing/HT 'omics Data] Cloud-scale genomics: examples and lessons ***SLIDES*** |
| 12:15-12:30 |
Enis Afgan |
[Cloud Computing/HT 'omics Data] Deploying Galaxy on the Cloud ***SLIDES*** |
| 12:30-2:00 |
|
Lunch |
| 2:00-2:20 |
Steffen Möller |
[Cloud Computing] Community-driven computational biology with Debian and Taverna ***SLIDES*** |
| 2:20-2:40 |
Darin London |
[Cloud Computing/HT 'omics Data] Dealing with the Data Deluge: What can the Robotics Community Teach us? ***SLIDES*** |
| 2:40-3:00 |
Nyasha Chambwe |
[HT 'omics Data] The Goby framework: towards efficient next-generation sequencing data analysis ***SLIDES*** |
| 3:00-3:15 |
Dana Robinson |
[HT 'omics Data] BioHDF: Open binary file formats for NGS data - current status and future directions ***SLIDES*** |
| 3:15-3:30 |
Jens Lichtenberg |
[HT 'omics Data] Concurrent Bioinformatics Software for Discovering Genome-wide Patterns and Word-based Genomic Signatures ***SLIDES*** |
| 3:30-3:38 |
Chris Hemmerich |
[HT 'omics Data] Automated Annotation of NGS Transcriptome Data using ISGA and Ergatis ***SLIDES*** |
| 3:38-4:00 |
|
Coffee Break |
| 4:00-4:20 |
Mark Wilkinson |
[Semantic Web] From Moby to SADI - Modeling Semantic Web Services with the Semantic Automated Discovery and Integration Framework ***SLIDES*** |
| 4:20-4:35 |
Aravind Venkatesan |
[Semantic Web] ONTO-ToolKit: enabling bio-ontology engineering via Galaxy ***SLIDES*** |
| 4:35-4:45 |
Kazuharu Arakawa |
[Semantic Web] G-language Bookmarklet: a gateway for Semantic Web, Linked Data, and Web Services ***SLIDES*** |
| 4:45-4:55 |
Christian M Zmasek |
[Semantic Web] Connecting TOPSAN to Computational Analysis ***SLIDES*** |
| 4:55-5:10 |
Jianjiong Gao |
[OS Software] Musite: Global Prediction of General and Kinase-Specific Phosphorylation Sites ***SLIDES*** |
| 5:10-5:18 |
Hervé Ménager |
[Lightning Talk] Mobyle Bioinformatics Web Portal: project update ***SLIDES*** |
| 5:18-5:26 |
Stuart Owen |
[Lightning Talk] The Taverna 2.2 Workflow Workbench with a case study using it for Next Gen Sequencing of African cows ***SLIDES*** |
| 5:26-5:34 |
Jiten Bhagat |
[Lightning Talk] BioCatalogue - the Public Curated Registry of Life Science Web Services ***SLIDES*** |
| 5:34-5:42 |
Christian M Zmasek |
[Software Demo] Evolutionary tree visualization and analysis with Archaeopteryx ***SLIDES*** |
| 5:42-5:50 |
Aleksi Kallio |
[Lightning Talk] Connecting Chipster genome browser to the cloud ***SLIDES*** |
| 5:50-5:58 |
Christopher Bottoms |
[Lightning Talk] SNP Allele Designations (Bio::SNP::Inherit) ***SLIDES*** |
| 5:58-6:06 |
Tomasz Puton |
[Lightning Talk] BioPython modules for handling RNA sequences containing modified nucleosides ***SLIDES*** |
| 6:06-6:15 |
Brad Chapman |
[Lightning Talk] Codefest 2010 Report |
| 6:15-6:45 |
|
Birds of a Feather |
| 6:45 |
|
OBF Board Meeting and No-host Dinner; Location: Legal Seafood |
|
|
|
| Day 2 |
Saturday |
July 10: Hynes Convention Center room 207 |
| 9:00-9:15AM |
Kam Dahlquist |
[Announcements] |
| 9:15-10:15 |
Ross Gardler |
[Keynote] Community Development at the Apache Software Foundation ***SLIDES*** |
| 10:15-10:45 |
|
Coffee Break |
| 10:45-11:05 |
Christopher Fields |
[Bio* Update] Towards a Modern BioPerl: BioPerl Update 2010 ***SLIDES*** |
| 11:05-11:20 |
Raoul J.P. Bonnal |
[Bio* Update] BioRuby 2010 updates: moving to agile bioinformatics ***SLIDES*** |
| 11:20-11:35 |
Peter Rice |
[Bio* Update] EMBOSS: The European Molecular Biology Open Software Suite ***SLIDES*** |
| 11:35-11:50 |
Brad Chapman |
[Bio* Update] Biopython Project Update 2010 ***SLIDES*** |
| 11:50-12:05PM |
Tiago Antao |
[OS software] interPopula: Database and tool integration for population genetics using Python ***SLIDES*** |
| 12:05-12:20 |
Laurent Gautier |
[Bio* Update] Bioconductor with Python, What else ? ***SLIDES*** |
| 12:20-12:30 |
Eric W Talevich |
[Bio* Update] Bio.Phylo: A unified phylogenetics toolkit for Biopython ***SLIDES*** |
| 12:30-2:00 |
|
Lunch |
| 2:00-2:20 |
Simon Mercer |
[OS Software Framework] The Microsoft Biology Foundation ***SLIDES*** |
| 2:20-2:40 |
William Crawford |
[OS Software/Code Generation] Building Bioinformatics Web Application with Clickframes |
| 2:40-3:00 |
Morris A. Swertz |
[OS Software/Code Generation] MOLGENIS: rapid prototyping of biosoftware at the push of a button ***SLIDES*** |
| 3:00-3:10 |
Alexandros Kanterakis |
[OS Software/Code Generation] Generating a data platform for microarray gene expression experiments using MOLGENIS and MAGE-TAB ***SLIDES*** |
| 3:10-3:25 |
Sebastian J. Schultheiss |
[Web Services] Long-term availability of bioinformatics web services ***SLIDES*** |
| 3:25-4:00 |
|
Coffee Break |
| 4:00-4:15 |
Lincoln Stein |
[Visualization] GBrowse2 ***SLIDES*** |
| 4:15-4:35 |
Gary D. Bader |
[Visualization] Cytoscape Web: An interactive, customizable web-based network browser ***SLIDES*** |
| 4:35-4:50 |
Nobuaki Kono |
[Visualization] Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API ***SLIDES*** |
| 4:50-5:05 |
James A. Morris |
[Visualization] Evoker: a visualization tool for genotype intensity data ***SLIDES*** |
| 5:05-5:20 |
Pavel Tomancak |
[Visualization] Fiji Is Just ImageJ - an Open Source platform for biological image analysis |
| 5:20-5:30 |
Iddo Friedberg |
[Visualization] IPRStats: visualization and analysis of InterProScan Results ***SLIDES*** |
| 5:30-6:00 |
|
Birds of a Feather |