Please visit our ***NEW*** OBF/BOSC website: https://www.open-bio.org/ |
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Difference between revisions of "BOSC 2012 Schedule"
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| Chair: | | Chair: | ||
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− | || | + | || 10:45 |
| [Cloud] Cloudgene - an execution platform for MapReduce programs in public and private clouds | | [Cloud] Cloudgene - an execution platform for MapReduce programs in public and private clouds | ||
| Sebastian Schoenherr | | Sebastian Schoenherr | ||
|- | |- | ||
− | | | + | | 11:10 |
| [Cloud] Data reduction and division approaches for assembling short-read data in the cloud | | [Cloud] Data reduction and division approaches for assembling short-read data in the cloud | ||
| C. Titus Brown | | 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 | | [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 | | Andrey Tovchigrechko | ||
|- | |- | ||
− | | | + | | 12:00 |
| [Cloud] Workflows on the Cloud - Scaling for National Service | | [Cloud] Workflows on the Cloud - Scaling for National Service | ||
| Shoaib Sufi | | Shoaib Sufi | ||
|- | |- | ||
− | | 15 | + | | 12:15 |
| [Cloud] How to use BioJava to calculate one billion protein structure alignments at the RCSB PDB website | | [Cloud] How to use BioJava to calculate one billion protein structure alignments at the RCSB PDB website | ||
| Andreas Prlic | | Andreas Prlic | ||
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| Chair: | | Chair: | ||
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− | | | + | | 2:00 |
| [Genome-scale] Using HDF5 to Work With Large Quantities of Biological Data | | [Genome-scale] Using HDF5 to Work With Large Quantities of Biological Data | ||
| Dana Robinson | | Dana Robinson | ||
|- | |- | ||
− | | 15 | + | | 2:15 |
| [Genome-scale] Large scale data management in Chipster 2 workflow environment | | [Genome-scale] Large scale data management in Chipster 2 workflow environment | ||
| Aleksi Kallio | | Aleksi Kallio | ||
|- | |- | ||
− | | | + | | 2:30 |
| [Genome-scale] JBrowse 2012 | | [Genome-scale] JBrowse 2012 | ||
| Ian Holmes | | Ian Holmes | ||
|- | |- | ||
− | | | + | | 2:45 |
| [Genome-scale] Khmer: A probabilistic approach for efficient counting of k-mers | | [Genome-scale] Khmer: A probabilistic approach for efficient counting of k-mers | ||
| Qingpeng Zhang | | Qingpeng Zhang | ||
|- | |- | ||
− | | | + | | 3:00 |
| [Genome-scale] AmiGO 2: a document-oriented approach to ontology software and escaping the heartache of an SQL backend | | [Genome-scale] AmiGO 2: a document-oriented approach to ontology software and escaping the heartache of an SQL backend | ||
| Seth Carbon | | Seth Carbon | ||
|- | |- | ||
− | | 15 | + | | 3:15 |
| [Genome-scale] Discovery of motif-based regulatory signatures in whole genome methylation experiments | | [Genome-scale] Discovery of motif-based regulatory signatures in whole genome methylation experiments | ||
| Jens Lichtenberg | | Jens Lichtenberg | ||
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| Chair: Jan Aerts | | 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 | | [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 | | Philippe Rocca-Serra | ||
|- | |- | ||
− | | 25 | + | | 4:25 |
| [Linked / Translational] Automated infrastructure for custom variant comparison and analysis | | [Linked / Translational] Automated infrastructure for custom variant comparison and analysis | ||
| Brad Chapman | | Brad Chapman | ||
|- | |- | ||
− | | | + | | 4:50 |
| [Linked / Translational] KUPKB: Sharing, Connecting and Exposing Kidney and Urinary Knowledge using RDF and OWL | | [Linked / Translational] KUPKB: Sharing, Connecting and Exposing Kidney and Urinary Knowledge using RDF and OWL | ||
| Julie Klein | | Julie Klein | ||
|- | |- | ||
− | | | + | | 5:05 |
| [Linked / Translational] eagle-i: development and expansion of a scientific resource discovery network | | [Linked / Translational] eagle-i: development and expansion of a scientific resource discovery network | ||
| Sophia Cheng | | Sophia Cheng |
Revision as of 00:37, 27 May 2012
Day 1: Friday, July 13
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: |
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 (Room TBA) | |
2:00-3:30 | Session: Genome-scale Data Management | Chair: |
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 (Room TBA)
Time | Topic | Speaker or Moderator |
---|---|---|
8:45-8:50 | Announcements | Nomi Harris |
8:50-9:50 | [Keynote] Title TBA | Carole Goble (University of Manchester) |
10:15-10:45 | Coffee Break | |
10:45-12:30 | Session: Software Interoperability | Chair: |
15 | [Interoperability] Take-aways from the Interoperability SIG (BSI-SIG) | Michael Reich (Co-Chair, BSI-SIG) |
15 | [Interoperability] Galaxy Project Update | Dannon Baker |
15 | [Interoperability] Zero to a Bioinformatics Analysis Platform in 4 Minutes | Enis Afgan |
25 | [Interoperability] PyPedia: A python crowdsourcing development environment for bioinformatics and computational biology | Alexandros Kanterakis |
15 | [Interoperability] InterMine - Embeddable Data-Mining Components | Alexis Kalderimis |
15 | [Interoperability] Creating biology pipelines with BioUno | Bruno Kinoshi ta |
15 | [Interoperability] A Framework for Interactive Visual Analysis of NGS Data using Galaxy | Jeremy Goecks |
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: |
15 | [Project Updates] Mobyle Web Framework: New Features | Hervé Ménager |
15 | [Project Updates] Biopython Project Update | Eric Talevich |
25 | [Project Updates] Biogem,Ruby UCSC API, and BioRuby | Hiroyuki Mishima |
15 | [Project Updates] scabio - a framework for bioinformatics algorithms in Scala | Markus Gumbel |
25 | [Project Updates] Why Scientists Should Contribute to Wikipedia | Spencer Bliven |
3:30-4:00 | Coffee Break | |
4:00-4:30 | Session: Lightning Talks | 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 |