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Difference between revisions of "BOSC 2012 Schedule"
From Open Bioinformatics Foundation
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|| 10:45 | || 10:45 | ||
| − | | [Cloud] Cloudgene - an execution platform for MapReduce programs in public and private clouds | + | | [Cloud] [http://www.slideshare.net/jandot/l-forer-cloudgene-an-execution-platform-for-mapreduce-programs-in-public-and-private-clouds Cloudgene - an execution platform for MapReduce programs in public and private clouds] |
| Sebastian Schönherr | | Sebastian Schönherr | ||
|- | |- | ||
| 11:10 | | 11:10 | ||
| − | | [Cloud] Data reduction and division approaches for assembling short-read data in the cloud | + | | [Cloud] [http://www.slideshare.net/jandot/ct-brown-doing-nextgen-sequencing-analysis-in-the-cloud Data reduction and division approaches for assembling short-read data in the cloud] |
| C. Titus Brown | | C. Titus Brown | ||
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| 2:00 | | 2:00 | ||
| − | | [Genome-scale] Using HDF5 to Work With Large Quantities of Biological Data | + | | [Genome-scale] [http://www.slideshare.net/jandot/d-robinson-using-hdf5-to-work-with-large-quantities-of-rich-biological-data Using HDF5 to Work With Large Quantities of Biological Data] |
| Dana Robinson | | Dana Robinson | ||
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| 10:45-11:00 | | 10:45-11:00 | ||
| − | | [Interoperability] GenomeSpace: An open source environment for frictionless bioinformatics | + | | [Interoperability] [http://www.slideshare.net/jandot/m-reich-genomespace GenomeSpace: An open source environment for frictionless bioinformatics] |
| Michael Reich | | Michael Reich | ||
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| 11:00-11:15 | | 11:00-11:15 | ||
| − | | [Interoperability] Galaxy Project Update | + | | [Interoperability] [http://www.slideshare.net/jandot/d-baker-galaxy-update Galaxy Project Update] |
| Dannon Baker | | Dannon Baker | ||
|- | |- | ||
| 11:15-11:30 | | 11:15-11:30 | ||
| − | | [Interoperability] Zero to a Bioinformatics Analysis Platform in 4 Minutes | + | | [Interoperability] http://www.slideshare.net/jandot/e-afgan-zero-to-a-bioinformatics-analysis-platform-in-four-minutes Zero to a Bioinformatics Analysis Platform in 4 Minutes] |
| Enis Afgan | | Enis Afgan | ||
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| 11:55-12:10 | | 11:55-12:10 | ||
| − | | [Interoperability] InterMine - Embeddable Data-Mining Components | + | | [Interoperability] [http://www.slideshare.net/jandot/a-kalderimis-intermine-embeddable-datamining-components InterMine - Embeddable Data-Mining Components] |
| Alexis Kalderimis | | Alexis Kalderimis | ||
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| 12:10-12:25 | | 12:10-12:25 | ||
| − | | [Interoperability] Creating biology pipelines with BioUno | + | | [Interoperability] [http://slidesha.re/MHApSM Creating biology pipelines with BioUno] |
| − | | Bruno Kinoshi | + | | Bruno Kinoshi ta |
|- | |- | ||
| '''12:30-1:30''' | | '''12:30-1:30''' | ||
Revision as of 06:18, 18 July 2012
Click here to download this schedule as PDF
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 ** Talk ** | 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 | |
| 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 is sick--instead we will see a short talk on JBrowse by Robert Buels) |
| 2:38 | Report on Codefest 2012 | Brad Chapman |
| 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 | Introduction to the Open Bioinformatics Foundation | Hilmar Lapp (President, Open Bioinformatics Foundation) |
| 5:30 | Announcements | Nomi Harris (Chair, BOSC 2012) |
| 5:30-6:30 | Poster Session II (Hall B)--there are still spots open for last-minute posters! | |
| 5:30-6:30 | BOFs | |
| 7:00 | Pay-your-own-way BOSC dinner ($25/person): George’s Greek Café, 135 Pine Avenue, Long Beach. (Registration for dinner is now closed.) |
Day 2: Saturday, July 14
| 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] http://www.slideshare.net/jandot/e-afgan-zero-to-a-bioinformatics-analysis-platform-in-four-minutes 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 | |
| 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 | 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] GMOD in the Cloud | Scott Cain |
| 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 |
Click here to download this schedule as PDF
Click here to download the complete BOSC program as PDF
