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Difference between revisions of "BOSC 2009 Schedule"

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| [Welcome]
 
| [Welcome]
 
|-
 
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| 9:15-10:15am
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| 9:15-10:15
 
| Alan Ruttenberg
 
| Alan Ruttenberg
 
| [Keynote] Semantic Web Technologies
 
| [Keynote] Semantic Web Technologies
 
|-
 
|-
| 10:15-10:45am
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| 10:15-10:45
 
| Coffee Break
 
| Coffee Break
 
|-
 
|-
| 10:45-11:05am
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| 10:45-11:05
 
| Jean-Stéphane Varré
 
| Jean-Stéphane Varré
 
| [Multicore & GPGPU Computing] Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics
 
| [Multicore & GPGPU Computing] Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics
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| [Multicore & GPGPU Computing Lightning Talk] Qnorm: A library of parallel methods for gene-expression Q-normalization
 
| [Multicore & GPGPU Computing Lightning Talk] Qnorm: A library of parallel methods for gene-expression Q-normalization
 
|-
 
|-
| 11:48-12:08
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| 11:48-12:08pm
 
| Hajo N. Krabbenhöft
 
| Hajo N. Krabbenhöft
 
| [Computational Grids] Taverna workflows across Grids, web services and the command line
 
| [Computational Grids] Taverna workflows across Grids, web services and the command line
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| 12:31-2:00
 
| 12:31-2:00
 
| Lunch
 
| Lunch
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|-
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| 2:00-2:20
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| Allan Kuchinsky
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| [Visualization] Cytoscape Springs Forward: Re-architecture for Version 3.0
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|-
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| 2:20-2:33
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| Frederik Decouttere
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| [Visualization] Bioinformatics simplified with seqpad
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|-
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| 2:33-2:46
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| Bernat Gel
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| [Visualization] DASGenExp: an interactive web-based DAS client with client-side rendering
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|-
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| 2:46-2:59
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| Kazuharu Arakawa
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| [OS Software] Web Service Interface for G-language Genome Analysis Environment
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|-
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| 2:59-3:12
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| Sylvain Brohée
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| [OS Software] Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases
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|-
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| 3:12-3:30
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| Bartek Wilczynski
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| [Regulatory Genomics] BNfinder: free software for effective Bayesian Network inference
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|-
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| 3:30-4:00
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| Coffee Break
 
|}
 
|}

Revision as of 19:58, 1 June 2009

Return to BOSC 2009 main page.

Keynote Speakers

The BOSC 2009 Organizing committee is pleased to announce our two Keynote Speakers:

Alan Ruttenberg

Alan Ruttenberg is a Principal Scientist at Science Commons. He works with Semantic Web technologies in computational biology, with an emphasis on the creation and application of structured biological knowledge to interpret experimental results. He is currently involved in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that will form the upper level ontology for the OBO foundry, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), the Information Artifact Ontology (IAO), and BioPAX-OBO for representing molecular and cellular pathways. These interests and efforts come together in my project at Science Commons - the Neurocommons, a large scale Semantic Web knowledge base of biological information aimed at supporting, initially, the neurosciences. He is also an active participant in W3C Semantic Web activities. In 2006 and 2007 he was a member of the Health Care Life Sciences Interest Group, and early work on the Neurocommons became the core of the prototype life sciences knowledge base that the group has documented. He is a chair of the OWL Working Group specifying OWL 2, and a coordinating editor of the OBO Foundry. His graduate work was at the MIT Media Lab in the Music and Cognition Group, and he has an undergraduate degree in Physics and Mathematics from Brandeis University.

Robert S. Hanmer

Robert S. Hanmer is a Consulting Member of Technical Staff in the Technical Component Management area in Alcatel-Lucent’s Operations area. He is based in Naperville, Illinois, USA. Current responsibilities include developing software-sourcing strategies for middleware and open source software. Previous positions within Lucent and Bell Laboratories have included development, architecture and evaluation of highly reliable systems focusing especially on the areas of reliability and performance. He is active in the software patterns community, including serving as program chair at several pattern conferences. He has authored or co-authored 14 journal articles, several book chapters and the book Patterns for Fault Tolerant Software. He is a member of the IEEE Computer Society, a Senior Member of the ACM and current President of The Hillside Group, the organization that sponsors the PLoP conference. He received his B.S. and M.S. degrees in Computer Science from Northwestern University in Evanston, Illinois.

His talk at BOSC will be entitled "Software Patterns for Reusable Design".

Multicore & GPGPU Computing

Click on the title to view the abstract.

Computational Grids

Click on the title to view the abstract.

Visualization

Click on the title to view the abstract.

Open Source Software

Click on the title to view the abstract.

Data & Analysis Management (shared session with D&AM SIG)

Click on the title to view the abstract.

Bio* Update

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Regulatory Genomics

Click on the title to view the abstract.

Design Patterns Panel Discussion

On the Applicability of Design Patterns for the Bioinformatics Open Source Community

Click on the author's name to view the abstract submitted for the panel.

Schedule

Day 1

Time Speaker Title
9:00-9:15am Kam Dahlquist [Welcome]
9:15-10:15 Alan Ruttenberg [Keynote] Semantic Web Technologies
10:15-10:45 Coffee Break
10:45-11:05 Jean-Stéphane Varré [Multicore & GPGPU Computing] Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics
11:25-11:40 Josh Buckner [Multicore & GPGPU Computing] Enabling GPU Computing in the R Statistical Environment
11:25-11:40 Mikhail Fursov [Multicore & GPGPU Computing] UGENE – A practical approach for complex computational analysis in molecular biology
11:40-11:48 Oswaldo Trelles [Multicore & GPGPU Computing Lightning Talk] Qnorm: A library of parallel methods for gene-expression Q-normalization
11:48-12:08pm Hajo N. Krabbenhöft [Computational Grids] Taverna workflows across Grids, web services and the command line
12:08-12:23 Ann-Kristin Grimm [Computational Grids] Grid-based expression QTL analysis
12:23-12:31 Joel Hedlund [Computational Grids Lightning Talk] The Nordic BioGrid project -- Bioinformatics for the grid
12:31-2:00 Lunch
2:00-2:20 Allan Kuchinsky [Visualization] Cytoscape Springs Forward: Re-architecture for Version 3.0
2:20-2:33 Frederik Decouttere [Visualization] Bioinformatics simplified with seqpad
2:33-2:46 Bernat Gel [Visualization] DASGenExp: an interactive web-based DAS client with client-side rendering
2:46-2:59 Kazuharu Arakawa [OS Software] Web Service Interface for G-language Genome Analysis Environment
2:59-3:12 Sylvain Brohée [OS Software] Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases
3:12-3:30 Bartek Wilczynski [Regulatory Genomics] BNfinder: free software for effective Bayesian Network inference
3:30-4:00 Coffee Break