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BOSC 2009 Schedule

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Revision as of 01:40, 2 June 2009 by Kdahlquist (talk) (abstracts linked to Bio* updates)
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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".

Bio* Update

Click on the title to view the abstract.

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 Saturday June 27
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
4:00-4:20 Morris Swertz [Data & Analysis Management] MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments
4:20-4:40 Robert Murphy [Data & Analysis Management] PSLID, the Protein Subcellular Location Image Database: Subcellular location assignments, annotated image collections, image analysis tools, and generative models of protein distributions
4:40-5:00 Mark Welsh [Data & Analysis Management] BioHDF: Open binary file formats for large-scale data management – Project Update
5:00-5:15 Brad Chapman [Data & Analysis Management] Lowering barriers to publishing biological data on the web
5:15-5:30 Kam Dahlquist [Data & Analysis Management] XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources
5:30-6:00   Lightning Talks and Birds of a Feather
7:00   O|B|F Board Meeting and No-host Dinner (location TBA)
Day 2 Sunday June 28
9:00-9:15am Kam Dahlquist [Announcements]
9:15-10:15 Robert Hanmer [Keynote] Software Patterns for Reusable Design
10:15-10:45 Coffee Break
10:45-11:00 Peter Rice [Bio* Update] EMBOSS: European Molecular Biology Open Software Suite
11:00-11:15 Peter Cock [Bio* Update] Biopython Project Update
11:15-11:30 Andreas Prlic [Bio* Update] BioJava 2009: an Open-Source Framework for Bioinformatics
11:30-11:45 Jim Procter [Bio* Update] Application of VAMSAS enabled tools for the investigation of protein evolution
11:45-12:00pm Martin Senger [Bio* Update] Soaplab: Open Source Web Services Framework for Bioinformatics Programs
12:00-12:20 Pjotr Prins [Bio* Update] BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA
12:20-12:28 Steffen Möller [OS Software Lightning Talk] Debian adopts and disseminates Bioinformatics Open Source Software
12:30-2:00 Lunch
2:00-2:20 Quinn Snell [OS Software] PSODA: Open Source Phylogenetic Search and DNA Analysis
2:20-2:40 Finn Drablos [Regulatory Genomics] Computational discovery of composite motifs in DNA
2:40-2:55 François Fauteux [Regulatory Genomics] SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY
2:55-3:10 Matias Piipari [Regulatory Genomics] Large-scale gene regulatory motif discovery and categorisation with NestedMICA
3:10-3:30 Sophie Schbath [Regulatory Genomics] R'MES:
3:30-4:00 Coffee Break
4:00-4:15 Lonnie Welch [Regulatory Genomics] Open Source Implementation of Batch-Extraction for Coding and Non-coding Sequences/An Open Source Framework for Bioinformatics Word Enumeration and Scoring
4:15-4:50 Robert Hanmer (moderator), Lonnie Welch, Aleksi Kallio, other panelists TBA [Panel Discussion] On the Applicability of Design Patterns for the Bioinformatics Open Source Community
4:50-5:30 Lightning Talks and Birds of a Feather
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