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BOSC 2009 Schedule
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Contents
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
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- Jean-Stéphane Varré - Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics (15 min.)
- Josh Buckner - Enabling GPU Computing in the R Statistical Environment (15 min.)
- Mikhail Fursov - UGENE – A practical approach for complex computational analysis in molecular biology (10 min.)
- Oswaldo Trelles - Qnorm: A library of parallel methods for gene-expression Q-normalization (5 min. Lightning Talk)
Computational Grids
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- Hajo N. Krabbenhöft - Taverna workflows across Grids, web services and the command line (15 min.)
- Ann-Kristin Grimm - Grid-based expression QTL analysis (10 min.)
- Joel Hedlund - The Nordic BioGrid project -- Bioinformatics for the grid (5 min. Lightning Talk)
Visualization
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- Allan Kuchinsky - Cytoscape Springs Forward: Re-architecture for Version 3.0 (15 min.)
- Frederik Decouttere - Bioinformatics simplified with seqpad (10 min.)
- Bernat Gel - DASGenExp: an interactive web-based DAS client with client-side rendering (10 min.)
Open Source Software
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- Kazuharu Arakawa - Web Service Interface for G-language Genome Analysis Environment (10 min.)
- Sylvain Brohée - Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases (10 min.)
- Quinn Snell - PSODA: Open Source Phylogenetic Search and DNA Analysis (15 min.)
Click on the title to view the abstract.
- Morris Swertz - MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments (15 min.)
- Mark Welsh - BioHDF: Open binary file formats for large-scale data management – Project Update (15 min.)
- Robert Murphy - PSLID, the Protein Subcellular Location Image Database: Subcellular location assignments, annotated image collections, image analysis tools, and generative models of protein distributions (15 min.)
- Kam Dahlquist - XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources (10 min.)
- Brad Chapman - Lowering barriers to publishing biological data on the web (10 min.)
Bio* Update
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- Martin Senger - Soaplab: Open Source Web Services Framework for Bioinformatics Programs (10 min.)
- Pjotr Prins - BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA (15 min.)
- Peter Rice - EMBOSS: European Molecular Biology Open Software Suite (10 min.)
- Peter Cock - Biopython Project Update (10 min.)
- Andreas Prlic - BioJava 2009: an Open-Source Framework for Bioinformatics (10 min.)
- Jim Procter - Application of VAMSAS enabled tools for the investigation of protein evolution (10 min.)
- Steffen Möller - Debian adopts and disseminates Bioinformatics Open Source Software (5 min. Lightning Talk)
Regulatory Genomics
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- Finn Drablos - Computational discovery of composite motifs in DNA (15 min.)
- Sophie Schbath - R'MES (15 min.)
- Matias Piipari - Large-scale gene regulatory motif discovery and categorisation with NestedMICA (10 min.)
- Bartek Wilczynski - BNfinder: free software for effective Bayesian Network inference (15 min.)
- Lonnie Welch - Open Source Implementation of Batch-Extraction for Coding and Non-coding Sequences/An Open Source Framework for Bioinformatics Word Enumeration and Scoring (10 min.)
- François Fauteux - SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY (10 min.)
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.
- Robert Hanmer - Moderator
- Lonnie Welch
- Aleksi Kallio
