BOSC 2009 Schedule

From Open Bioinformatics Foundation
Revision as of 14:44, 29 May 2009 by Kdahlquist (talk) (Bio* Update: added links to abstracts)
Jump to: navigation, search

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.


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

Click on the title to view the abstract.

Regulatory Genomics

  • 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.)

Design Patterns Panel Discussion

Confirmed speakers for the Panel include:

  • Robert Hanmer - Moderator
  • Lonnie Welch - The WORDIFIER Pattern for Functional and Regulatory Genomics (5 min.)
  • Aleksi Kallio - Robust architectural patterns for bioinformatics: experiences with Chipster (5 min.)