Birds of a Feather (BoF)

Topic: Cytoscape User Group

Leader: Allan Kuchinsky
Affiliation: Agilent Technologies

Time: Tuesday, June 30 1:00-2:00
Room: T1

Desc: Cytoscape is free, open-source software for network visualization and analysis. Users and plugin developers are invited to join core developers for Cytoscape discussion.

Topic: Concept Web Alliance

Leader: Barend Mons
Affiliation: Netherlands Bioinformatics Center

Time: Tuesday, June 30 1:00 p.m. - 2:00 p.m.
Room: T1

Desc: Many of the "magnet group members" of the Concept Web Alliance will be at ISMB this year (see This BoF will explain the goals and governance of the CWA. We anticipate several magnet group members to attend and speak if needed. The target audience is all participants in principle, but mainly the younger generation involved in massive data interoperability challenges.

Topic: Protein protein interactions and evolution

Leader: Emmanuel Levy
Affiliation: Universite de Montreal, Biochemistry Department

Time: Tuesday, 1:00 p.m - 2:00 p.m.
Room: K2

Desc: Any engineered device should certainly not contain non-functional components, for this would be a waste of energy and money. In contrast, evolutionary theory tells us that biological systems need not be optimized and may very well accumulate non-functional elements, e.g., large non-coding DNA regions or spurious DNA binding sites. I would like to propose a debate around the question: could protein-protein interaction networks have accumulated non-functional elements as well? That is, non-functional interactions - and if yes, how many?

Topic: BioHDF: Applying HDF to Next-Gen Sequence Analysis

Leader: Mark Welsh
Affiliation: Geospiza, Inc.

Time: Wednesday, July 1 1:00 p.m. - 2:00 p.m.
Room: T1

Desc: To handle next-gen sequencing's huge data volumes, Geospiza and The HDF Group are designing open-source tools around the Hierarchical Data Format. In this session, we'll review prototype BioHDF data models and tools, and experiment with data storage, analysis, and report generation. Bring a Unix-based laptop if you can.


Leader: Peter Rice
Affiliation: European Bioinformatics Institute

Time: Wednesday, 1:00 p.m - 2:00 p.m.
Room: K2

Desc: For users and developers of EMBOSS to discuss plans for the next 3 years. As a follow-on to last year's BoF, EMBOSS will extend data and metadata handling, integrate bio-ontologies, add a comprehensive set of public data sources, support next-generation sequencing, provide online training resources and develop 100 new applications.

Topic: Visualizing Biological Data (VizBi)

Leader: Nils Gehlenborg
Affiliation: European Bioinformatics Institute

Time: Wednesday, 1:00 p.m - 2:00p.m.
Room: K1

Desc: This is a BoF for everyone actively developing or using systems to visualize biological data. We will discuss plans for an upcoming EMBO Workshop on Visualizing Biological Data ( in March 2010 that provides an opportunity to bring this diverse group of researchers together for the first time.

Topic: Semantic Web-Linked Data

Leader: Eric Neumann
Affiliation: CSG W3C

Time: Wednesday July 1, 1:00 - 2:00
Room: T5

Desc: Gathering of interested folks to discuss upcoming open linked data projects, open knowledge spaces, and semantic mash-ups for bioinformatics.

Topic: Galaxy: Data Managenement and Tool Integration

Leader: Taylor/Nekrutenko

Time: Wednesday July 1, 1:00 - 2:00
Room: T2

Desc: This BoF is aimed at answering questions related to using Galaxy ( for data analysis, management, and tool integration. The topics will include data libraries, building and sharing of workflows, integration of complex tools, and configuration of compute back-ends.

Topic: Beyond microblogging

Leader: Roland Krause
Affil: MPI for Molecular Genetics

Time: Wednesday July 1, 1:00 - 2:00
Room: C8

Desc: Microblogging scientific conferences is establishing itself as a useful supplement for ISMB and others. Let's discuss where the field is going, technologically, organizationally and socially.