Sunday, July 20

Cytoscape User Group

Leader: Gary Bader

Sunday, July 20 - 12:45 p.m. - 2:00 p.m.

Room: 701B

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

Bioinformatics Core Facilities - Next Gen Sequencing

Leader: Fran Lewitter

Sunday, July 20 - 12:45 p.m. - 2:00 p.m.

Room: 718A

Description: This session is geared towards support issues related to next gen sequencing and will include short talks on how to set up the infrastructure, LIMs systems for handling the data, and software tools for working with the data. Ample time will be allotted for discussion.

Personal Genome Interpretation and the Genome Commons

Leader: Steven E. Brenner

Sunday, July 20 - 12:45 p.m. - 2:00 p.m.

Room: 718B

Description: This BoF will discuss public efforts to assemble genotype-phenotype relationship data, and to use this information to interpret individuals' genomes. The current status of the Genome Commons and the Genome Commons Navigator will be presented.

Monday, July 21

Pathway Tools Software

Leader: Peter Karp

Monday, July 21 12:45 p.m. 2:00 p.m.

Room: 718A

Description: Discussion by users and developers of the Pathway Tools software developed at SRI International. Topics are likely to include recent developments in the software, users suggestions, user experiences, new databases and software add-ons developed by users.

EMBOSS Users and Developers

Leader: Peter Rice

Room 701A

Monday, July 21 1:00 p.m. - 2:15 p.m.

Monday, July 21

Sharing Biological Pathway Information (e.g. BioPAX)

Leader: Gary Bader

Monday, July 21 - 12:45 p.m. - 2:00 p.m.

Room: 718B

Description: This BOF is aimed at pathway data providers and users for discussion about sharing biological pathway information. Discussion will include the BioPAX (www.biopax.org) pathway exchange format, pathway data registries and author data entry systems.

Tuesday, July 22

Effective Implementation of Software Sharing

Leader: David States

Tuesday, July 22 - 1:00 p.m.- 2:15 p.m.

Room: 801

Description: This session will explore options for Data and Software Sharing and is open to all to provide feedback to ISCB.

Running a Bioinformatics Core Facility

Leader: Fran Lewitter

Tuesday, July 22 - 1:00 p.m.- 2:15 p.m.

Room: 718A

Description: We have met annually since 2002 and have participated in conference calls since ISMB/ECCB 2007. Today's meeting will address best practices for running a bioinformatics core facility and will include short talks from people from different types of facilities - universities (public and private), research institutes, and industry. Ample time will be allotted for discussion.

Topic: Science blogging and Web 2.0
Leader: Shirley Wu, Stanford University
Day: Tuesday, July 22 - 12:45 p.m. - 2:00 p.m
Room: 718B
Description: The web has changed the way people communicate, interact, and operate. In some ways, science has embraced the web, but in many ways it has yet to realize the full potential the web offers. This session is for anyone who participates at the intersection of science and the web - bloggers, twitterers, friends feeding the ISMB 2008 room, science social networkers, open notebook science folks, wiki-users, etc. People interested in learning more about these tools and the potential of "science 2.0" and "open science" are also welcome.