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.
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.
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.
Description: We have met annually since 2002 and have participated in conference calls since ISMB2007. 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.
Description: This session will explore options for Data and Software Sharing and is open to all to provide feedback to ISCB.
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.
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.
Description: For EMBOSS (European Molecular Biology Open Software Suite) experts and newcomers to meet up and to discuss the latest release and future directions (new applications, extended features, next generation sequencing and other challenges)
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 that Web 2.0 offers. This session is for anyone who participates at the intersection of science and the Internet - 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.
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.
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Description: 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 (http://www.vizbi.org) in March 2010 that provides an opportunity to bring this diverse group of researchers together for the first time.
Description: 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?
Description: 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.
Description: 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.
Description: Many of the 'magnet group members' of the Concept Web Alliance will be at ISMB this year (see http://conceptweblog.wordpress.com/magnet-group/)
We wish to host a BoF meeting to 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.
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.
Description: Gathering of interested folks to discuss upcoming open linked data projects, open knowledge spaces, and semantic mash-ups for bioinformatics.
Description: Official meeting of SC/RSG Leaders
Description: This BoF is aimed at answering questions related to using Galaxy (http://galaxyproject.org) 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.
Description: (Wednesday preferred)
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.
