Birds of a Feather (BoF) Schedule

Topic: Visualizing Biological Data

Leader: Seán O'Donoghue
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Affiliation: European Molecular Biology Laboratory

Time: Monday, July 12, 6:00 p.m. - 7:00 p.m.
Room: 304

Description:
 Visualization is one of the primary ways that biologists interact with their data, however today’s systems are inadequate for many high-throughput data sets. We invite those interested to a discussion of recent and ongoing community efforts aimed at improving integration, effectiveness, and usability of visualization in biology (e.g.,http://vizbi.orghttp://www.nature.com/nmeth/journal/v7/n3s).


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Topic: Scaling up Biomedical Knowledge Bases

Leader: Kevin Livingston
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Affiliation: Center for Computational Pharmacology, University of Colorado Denver

Time: Monday, July 12, 6:00 p.m. - 7:00 p.m.
Room: 306

Extensive semantic resources and new standards and technologies have transformed biomedical knowledge-bases, but challenges remain in building, using, sharing, and maintaining them.  This BoF will discuss technologies, scaling issues, and potential community-wide collaborations.

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Topic: Network visualization and analysis using Cytoscape

Leader: Gary Bader
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Affiliation: University of Toronto

Time: Tuesday, July 13, 1:00 p.m. - 2:00 p.m.
Room: 302

Description:
Network visualization and analysis is frequently used in computational biology and biology. Cytoscape is one software system that handles this task. The Cytoscape team is interested in connecting with users and developers of network visualization and analysis software to get feedback on Cytoscape and to discuss challenges and opportunities in this area.
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Topic: A practical approach to web semantics using Reflect

Leader: Seán O'Donoghue
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Affiliation: European Molecular Biology Laboratory

Time: Tuesday, July 13, 1:00 p.m. - 2:00 p.m.
Room: 304

Description:
Semantic tagging of biochemical entities in webpages helps life scientists deal with the large number of protein and chemicals names and synonyms. Released in 2009, Reflect is used by 40,000+ life scientists to tag biochemical entities in webpages. The Reflect team is interested to meet users and content providers to get feedback and discuss opportunities.


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Topic: BioHDF

Leader: Dana Robinson
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Affiliation: The HDF Group

Time: Tuesday, July 13, 1:00 p.m. - 2:00 p.m.
Room: 306

Description:
This BoF discussion will be about using BioHDF to store next-generation sequencing (NGS) data with a special focus SAM/BAM interoperability.

 

Topic: BioPAX

Leader: Nadia Anwar
Email:
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Affiliation: Memorial Sloan Kettering Cancer Center

Time: Tuesday, July 13, 1:00 p.m. - 2:00 p.m.
Room: 312


Desc: The BioPAX ontology (www.biopax.org) is a standard language for formally representing biological pathways and is available to the biological community to enable exchange and integration of pathway data. To get involved, or learn more about BioPAX please join us for an informal tutorial/round table session.