The UCSF Resource for Biocomputing, Visualization, and Informatics Tools and Resources for Life Sciences Computing

Wednesday, April 18, 2007 - 17:30
TH 331
John "Scooter" Morris & Conrad Huang, UCSF

The field of bioinformatics (or more broadly life sciences computing) can be broken up in a number of different ways. At the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI), we tend to see four different major aspects to bioinformatics: algorithm development, data analysis and visualization, data mining and management, and computing infrastructure for life sciences. The RBVI is an NIH NCRR (National Center for Research Resources) Biomedical Technology Resource Center focused on providing tools and resources for solving a wide range of genomic and molecular recognition problems within the complex sequence->structure->function triad. Our focus as a resource is on the middle two aspects of bioinformatics: data analysis and visualization; and data mining and management. For our presentation, we will be working through an example demonstrating the use of RBVI tools and resources including the Structure-Function Linkage Database to provide curated information about enzyme function, Cytoscape and various Cytoscape plugins to explore an enzyme superfamily, and UCSF Chimera to visualize the sequence and structural relationships among some of the members of enzyme families. Through this talk, we will point out areas where we have applied our tools and technologies and areas where there are opportunities for further work.


John "Scooter" Morris is the Executive Director of the UCSF Resource for Biocomputing, Visualization, and Informatics. His research interests include Information Visualization, HCI, and more specifically, how to integrate visualizations of biological context with more detailed analysis of molecular interactions. He is a core developer for the Cytoscape open source package for visualizing biological networks, and a contributer to the SVG component of the Gecko engine which underlies Firefox. Before joining UCSF, Scooter was a Distinguished Systems Architect at Genentech, Inc., where for 19 years he helped develop the computing infrastructure for the company. Scooter was the co-chair of CHI'92, a past member of ACM Council, and is currently on the SIGCHI Conference Management Committee and the SIGCHI Executive Committee.

Conrad Huang is the Director of Software Development for the UCSF RBVI. His primary research interest is molecular visualization. He is the lead developer of UCSF Chimera and its predecessor, UCSF MidasPlus. He is also involved with informatics aspects of two projects: the Pharmacogenetics of Membrane Transporters (PMT) and the International Gene Trap Consortium (IGTC). The PMT is a project for studying the effects of genetics on pharmacological response. The IGTC is a project for identifying knock-out mouse cell lines with their deactivated genes. Conrad is also an adjunct assistant professor at UCSF and teaches an introductory programming course for graduate students in the School of Pharmacy.