For our second quarter seminar, I am pleased to announce that Dr. Peter Karp Director of the Bioinformatics Research Group at SRI International will present "Databases and Algorithms for Pathway Bioinformatics". Since this is a quarterly seminar, Dr. Karp's talk will take up most of the allotted time and there will be no lightning talks.

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Directions:

The seminar will be held in the International Building at
SRI International.

Driving:
o SRI International is at 333 Ravenswood Ave in Menlo Park,
between Middlefield Rd and El Camino. 101 exit: Willow Road.

o There are two entrances to SRI on Ravenswood Ave. When coming to
the International Building, please use the eastern entrance on
Ravenswood, closer to Middlefield than to Laurel Ave. It is the main
SRI entrance. Park in the right side parking lot (west side). After parking,
walk east (toward Middlefield), up the stairs, and onto the brick patio at
the center of the International Building. The entry to the seminar will be
directly off the patio.

Caltrain:
o Take Caltrain to the Menlo Park stop. Walk south along
the tracks to the first street (Ravenswood Ave), and turn east (left).
Walk ~7 minutes along Ravenswood Ave to the above driveway entry
toward Building A. Walk east (toward Middlefield), up
the stairs, and onto the brick patio at the center of the International
Building. The entry to the seminar will be directly off the patio.

General directions to SRI:
http://www.sri.com/contact/maps.html

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Agenda:
7:00-7:30 - Networking
7:30-8:30 - Dr. Karp Presents "Databases and Algorithms for Pathway Bioinformatics"
8:30-9:00 - Questions and follow-up discussions

Speaker Info:
Peter D. Karp, Ph.D.
Director, Bioinformatics Research Group
SRI International

Abstract:
Comprehensive knowledge of metabolic pathways is required in a variety of applications including biofuels and drug discovery. A family of hundreds of Pathway/Genome Databases (PGDBs) now exists for organisms with sequenced genomes. These databases share a common schema, facilitating interoperation and comparative analysis. Many are highly curated, including PGDBs for E. coli, yeast, mouse, and Arabidopsis. The BioCyc PGDB collection developed by SRI contains PGDBs for more than 500 organisms. Common to these PGDBs is their derivation from the MetaCyc PGDB. MetaCyc contains 1,400 experimentally elucidated metabolic pathways found in 1,800 organisms. The MetaCyc data were curated from 21,000 publications.

Also common to these PGDBs is the Pathway Tools Software, which contains a large suite of algorithms for manipulating biological networks and genome data. Pathway Tools includes inference modules for inferring the metabolic pathways of an organism, and for predicting which genes fill missing reactions in the predicted pathways. It includes extensive visualization tools for individual metabolic pathways, for complete metabolic networks, and for complete regulatory networks. These visualization tools can also be used for analysis of omics datasets. Pathway Tools also contains algorithms for systems biology analyses of metabolic networks, including detection of dead-end metabolites and reachability analysis.

Blogging is allowed at this event. Please see the BayBIFX blog policy for more details.

Thanks

Hope to see you all there!

• 
  Doug Hershberger

  Thanks to all who attended and especially to Peter Karp, our esteemed speaker. The setting was beautiful! With a gorgeous patio that made me want to bring my barbeque. Peter delivered an excellent talk and even though I have been following MetaCyc since about 1997 I continue to be amazed at the richness of the pathway tools interface and the breadth and depth of the database. The informal atmosphere led to an illuminating discussion of the philosophy behind MetaCyc. Truly an outstanding talk.

  Posted May 13, 2010 at 8:34 AM