Blogging the biotechnology revolution

Systems Biology is changing the way biology is done. Is it a fad or is it effective? This blog tracks current happenings and helps you stay on top of the field. You can find a list of relevant papers at systems biology paper watch Have you heard a talk or read a paper in bioinformatics / systems biology you would like to tell other people about? Email: and get the word out!

Friday, December 02, 2005

David Dill, SRI International

"The Pathalyzer: a tool for visualization and analysis of signal transduction pathways"

Petri Nets as a method for monitoring signal transduction pathways. This group developed software to find active pathways in a network of reactions. Encoded in Maude language layed out using Dot. A query (can gene x,y,z be activated), is known as the reachability problem, and can be solved uning 'stubborn sets' otherwise would be an NP hard problem. He mentions that Petri nets are used alot in biology. I havent seen anything like it, does anyone know of any papers using Petri nets?


Blogger ploriaux said...

This is cool -- what's with the title? I did some futzing with petri nets once. Earliest papers were by a guy named Reddy (early 90's?) and were applied to metabolism. There have been several more since, but I don't know if that qualifies as "a lot" of application. I gather they have a lot of nice theory behind them, so there's interest in applying them to bio problems. Here's a 30,000 ft review:

4:48 PM  

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