HOME	MEBI 534 , Autumn 2008 Biology and Informatics
	Biochemistry Informatics: Pathway databases  Assignment A. Read the following articles Karp 2001, Pathway databases: a case study in computational symbolic theories Luciano2005 BioPaX B. Skim this article Cortassa 2003 - includes a mathematical model of the Krebs Cycle. No need to read this carefully, just enough to answer question 1 below. C. Optional Reading Schaefer 2004, Pathway databases, an abstract review of different types of pathway databases, together with a listing of several of these as of 2004. JiangPathwayIntegration2005 An architecture for integrating multiple pathway databases, using the BioPax ontology for semantic interoperability CookChalkboard2007 Example by Cook and Gennari that is similar to Karp's work. D. Provide written answers to the following questions, to be turned in prior to the Wed class, as per these instructions. These questions are based the readings in A and B. 1. Both the Karp and Cortessa papers discuss simulation of biochemical pathways. Describe the differences in the two approaches. 2. What is EcoCyc? 3. What is BioPAX and why is it needed? 4. Go to the EcoCyc website at ecocyc.org, search for the TCA cycle, and provide two screenshots: one showing a graphical view of the pathway and the second showing a view in BioPAX format (just a snippet to show you've found it). 5. What is the point of Ecycyc providing both views in question 4?
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