One view of bioinformatics is that the field strives to define both representations of key biological datatypes, and algorithms and inference procedures that operate on those datatypes. Some of the key datatypes in bioinformatics thus far have been sequences and structures. Biological pathways and reactions are two other key datatypes for bioinformatics.
This tutorial addresses computational problems in representing and computing with metabolic pathways. The presentation will cover the following topics: (1) Database aspects -- ontologies for representing metabolic knowledge; a summary of existing metabolic databases; user interfaces for these databases. (2) Biological issues -- physico-chemical properties of enzymes and their substrates in biological systems; pathway analysis of whole genomes; common patterns across species, and species differences. (3) Algorithmic problems -- enumeration of flux routes; tracing radioactive atoms; estimating the feasibility of pathways. Finally, future directions towards representing integral cellular processes are discussed.
This document is an outline of the tutorial, reflecting the basic structure of the course. The material is aimed towards computer scientists interested in both representation and user interfaces, and biologists interested in the global study of cellular processes and the impact of whole genome data in their research.
Additional background material provided as part of this tutorial includes: