Conservation analysis in biochemical networks: computational issues for software writers.
Large scale genomic studies are generating significant amounts of data on the structure of cellular networks. This is in contrast to kinetic data, which is frequently absent, unreliable or fragmentary. There is, therefore, a desire by many in the community to investigate the potential rewards of analyzing the more readily available topological data. This brief review is concerned with a particular property of biological networks, namely structural conservations (e.g. moiety conserved cycles). There has been much discussion in the literature on these cycles but a review on the computational issues related to conserved cycles has been missing. This review is concerned with the detection and characterization of conservation relations in arbitrary networks and related issues, which impinge on simulation simulation software writers. This review will not address flux balance constraints or small-world type analyses in any significant detail.
Sauro
Herbert M
HM
Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA. hsauro@kgi.edu
Ingalls
Brian
B
D001669:Biochemical Phenomena; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008432:Mathematical Computing; D012984:Software