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Automatic Analysis of Computation in BioChemical Reactions

<12> This paper automates detection of hierarchical structure in finitary dynamical systems, a major problem in systems biology. For the first time it is possible to extract hierarchical coordinate systems and detect reversible subsystems automatically, thus achieving within kiloseconds what previously took the few humans who could do it weeks of laborious computation. This is exemplified by applications to Krebs citric acid cycle models. UH consequently received €80K from FP6 OPAALS project to augment the tools with full Krohn-Rhodes decomposition, now available and downloaded hundreds of times worldwide as the open-source SgpDec package for the GAP computer algebra system.