%0 Journal Article
%T Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem
%A Sylvain Soliman
%J Algorithms for Molecular Biology
%D 2012
%I BioMed Central
%R 10.1186/1748-7188-7-15
%X In our case, this analysis brings both qualitative and quantitative information on the models, in the form of conservation laws, consistency checking, etc. thanks to finite domain constraint programming. It is noticeable that some of the most recent optimizations of standard invariant computation techniques in Petri nets correspond to well-known techniques in constraint solving, like symmetry-breaking. Moreover, we show that the simple and natural encoding proposed is not only efficient but also flexible enough to encompass sub/sur-invariants, siphons/traps, etc., i.e., other Petri net structural properties that lead to supplementary insight on the dynamics of the biochemical system under study.A simple implementation based on GNU-Prolog's finite domain solver, and including symmetry detection and breaking, was incorporated into the BIOCHAM modelling environment and in the independent tool Nicotine. Some illustrative examples and benchmarks are provided.Reaction models like those of reactome.org, KEGG pathway database [1] or biomodels.net represent a growing part of Systems Biology especially for metabolic or signalling pathways, cell-cycle and more generally post-genomic regulation systems. They build on established standards like BioPAX or SBML [2] to facilitate the exchange and comparison of models and benefit from a large number of available tools, especially ODE integration based simulators.The use of Petri nets to represent those models, taking into account the difference between compounds and reactions in the graph, and make available various kinds of analyses is quite old [3], however it remains somehow focused towards mostly qualitative and structural properties. Some have been used for module decomposition, like (I/O) T-invariants [4,5], related to dynamical notions of elementary flux modes [6]. However, there is, to our knowledge, very little use of P-invariant computation, which provides both qualitative information about some notion of module related to
%U http://www.almob.org/content/7/1/15