GraTeLPy: graph-theoretic linear stability analysis

BMC Systems Biology

Maya Mincheva²  Matthew Hartley¹  Georg R Walther¹ 

[1] Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK;Department of Mathematical Sciences, Northern Illinois University, DeKalb, IL 60115, USA

关键词: Parameter-free model discrimination;    Oscillations;    Turing instability;    Multistability;    Bipartite digraph;    Biochemical mechanism;   

Others  :  1141339
DOI  :  10.1186/1752-0509-8-22

 received in 2013-09-09, accepted in 2014-02-14,  发布年份 2014

【 摘 要 】

Background

A biochemical mechanism with mass action kinetics can be represented as a directed bipartite graph (bipartite digraph), and modeled by a system of differential equations. If the differential equations (DE) model can give rise to some instability such as multistability or Turing instability, then the bipartite digraph contains a structure referred to as a critical fragment. In some cases the existence of a critical fragment indicates that the DE model can display oscillations for some parameter values. We have implemented a graph-theoretic method that identifies the critical fragments of the bipartite digraph of a biochemical mechanism.

Results

GraTeLPy lists all critical fragments of the bipartite digraph of a given biochemical mechanism, thus enabling a preliminary analysis on the potential of a biochemical mechanism for some instability based on its topological structure. The correctness of the implementation is supported by multiple examples. The code is implemented in Python, relies on open software, and is available under the GNU General Public License.

Conclusions

GraTeLPy can be used by researchers to test large biochemical mechanisms with mass action kinetics for their capacity for multistability, oscillations and Turing instability.

【 授权许可】

   
2014 Walther et al.; licensee BioMed Central Ltd.

【 图 表 】

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