Walther GR, Hartley M, Mincheva M. GraTeLPy: graph-theoretic linear stability analysis.
BMC SYSTEMS BIOLOGY 2014;
8:22. [PMID:
24572152 PMCID:
PMC4016541 DOI:
10.1186/1752-0509-8-22]
[Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 02/14/2014] [Indexed: 11/10/2022]
Abstract
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.
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