Symbolic versus numerical computation and visualization of parameter regions for multistationarity of biological networks

DOI10.1007/978-3-319-66320-3_8MaRDI QIDQ1701474zbMATH OpenOpenAlexWikidataFDO

Authors Matthew England, Hassan Errami, Ovidiu Radulescu, Thomas Sturm, Andreas Weber, Dima Grigoriev

Publication date 23 February 2018

Full work available at URL https://arxiv.org/abs/1706.08794

Mathematics Subject Classification ID

Symbolic computation and algebraic computation (68W30) Systems biology, networks (92C42)

Abstract: We investigate models of the mitogenactivated protein kinases (MAPK) network, with the aim of determining where in parameter space there exist multiple positive steady states. We build on recent progress which combines various symbolic computation methods for mixed systems of equalities and inequalities. We demonstrate that those techniques benefit tremendously from a newly implemented graph theoretical symbolic preprocessing method. We compare computation times and quality of results of numerical continuation methods with our symbolic approach before and after the application of our preprocessing.

Recommendations

• Identifying the parametric occurrence of multiple steady states for some biological networks
• A case study on the parametric occurrence of multiple steady states
• Graph-theoretic analysis of multistationarity using degree theory
• Symbolic analysis of multiple steady states in a MAPK chemical reaction network
• Multistationarity in the activation of a MAPK: parametrizing the relevant region in parameter space

Cited in

(13)

• Parametric toricity of steady state varieties of reaction networks
• Symbolic analysis of multiple steady states in a MAPK chemical reaction network
• Using machine learning to improve cylindrical algebraic decomposition
• Multistationarity in the activation of a MAPK: parametrizing the relevant region in parameter space
• Testing binomiality of chemical reaction networks using comprehensive Gröbner systems
• Cylindrical algebraic decomposition with equational constraints
• Symbolic computations of the equilibrium orientations of a system of two connected bodies moving on a circular orbit around the Earth
• A case study on the parametric occurrence of multiple steady states
• Algorithmic reduction of biological networks with multiple time scales
• Identifying the parametric occurrence of multiple steady states for some biological networks
• Computer algebra methods for searching the stationary motions of the connected bodies system moving in gravitational field
• MAPK's networks and their capacity for multistationarity due to toric steady states
• Exotic bifurcations in three connected populations with Allee effect

Describes a project that uses

Uses Software

• BioModels
• Bertini
• REDLOG

This page was built for publication: Symbolic versus numerical computation and visualization of parameter regions for multistationarity of biological networks

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q1701474)