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ODEion — A SOFTWARE MODULE FOR STRUCTURAL IDENTIFICATION OF ORDINARY DIFFERENTIAL EQUATIONS

PETER GENNEMARK

Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden

Department of Mathematics, Uppsala University, Uppsala, Sweden

Corresponding author.

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and

DAG WEDELIN

Department of Computer Science and Engineering, Chalmers University of Technology, Sweden

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https://doi.org/10.1142/S0219720013500157Cited by:4 (Source: Crossref)

Abstract

In the systems biology field, algorithms for structural identification of ordinary differential equations (ODEs) have mainly focused on fixed model spaces like S-systems and/or on methods that require sufficiently good data so that derivatives can be accurately estimated. There is therefore a lack of methods and software that can handle more general models and realistic data.

We present ODEion, a software module for structural identification of ODEs. Main characteristic features of the software are:

• The model space is defined by arbitrary user-defined functions that can be nonlinear in both variables and parameters, such as for example chemical rate reactions.

• ODEion implements computationally efficient algorithms that have been shown to efficiently handle sparse and noisy data. It can run a range of realistic problems that previously required a supercomputer.

• ODEion is easy to use and provides SBML output.

We describe the mathematical problem, the ODEion system itself, and provide several examples of how the system can be used.

Available at: http://www.odeidentification.org.

Keywords:

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