Building Mathematical Models of Biological Systems with modelbase

Oliver Ebenhöh; Marvin van Aalst; Nima P. Saadat; Tim Nies; Anna Matuszyńska

doi:10.5334/jors.236

Building Mathematical Models of Biological Systems with modelbase

Journal of Open Research Software

Volume 6 (2018): Issue 1

By: Oliver Ebenhöh , Marvin van Aalst, Nima P. Saadat, Tim Nies and Anna Matuszyńska

Open Access

|Nov 2018

Abstract

The modelbase package is a free expandable Python package for building and analysing dynamic mathematical models of biological systems. Originally it was designed for the simulation of metabolic systems, but it can be used for virtually any deterministic chemical processes. modelbase provides easy construction methods to define reactions and their rates. Based on the rates and stoichiometries, the system of differential equations is assembled automatically. modelbase minimises the constraints imposed on the user, allowing for easy and dynamic access to all variables, including derived ones, in a convenient manner. A simple incorporation of algebraic equations is, for example, convenient to study systems with rapid equilibrium or quasi steady-state approximations. Moreover, modelbase provides construction methods that automatically build all isotope-specific versions of a particular reaction, making it a convenient tool to analyse non-steady state isotope-labelling experiments.

Funding statement: This work was financially supported by the Deutsche Forschungsgemeinschaft “Cluster of Excellence on Plant Sciences” CEPLAS (EXC 1028).

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Articles in this issue

DOI: https://doi.org/10.5334/jors.236 | Journal eISSN: 2049-9647

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Language: English

Submitted on: Jun 27, 2018

Accepted on: Oct 16, 2018

Published on: Nov 16, 2018

Published by: Ubiquity Press

In partnership with: Paradigm Publishing Services

Publication frequency: 1 issue per year

Keywords:

isotope labelling,

mathematical modelling,

metabolic networks,

Python,

ODEs,

© 2018 Oliver Ebenhöh, Marvin van Aalst, Nima P. Saadat, Tim Nies, Anna Matuszyńska, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.

Volume 6 (2018): Issue 1