ODEbase: a repository of ODE systems for systems biology.

Authors :: Lüders C
Sturm T
Radulescu O
Source :: Bioinformatics advances [Bioinform Adv] 2022 Apr 26; Vol. 2 (1), pp. vbac027. Date of Electronic Publication: 2022 Apr 26 (Print Publication: 2022).
Publication Year :: 2022
Abstract: Summary: Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to biological questions. Qualitative methods analyze dynamical input systems as formal objects, in contrast to investigating only part of the state space, as is the case with numerical simulation. However, corresponding tools and libraries have a different set of requirements for their input data than their numerical counterparts. A common format used in mathematical modeling of biological processes is Systems Biology Markup Language (SBML). We illustrate that the use of SBML data in symbolic computation requires significant pre-processing, incorporating external biological and mathematical expertise. ODEbase provides suitable input data derived from established existing biomodels, covering in particular the BioModels database.<br />Availability and Implementation: ODEbase is available free of charge at https://odebase.org.<br /> (© The Author(s) 2022. Published by Oxford University Press.)