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ODEbase: A Repository of ODE Systems for Systems Biology


Sturm,  Thomas       
Automation of Logic, MPI for Informatics, Max Planck Society;

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Lüders, C., Sturm, T., & Radulescu, O. (2022). ODEbase: A Repository of ODE Systems for Systems Biology. Retrieved from https://arxiv.org/abs/2201.08980.

Cite as: https://hdl.handle.net/21.11116/0000-000B-654F-C
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,
symbolic computation 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 SBML. We illustrate that the
use of SBML data in symbolic computation requires significant pre-processing,
incorporating external biological and mathematical expertise. ODEbase provides
high quality symbolic computation input data derived from established existing
biomodels, covering in particular the BioModels database.