We (T. Sturm, O.Radulescu, and me) have written a paper on ODEbase, A Repository of ODE Systems for Systems Biology. It’s available on arXiv. Furthermore, we have redesigned and updated ODEbase and got it a new domain name: odebase.org.
If you use our data in a publication, please cite us:
Christoph Lüders, Thomas Sturm, Ovidiu Radulescu. ODEbase: A Repository of ODE Systems for Systems Biology, CoRR:abs/2201.08980, 2022 [bibtex]
Abstract: We present a symbolic algorithmic approach that allows to compute invariant manifolds and corresponding reduced systems for differential equations modeling biological networks which comprise chemical reaction networks for cellular biochemistry, and compartmental models for pharmacology, epidemiology and ecology. Multiple time scales of a given network are obtained by scaling, based on tropical geometry. Our reduction is mathematically justified within a singular perturbation setting using a recent result by Cardin and Teixeira. The existence of invariant manifolds is subject to hyperbolicity conditions, which we test algorithmically using Hurwitz criteria. We finally obtain a sequence of nested invariant manifolds and respective reduced systems on those manifolds. Our theoretical results are generally accompanied by rigorous algorithmic descriptions suitable for direct implementation based on existing off-the-shelf software systems, specifically symbolic computation libraries and Satisfiability Modulo Theories solvers. We present computational examples taken from the well-known BioModels database using our own prototypical implementations.
(with Niclas Kruff, Ovidiu Radulescu, Thomas Sturm and Sebastian Walcher)
The paper has been submitted to a journal and a preprint is available on arXiv.