ODEbase: A Repository of ODE Systems for Systems Biology

TL;DR

ODEbase offers a curated collection of biological ODE systems derived from established models, facilitating symbolic computation in systems biology and addressing data format challenges.

Contribution

It provides a repository of high-quality ODE systems from existing biomodels, streamlining symbolic computation workflows in systems biology.

Findings

Enables qualitative analysis of biological systems using symbolic methods.

Addresses data pre-processing challenges for SBML in symbolic computation.

Supports research in systems biology with standardized ODE models.

Abstract

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.