Efficiently and Effectively Recognizing Toricity of Steady State Varieties

Journal article

Recently, symbolic computation and computer algebra systems have beensuccessfully applied in systems biology, especially in chemical reactionnetwork theory. One advantage of symbolic computation is its potential forqualitative answers to biological questions. Qualitative methods analyzedynamical input systems as formal objects, in contrast to investigating onlypart of the state space, as is the case with numerical simulation. However,symbolic computation tools and libraries have a different set of requirementsfor their input data than their numerical counterparts. A common format used inmathematical modeling of biological processes is SBML. We illustrate that theuse of SBML data in symbolic computation requires significant pre-processing,incorporating external biological and mathematical expertise. ODEbase provideshigh quality symbolic computation input data derived from established existingbiomodels, covering in particular the BioModels database.

Authors: Grigoriev, D; Iosif, A; Rahkooy, H; Sturm, T; Weber, A

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Springer
• Journal: Mathematics in Computer Science
• Volume: 15
• Issue: 2
• Pages: 199-232
• Publication date: 2020-07-21
• DOI: 10.1007/s11786-020-00479-9
• EISSN: 1661-8289
• ISSN: 1661-8270
• Language: English