ODEbase: A Repository of ODE Systems for Systems Biology
@article{Lders2022ODEbaseAR, title={ODEbase: A Repository of ODE Systems for Systems Biology}, author={Christoph L{\"u}ders and Thomas Sturm and Ovidiu Radulescu}, journal={ArXiv}, year={2022}, volume={abs/2201.08980} }
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…
References
SHOWING 1-10 OF 16 REFERENCES
Algorithmic Reduction of Biological Networks With Multiple Time Scales
- Computer Science, MathematicsMath. Comput. Sci.
- 2021
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…
BIOCHEMICAL REACTION NETWORKS : AN INVITATION FOR ALGEBRAIC
- Mathematics
- 2015
This article is a survey of the recent use of some techniques from computational algebraic geometry to address mathematical challenges in systems biology. (Bio)chemical reaction networks de ne…
Algebraic Systems Biology: A Case Study for the Wnt Pathway
- MathematicsBulletin of mathematical biology
- 2016
This case study explores multistationarity, model comparison, dynamics within regions of the state space, identifiability, and parameter estimation, from a geometric point of view using current methods from computational algebraic geometry, polyhedral geometry, and combinatorics.
Identifying the Parametric Occurrence of Multiple Steady States for some Biological Networks
- MathematicsJ. Symb. Comput.
- 2020
BioModels—15 years of sharing computational models in life science
- Biology, Computer ScienceNucleic Acids Res.
- 2020
BioModels has become the world’s largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research.
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
- Computer Science, BiologyNucleic Acids Res.
- 2006
BioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is…
Detection of Hopf bifurcations in chemical reaction networks using convex coordinates
- Mathematics, Computer ScienceJ. Comput. Phys.
- 2015
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
- Biology, Computer ScienceBioinform.
- 2003
This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems
- Computer ScienceBioinform.
- 2020
SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models is presented, showing that the major open-source Modelica and FMU simulators achieve performance comparable to state-of-the-art specialised SBML simulators.
MathSBML: a package for manipulating SBML-based biological models
- Computer ScienceBioinform.
- 2004
UNLABELLED MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models and provides a platform for manipulating and evaluating these models.