BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. BioModels Database (, part of the international initiative, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.

References in zbMATH (referenced in 32 articles )

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  1. Kruff, Niclas; Lüders, Christoph; Radulescu, Ovidiu; Sturm, Thomas; Walcher, Sebastian: Algorithmic reduction of biological networks with multiple time scales (2021)
  2. Hinze, Thomas: Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis (2020)
  3. Stalidzans, Egils; Landmane, Katrina; Sulins, Jurijs; Sahle, Sven: Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs (2019)
  4. Suderman, Ryan; Mitra, Eshan D.; Lin, Yen Ting; Erickson, Keesha E.; Feng, Song; Hlavacek, William S.: Generalizing Gillespie’s direct method to enable network-free simulations (2019)
  5. Bradford, Russell; Davenport, James H.; England, Matthew; Errami, Hassan; Gerdt, Vladimir; Grigoriev, Dima; Hoyt, Charles; Košta, Marek; Radulescu, Ovidiu; Sturm, Thomas; Weber, Andreas: A case study on the parametric occurrence of multiple steady states (2017)
  6. England, Matthew; Errami, Hassan; Grigoriev, Dima; Radulescu, Ovidiu; Sturm, Thomas; Weber, Andreas: Symbolic versus numerical computation and visualization of parameter regions for multistationarity of biological networks (2017)
  7. Johnston, Matthew D.: A computational approach to extinction events in chemical reaction networks with discrete state spaces (2017)
  8. Shafaghati, Leila; Razaghi-Moghadam, Zahra; Mohammadnejad, Javad: A systems biology approach to understanding alcoholic liver disease molecular mechanism: the development of static and dynamic models (2017)
  9. Nabli, Faten; Martinez, Thierry; Fages, François; Soliman, Sylvain: On enumerating minimal siphons in Petri nets using CLP and SAT solvers: theoretical and practical complexity (2016)
  10. Fages, François; Gay, Steven; Soliman, Sylvain: Inferring reaction systems from ordinary differential equations (2015)
  11. Heinle, Albert; Levandovskyy, Viktor: The \textscSDEvalbenchmarking toolkit (2015)
  12. Samal, Satya Swarup; Grigoriev, Dima; Fröhlich, Holger; Radulescu, Ovidiu: Analysis of reaction network systems using tropical geometry (2015)
  13. Samal, Satya Swarup; Grigoriev, Dima; Fröhlich, Holger; Weber, Andreas; Radulescu, Ovidiu: A geometric method for model reduction of biochemical networks with polynomial rate functions (2015)
  14. Paulevé, Loïc; Craciun, Gheorghe; Koeppl, Heinz: Dynamical properties of discrete reaction networks (2014)
  15. De Matteis, Giovanni; Graudenzi, Alex; Antoniotti, Marco: A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development (2013)
  16. Kourdis, Panayotis D.; Goussis, Dimitris A.: Glycolysis in saccharomyces cerevisiae: algorithmic exploration of robustness and origin of oscillations (2013)
  17. Campbell, David; Steele, Russell J.: Smooth functional tempering for nonlinear differential equation models (2012)
  18. Rybiński, Mikołaj; Gambin, Anna: Model-based selection of the robust JAK-STAT activation mechanism (2012)
  19. Samal, Satya Swarup; Errami, Hassan; Weber, Andreas: PoCaB: a software infrastructure to explore algebraic methods for bio-chemical reaction networks (2012)
  20. Liu, Bing; Hsu, David; Thiagarajan, P. S.: Probabilistic approximations of ODEs based bio-pathway dynamics (2011)

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