GEPASI

Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and linear stability analysis. Gepasi simplifies the task of model building by assisting the user in translating the language of chemistry (reactions) to mathematics (matrices and differential equations) in a transparent way. This is combined with a set of sophisticated numerical algorithms that assure the results are obtained fast and accurate. Gepasi is intended primarily for research purposes but because of its user-friendly interface it is equally good for education.


References in zbMATH (referenced in 16 articles )

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  1. Archetti, Marco; Scheuring, István: Review: Game theory of public goods in one-shot social dilemmas without assortment (2012)
  2. Bakalis, Evangelos; Kosmas, Marios; Papamichael, Emmanouel M.: Perturbation theory in the catalytic rate constant of the Henri-Michaelis-Menten enzymatic reaction (2012)
  3. Chen, Ming; Hariharaputran, Sridhar; Hofestädt, Ralf; Kormeier, Benjamin: Petri net models for the semi-automatic construction of large scale biological networks (2011)
  4. Ribeiro, Andre S.: Stochastic and delayed stochastic models of gene expression and regulation (2010)
  5. Aleman-Meza, Boanerges; Yu, Yihai; Schüttler, Heinz-Bernd; Arnold, Jonathan; Taha, Thiab R.: KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networks (2009)
  6. Miller, David J.; Ghosh, Avijit: A fully adaptive reaction-diffusion integration scheme with applications to systems biology (2007)
  7. Demir, Ozlem; Kurnaz, Isil Aksan: An integrated model of glucose and galactose metabolism regulated by the GAL genetic switch (2006)
  8. Gilbert, David; Heiner, Monika: From Petri nets to differential equations -- an integrative approach for biochemical network analysis (2006)
  9. Wang, Kai; Nemenman, Ilya; Banerjee, Nilanjana; Margolin, Adam A.; Califano, Andrea: Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes (2006)
  10. Webb, Ken; White, Tony: Cell modeling with reusable agent-based formalisms (2006)
  11. Heiner, Monika; Koch, Ina: Petri net based model validation in systems biology (2004)
  12. Corpas, Manuel: Integrating simulation packages via systems biology mark-up language (2003)
  13. Weitzke, Elizabeth L.; Ortoleva, Peter J.: Simulating cellular dynamics through a coupled transcription, translation, metabolic model. (2003)
  14. Tomita, Masaru; Hashimoto, Kenta; Takahashi, Koichi: The E-CELL project: Towards integrative simulation of cellular processes. (2000)
  15. Tomita, Masaru; Hashimoto, Kenta; Takahashi, Koichi: The E-CELL project: Towards integrative simulation of cellular processes. (2000)
  16. Stirbet, Alexandrina D.; Strasser, Reto J.: Numerical simulation of the in vivo fluorescence in plants (1996)