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 34 articles )

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  1. Archetti, Marco; Scheuring, István: Trading public goods stabilizes interspecific mutualism (2013)
  2. Lazár, Dušan: Simulations show that a small part of variable chlorophyll (a) fluorescence originates in photosystem I and contributes to overall fluorescence rise (2013)
  3. Archetti, Marco; Scheuring, István: Review: Game theory of public goods in one-shot social dilemmas without assortment (2012)
  4. Bakalis, Evangelos; Kosmas, Marios; Papamichael, Emmanouel M.: Perturbation theory in the catalytic rate constant of the Henri-Michaelis-Menten enzymatic reaction (2012)
  5. Chen, Ming; Hariharaputran, Sridhar; Hofestädt, Ralf; Kormeier, Benjamin: Petri net models for the semi-automatic construction of large scale biological networks (2011)
  6. Hawari, Aliah Hazmah; Mohamed-Hussein, Zeti-Azura: Simulation of a Petri net-based model of the terpenoid biosynthesis pathway (2010) ioport
  7. Ribeiro, Andre S.: Stochastic and delayed stochastic models of gene expression and regulation (2010)
  8. 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)
  9. Lazár, Dušan; Jablonský, Jiří: On the approaches applied in formulation of a kinetic model of photosystem II: different approaches lead to different simulations of the chlorophyll \textitafluorescence transients (2009)
  10. Jonker, C. M.; Snoep, J. L.; Treur, J.; Westerhoff, H. V.; Wijngaards, W. C. A.: BDI-modelling of complex intracellular dynamics (2008)
  11. Kell, Douglas B.; Mendes, Pedro: The markup is the model: reasoning about systems biology models in the semantic web era (2008)
  12. Miller, David J.; Ghosh, Avijit: A fully adaptive reaction-diffusion integration scheme with applications to systems biology (2007)
  13. Demir, Ozlem; Kurnaz, Isil Aksan: An integrated model of glucose and galactose metabolism regulated by the GAL genetic switch (2006)
  14. Gilbert, David; Heiner, Monika: From Petri nets to differential equations -- an integrative approach for biochemical network analysis (2006)
  15. Hayot, F.; Jayaprakash, C.: \textitNF-(\kappaB) oscillations and cell-to-cell variability (2006)
  16. Mendoza-Cózatl, David G.; Moreno-Sánchez, Rafael: Control of glutathione and phytochelatin synthesis under cadmium stress. Pathway modeling for plants (2006)
  17. Wang, Kai; Nemenman, Ilya; Banerjee, Nilanjana; Margolin, Adam A.; Califano, Andrea: Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes (2006)
  18. Webb, Ken; White, Tony: Cell modeling with reusable agent-based formalisms (2006) ioport
  19. Lazár, Dušan; Ilík, Petr; Kruk, Jerzy; Strzałka, Kazimierz; Nauš, Jan: A theoretical study on effect of the initial redox state of cytochrome (b_559) on maximal chlorophyll fluorescence level ((F_M)): implications for photoinhibition of photosystem II (2005)
  20. Marée, Athanasius F. M.; Komba, Mitsuhiro; Dyck, Cheryl; Łabęcki, Marek; Finegood, Diane T.; Edelstein-Keshet, Leah: Quantifying macrophage defects in type 1 diabetes (2005)

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