COPASI: biochemical network simulator. COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie’s stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams. (list of features).

References in zbMATH (referenced in 67 articles )

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  1. Heath, Allison P.; Kavraki, Lydia E.: Computational challenges in systems biology (2009)
  2. Jack, John; Păun, Andrei: Discrete modeling of biochemical signaling with memory enhancement (2009)
  3. Menolascina, Filippo; Bellomo, Domenico; Maiwald, Thomas; Bevilacqua, Vitoantonio; Ciminelli, Caterina; Paradiso, Angelo; Tommasi, Stefania: Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering (2009) ioport
  4. Petre, Ion; Mizera, Andrzej; Back, Ralph-Johan: Computational heuristics for simplifying a biological model (2009)
  5. Ciocchetta, Federica; Hillston, Jane; Kos, Martin; Tollervey, David: Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA (2008)
  6. Kell, Douglas B.; Mendes, Pedro: The markup is the model: reasoning about systems biology models in the semantic web era (2008)
  7. Hoops, Stefan; Sahle, Sven; Gauges, Ralph; Lee, Christine; Pahle, Jürgen; Simus, Natalia; Singhal, Mudita; Xu, Liang; Mendes, Pedro; Kummer, Ursula: Copasi---a complex pathway simulator (2006) ioport