COPASI - A COmplex PAthway SImulator

Stefan Hoops, Ralph Gauges, Christine Lee, Jürgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Motivation: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods. Results: Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features. We discuss numerical issues with these features; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation. © 2006 Oxford University Press.
    Original languageEnglish
    Pages (from-to)3067-3074
    Number of pages7
    JournalBioinformatics
    Volume22
    Issue number24
    DOIs
    Publication statusPublished - 15 Dec 2006

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