SoftwareApplication
name: COPASI
description: COPASI is an open source software for simulation and analysis of biochemical networks and their dynamics. It provides simulations using ODEs, SDEs, or Gillespie's stochastic simulation algorithm, with optional discrete events. COPASI provides several analyses, optimization, and parameter estimation.
description: - run simulations of chemical networks based on differential equations - run simulations of chemical networks based on stochastic processes - easily switch between differential equations and stochastic processes within a single model - calculate steady states and determine their stability - estimate model parameter values using experimental data - optimize arbitrary model variables using a menu of many optimization algorithms - perform sensitivity analysis of model variables - import/export models in the standard SBML format, or through OMEX files COPASI is one of the the most widely used software for simulations of bio/chemical reaction networks. COPASI is widely used to model metabolic and signaling pathways, pharmacology, genetics, and many areas of chemistry, with special emphasis on microkinetic modeling. Users define models in COPASI by focusing on the biochemistry components (species, reactions, kinetic rate laws, etc.) and the software automatically builds the corresponding mathematical equations. This feature makes it quickly accessible to biologists and chemists as model-building strongly relies on their domain knowledge, and minimizes the mathematical and programming skills required to a minimum. COPASI allows many different types of time-dependent models (i.e. models where diffusion is not explicit), using several formalisms: ODEs, stochastic differential equations (SDEs), stochastic simulation with the Gillespie algorithm, and hybrid models where some variables are modeled with ODEs and others with the Gillespie approach. Additionally all the models can include discrete events, making such models hybrid continuous-discrete. The most widely used functionality of COPASI is parameter estimation, where one fits parameter values of a model to experimental data. Users are able to associate an arbitrary number of experiments with the model variables and COPASI automatically builds a least-squares objective function for minimization which is carried out by nonl…
code repository: https://github.com/copasi/COPASI
author: https://orcid.org/0000-0001-6507-9168
author: https://orcid.org/0000-0001-8503-8371
author: https://orcid.org/0000-0001-5553-4702
author: https://orcid.org/0000-0002-5458-7404
author: Person
  given name: Ursula
  family name: Kummer
  name: Ursula Kummer
  role name: Founder
  affiliation: Organization
    name: Heidelberg University
author: https://orcid.org/0000-0002-4690-9944
author: https://orcid.org/0000-0002-7637-7547
author: Person
  given name: Ralph
  family name: Gauges
  name: Ralph Gauges
  role name: developer
  affiliation: Organization
    name: University of Applied Sciences Albstadt-Sigmaringen
author: https://orcid.org/0000-0002-4489-5876
author: https://orcid.org/0000-0002-0212-3958
author: https://orcid.org/0000-0002-8765-2604
author: Person
  given name: Aejaaz
  family name: Kamal
  name: Aejaaz Kamal
  role name: developer
  affiliation: Organization
    name: Virginia Tech
keywords: optimization
keywords: simulation modelling
keywords: Reaction networks
keywords: Parameter estimation
keywords: Simulation
keywords: Dynamics
programming language: Batchfile
programming language: C
programming language: C#
programming language: C++
programming language: CMake
programming language: CSS
programming language: Fortran
programming language: HTML
programming language: Inno Setup
programming language: Java
programming language: Makefile
programming language: Perl
programming language: Python
programming language: R
programming language: Redcode
programming language: Rich Text Format
programming language: SWIG
programming language: Shell
programming language: XSLT
programming language: sed
license:
  creative work: creativeWork
    name: Artistic-2.0
reference publication: btl485
reference publication: j.jbiotec.2017.06.1200
reference publication: 978-1-59745-525-1 2

https://orcid.org/0000-0001-6507-9168
type: Person
given name: Pedro
family name: Mendes
name: Pedro Mendes
role name: Founder
affiliation: Organization
  name: University of Connecticut School of Medicine

https://orcid.org/0000-0001-8503-8371
type: Person
given name: Stefan
family name: Hoops
name: Stefan Hoops
role name: Architect and developer
affiliation: Organization
  name: University of Virginia

https://orcid.org/0000-0001-5553-4702
type: Person
given name: Frank
family name: Bergmann
name: Frank Bergmann
role name: Architect and developer
affiliation: Organization
  name: Ruprecht Karls Universität Heidelberg

https://orcid.org/0000-0002-5458-7404
type: Person
given name: Sven
family name: Sahle
name: Sven Sahle
role name: Architect and developer
affiliation: Organization
  name: Heidelberg University

https://orcid.org/0000-0002-4690-9944
type: Person
given name: Brian
family name: Klahn
name: Brian Klahn
role name: developer
affiliation: Organization
  name: University of Virginia

https://orcid.org/0000-0002-7637-7547
type: Person
given name: Jürgen
family name: Pahle
name: Jürgen Pahle
role name: developer
affiliation: Organization
  name: Ruprecht Karls Universität Heidelberg

https://orcid.org/0000-0002-4489-5876
type: Person
given name: Joseph Olufemi
family name: Dada
name: Joseph Olufemi Dada
role name: developer
affiliation: Organization
  name: Afe Babalola University

https://orcid.org/0000-0002-0212-3958
type: Person
given name: Abhishekh
family name: Gupta
name: Abhishekh Gupta
role name: developer

https://orcid.org/0000-0002-8765-2604
type: Person
given name: Hasan
family name: Baig
name: Hasan Baig
role name: developer
affiliation: Organization
  name: University of Connecticut Health Center

btl485
type: ScholarlyArticle
name: COPASI—a COmplex PAthway SImulator
pagination: 3067-3074
url: https://doi.org/10.1093%2Fbioinformatics%2Fbtl485

j.jbiotec.2017.06.1200
type: ScholarlyArticle
name: COPASI and its applications in biotechnology
pagination: 215-220
url: https://doi.org/10.1016%2Fj.jbiotec.2017.06.1200

978-1-59745-525-1 2
type: ScholarlyArticle
name: Computational Modeling of Biochemical Networks Using COPASI
pagination: 17-59
url: https://doi.org/10.1007%2F978-1-59745-525-1_2