COPASI 4.6 Build 32

A tool for simulation and modeling of biochemical networks.
COPASI is a tool for simulation and modeling of biochemical networks. The software package has a GUI that lets users define biochemical network models by entering chemical reactions and kinetic equations. A powerful simulation engine can then perform simulations of the dynamics of the networks and carry out many different computational analyses. COPASI can simulate dynamics using either an ODE approach or a stochastic chemical kinetics approach (Gillespie-type algorithms).

Main features:

  • Model:
  • Chemical reaction network.
  • Arbitrary kinetic functions.
  • ODEs for compartments, species, and global quantities.
  • Assignments for compartments, species, and global quantities.
  • Initial assignments for compartments, species, and global quantities.
  • Analysis:
  • Stochastic and deterministic time course simulation
  • Steady state analysis (including stability).
  • Metabolic control analysis/sensitivity analysis.
  • Elementary mode analysis .
  • Mass conservation analysis.
  • Calculation of Lyapunov exponents.
  • Parameter scans.
  • Optimization of arbitrary objective functions.
  • Parameter estimation using data from time course and/or steady state experiments simultaneously.
  • Graphical User Interface (CopasiUI)
  • Sliders for interactive parameter changes.
  • Plots and Histograms.
  • Command Line (CopasiSE) for batch processing.
  • SBML import (L1V1+2, L2V1-3) and export (L1V2, L2V1-3).
  • Loading of Gepasi files.
  • Export to Berkeley Madonna, XPPAUT, and C source code of the ODE system generated from the model.
  • Versions for MS Windows, Linux, Mac OS X, and Solaris SPARC.
  • What's New in This Release:
  • New Features
  • There are no new features in this release.This is a bug fix release for COPASI 4.3 (Build 25)
  • Bug Fixes
  • Graphical User Interface (CopasiUI)
  • Initial expression depending only on fixed numerical values are now properly updated.
  • Fixed problem which may lead to a crash when running the Mass Conservation task.
  • Fixed crash in the dialog for specifying the experimental data of the parameter estimation which occurred in rare cases.
  • Fixed problem where cut and paste of mathematical expressions for ODEs assignments and initial assignments could lead to spurious results after committing the data.
  • Simulation Engine
  • Fixed possible crash in MCA calculation which may occur if the model contains species of type ODE or assignment.
  • SBML
  • Fixed multiple use of the same SId in SBML exports. This problem only occurred when the model has been previously imported from SBML.
  • The constant flag is now set correctly if a species is changed from constant to determined by reactions in COPASI. This problem only occurred when the model has been previously imported from SBML.

last updated on:
July 22nd, 2010, 16:39 GMT
price:
FREE!
developed by:
Pedro Mendes, Virginia Tech Intellectu...
homepage:
www.copasi.org
license type:
Free for non-commercial use
category:
ROOT \ Science and Engineering \ Bioinformatics

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COPASICOPASICOPASI
What's New in This Release:
  • Graphical User Interface (CopasiUI):
  • Sorting and filtering in tables, which eases handling of large models.
  • Enhanced result representation of elementary flux mode analysis.
  • Improved SBW registration to handle multiple COPASI installations.
read full changelog

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