COPASI A tool for simulation and modeling of biochemical networks.
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simulation networks biochemical biochemical networks modeling kinetic equations

COPASI Description

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). Here are some key features of "COPASI": 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. What's New in This Release: · Bugfixes.

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