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).
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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: [ read full changelog ]
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.
Simulation Engine:
· Support of conditional events, which are discrete changes to the model.
· 2 new stochastic simulation algorithms, which implements the direct Gillespie algorithm and Tau-Leap method.
· Eigenvalues of the steady-state Jacobians are now available for further processing or output.
SBML:
· Import and export of SBML Level 2 Version 4.
· Full support for SBML event import/export
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