COPASI Biochemical networks analysis and simulation made easy.
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COPASI Description

COPASI is a reliable tool designed to help you analyze biochemical networks and their dynamics. It feature an easy to use GUI which allows you to configure the networks, add tasks and generate reports. This tool comes as a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams 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. SBML import (L1V1+2, L2V1-4) and export (L1V2, L2V1-4). Analysis: Stochastic and deterministic time course simulation Steady state analysis (including stability). Metabolic control analysis/sensitivity analysis. Elementary mode analysis . Mass conservation analysis. Time scale separation 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. Color-coded tables 3D bar charts Plots and Histograms. Network diagram visualization of results. Command Line (CopasiSE) for batch processing. Versions for MS Windows, Linux, Mac OS X, and Solaris SPARC. Loading of legacy Gepasi files. Export to Berkeley Madonna, XPPAUT, and C source code of the ODE system generated from the model. Saving of mathematical formulas and ODEs in MathML or LaTeX

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