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<component type="desktop">
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<id>COPASI.desktop</id>
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<metadata_license>CC0-1.0</metadata_license>
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<summary>The COPASI graphical user interface</summary>
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<name>COPASI</name>
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<project_license>Artistic-2.0 and GPL-3.0+ and BSD</project_license>
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<categories>
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<category>Science</category>
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</categories>
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<description>
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COPASI is a software application for simulation and analysis of biochemical
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networks and their dynamics.
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COPASI is a stand-alone program that supports models in the SBML standard
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and can simulate their behavior using ODEs or Gillespie's stochastic
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simulation algorithm; arbitrary discrete events can be included in such
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simulations.
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COPASI carries out several analyses of the network and its dynamics and
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has extensive support for parameter estimation and optimization.
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COPASI provides means to visualize data in customizable plots, histograms and
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animations of network diagrams.
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MODELS
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Models in COPASI are based on reactions that convert a set of species into another set of species. Each species is located in a compartment,
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which is a physical location with a size (volume, area, etc). This maps directly to biochemical reaction networks,
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but can also represent other types of processes (for example, the species could be cell types).
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COPASI automatically converts the reaction network to a set of differential equations or to a system of stochastic reaction events
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— the user does not have to write down the math explicitly, the software does that.
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Models can also have:
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* Unlimited number of species, reactions, and compartments.
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* Arbitrary discrete events; these can be used to change the model, or just to monitor the progress of simulations.
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* Arbitrary differential equations; these have to be added explicitly by the user and can be mapped to species, compartments, or generic variables.
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* Compartments can have variable sizes (ie they can be variables of the model).
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* The rates of reaction can be picked from a set of predefined kinetic functions (the most common in biochemistry), or arbitrary functions defined by the user.
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Models can be visualized through
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* the GUI interface, with tables for reactions, species, compartments, etc.;
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* an arbitrary number of network diagrams (including an SBGN-compliant option);
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* the full set of differential equations; these can be exported in Latex or MathML formats.
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COPASI can import and export models in the SBML format (levels 1 to 3). Models can also be exported in XPP format,
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Berkeley Madonna format, and as C code (in addition to MathML and Latex).
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SIMULATION
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Simulation can be performed either with stochastic kinetics or with differential equations, and the software easily allows
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switching between them. The software provides an interface to create parameter scans (sweeps),
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parameter sampling and repeated simulations — including complex simulation scenarios mixing parameter samples
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with scans and repeats of simulations (or other analyses).
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Algorithms available for simulation:
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* LSODAR for ordinary differential equation modeling.
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* Gillespie's direct method for exact stochastic kinetics.
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* Gibson-Brooke's version of Gillespie's algorithm for exact stochastic kinetics.
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* τ-leap algorithm for faster (approximate) stochastic kinetics.
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* Adaptive SSA/τ-leap algorithm for faster (approximate) stochastic kinetics.
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* Hybrid Runge-Kutta/SSA for hybrid simulations with stochastic kinetics and differential equations.
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* Hybrid LSODA/SSA for hybrid simulations with stochastic kinetics and differential equations.
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Simulations can be of time courses or steady states.
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ANALISYS
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Models can be analyzed and modified with a large set of methods:
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* Stoichiometric analysis of the reaction network, including mass conservation analysis and elementary flux modes.
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* Optimization of arbitrary components of the model using a range of diverse algorithms.
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* Parameter estimation using a range of diverse optimization algorithms. This can be done over several different experiments simultaneously,
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including mixtures of steady-state and time course experiments.
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* Local sensitivity analysis.
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* Metabolic control analysis (a special form of sensitivity analysis).
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* Time scale separation analysis; this allows definition of fast and slow components of the model, in a time-dependent way.
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* Analysis of stochasticity using the linear noise approximation (allows estimating variances and co-variances even in the presence
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of large numbers of particles).
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* Cross sections, which allow to characterize non-linear dynamics properties, such as oscillations and chaos.
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* Lyapunov exponents, which allows to establish if the system dynamics are chaotic.
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DATA VISUALIZATION
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COPASI allows users to visualize data in various ways:
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* Network diagrams can be used to visualize time course simulations as movies;
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* Network diagrams can also be used to visualize mass conservation moieties, and elementary flux modes;
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* Arbitrary 2D plots of any model variables and parameters (including trajectories in phase space);
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* A series of plots that are most commonly used are already pre-defined;
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* Color-coded matrices, for easily identifying large and small values;
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* 3D bar chart representation of matrices
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DATA OUTPUT
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COPASI allows users to define report files where data is written to during simulations and analyses.
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These report files are useful for importing data onto other applications for further analysis and visualization.
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</description>
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<url type="homepage">http://copasi.org/</url>
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<screenshots>
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<screenshot type="default">
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<image>https://sagitter.fedorapeople.org/copasi/COPASI-TSSATask_03.png</image>
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</screenshot>
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<screenshot>
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<image>https://sagitter.fedorapeople.org/copasi/COPASI-maxresdefault.jpg</image>
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</screenshot>
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<screenshot>
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<image>https://sagitter.fedorapeople.org/copasi/COPASI-Diagrams_02.png</image>
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</screenshot>
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<screenshot>
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<image>https://sagitter.fedorapeople.org/copasi/COPASI-Diagrams_03.png</image>
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</screenshot>
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<screenshot>
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<image>https://sagitter.fedorapeople.org/copasi/COPASI-MCATask_02.png</image>
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</screenshot>
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<screenshot>
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<image>https://sagitter.fedorapeople.org/copasi/COPASI-MCATask_03.png</image>
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</screenshot>
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<screenshot>
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<image>https://sagitter.fedorapeople.org/copasi/COPASI-ParameterScan_08.png</image>
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</screenshot>
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<screenshot>
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<image>https://sagitter.fedorapeople.org/copasi/COPASIF5.large.jpg</image>
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</screenshot>
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</screenshots>
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<updatecontact>sagitter_at_fedoraproject.org</updatecontact>
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</component>
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