![]() ![]() * 3D bar chart representation of matricesĬOPASI allows users to define report files where data is written to during simulations and analyses.* Color-coded matrices, for easily identifying large and small values.* A series of plots that are most commonly used are already pre-defined. ![]() * Arbitrary 2D plots of any model variables and parameters (including trajectories in phase space).* Network diagrams can also be used to visualize mass conservation moieties, and elementary flux modes.* Network diagrams can be used to visualize time course simulations as movies.* Lyapunov exponents, which allows to establish if the system dynamics are chaotic.ĬOPASI allows users to visualize data in various ways:.* Cross sections, which allow to characterize non-linear dynamics properties, such as oscillations and chaos.* Analysis of stochasticity using the linear noise approximation (allows estimating variances and co-variances even in the presence of large numbers of particles).* Time scale separation analysis this allows definition of fast and slow components of the model, in a time-dependent way.* Metabolic control analysis (a special form of sensitivity analysis).This can be done over several different experiments simultaneously, including mixtures of steady-state and time course experiments. * Parameter estimation using a range of diverse optimization algorithms.* Optimization of arbitrary components of the model using a range of diverse algorithms.* Stoichiometric analysis of the reaction network, including mass conservation analysis and elementary flux modes.Models can be analyzed and modified with a large set of methods: Simulations can be of time courses or steady states. ![]() * Hybrid LSODA/SSA for hybrid simulations with stochastic kinetics and differential equations.* Hybrid Runge-Kutta/SSA for hybrid simulations with stochastic kinetics and differential equations.* Adaptive SSA/τ-leap algorithm for faster (approximate) stochastic kinetics.* τ-leap algorithm for faster (approximate) stochastic kinetics.* Gibson-Brooke's version of Gillespie's algorithm for exact stochastic kinetics.* Gillespie's direct method for exact stochastic kinetics.* LSODAR for ordinary differential equation modeling. ![]() The software provides an interface to create parameter scans (sweeps), parameter sampling and repeated simulations - including complex simulation scenarios mixing parameter samples with scans and repeats of simulations (or other analyses). Simulation can be performed either with stochastic kinetics or with differential equations, and the software easily allows switching between them. Models can also be exported in XPP format, Berkeley Madonna format, and as C code (in addition to MathML and Latex).
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