Kinetic modeling of complex biochemical systems is central to the emerging field of systems biology. Kinetic models require definition of numerous free parameters, usually obtained by calibration to experimental data, that specify initial species concentrations and kinetic rate constants. Once calibrated, a model should be analyzed for its sensitivity and predictive power over ranges of parameter values. Both model calibration and analysis can require thousands to millions of model simulations for statistical convergence and significance. In many cases, the computational expense of simulation at this scale makes detailed model analysis infeasible.
A software application for simulation and analysis of biochemical networks and their dynamics. COPASI is 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.
A structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver, SBML Simulation Core and Copasi. By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface.
Provides an ordinary differential equations (ODE) solver. XPP-AUT is an application that solves differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations. It draws nullclines, direction fields, and two- and three-dimensional plots of solutions as well as find equilibrium points and their stability. This resource is available as a desktop app and as a mobile app.
Allows simulation of movements and reactions of molecules within and between cells. MCell permits simulation of specific instance of chemical signaling, diffusion, and reaction of discrete neurotransmitter molecules in synaptic spaces. It can be useful for Monte Carlo simulation of diffusion in a volume or on a surface. This tool employs a Model Description Language (MDL) to define simulation input conditions and user-requested output.
Allows users to mathematically model dynamical systems. PottersWheel is a comprehensive framework for data-based modelling in Systems Biology comprising multi-experiment fitting in normal and logarithmic parameter space. The software integrates statistical tests for model-data-compliance, model discrimination and identifiability analysis for non-linear relationships between an arbitrary number of parameters.
Permits numerical study of parameterized continuous and discrete dynamical systems. MatCont computes phase response curves and their derivatives as a by-product of the continuation of limit cycles. It supports numerical normalization for all codim 1 cycle bifurcations. This tool allows computation of critical coefficients of periodic normal forms. It integrates a general Starter-Generator-Processor technique to compute solutions.
A problem solving environment, built on a central database, for analysis, modelling and simulation of cell biological processes. VCell integrates a growing range of molecular mechanisms, including reaction kinetics, diffusion, flow, membrane transport, lateral membrane diffusion and electrophysiology, and can associate these with geometries derived from experimental microscope images. It has been developed and deployed as a web-based, distributed, client-server system, with more than a thousand world-wide users.