Bio Models

BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats.

Models in this database are primarily distinguished by their identifier, which is in the form BIOMDxxxxxxxxxx where the x’s represent a number

COPASI

COmplex PAthway SImulator

COPASI

COPASI is 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.

Each chemical species in the network is represented by an ODE that describes the rate of change of that species along time. The ODE is composed by an algebraic sum of terms that represent the rates of the reactions that affect the chemical species. For a chemical species X

where si is a stoichiometry coefficient that is the number of molecules of X consumed or produced in one cycle of reaction i, with a positive sign if it is produced or negative if consumed, and vi is the velocity of reaction i. Obviously, for reactions that do not produce or consume X the corresponding s i is zero

These ODE models can be used to simulate the dynamics of the concentrations of the chemical species along time given their initial values. This is achieved by numerical integration of the system of ODE which can be carried out with well-established algorithms

Steady states can be found using the Newton–Raphson method which finds the roots of the right-hand side of the ODE (which must be zero by the definition of steady state). Alternatively steady states can also be found by integration of the ODE. COPASI can use either one of these strategies or a combination of the two

Stochastic Models