Systems Biology Markup Language (SBML)

Systems Biology Markup Language (SBML)

What Is SimBiology?

SimBiology is an integrated environment for modeling biological processes, simulating the dynamic behavior of these processes, and analyzing the model with simulation and experimental data. Biological processes include metabolic, genetic, and signaling pathways with transform, binding, and transport reactions.

Model

Design and build models by entering reactions, species, parameters, kinetic laws, rules, and submodels with a graphical user interface, a block diagram editor, or using the MATLAB® Command Window. Verify that the model can be simulated, and use the verification results to fix any incompatibilities in the model.

Import SBML models created with SimBiology or other modeling software that is compliant with the Systems Biology Markup Language (SBML) standard.

Export models created with the SimBiology desktop to MATLAB and continue your simulations and analysis with command-line functions. For more information, see Modeling.

Simulate

Observe changes in species amounts and parameter values over time. Convert your model to a system of differential equations and simulate the model numerically with various differential equation solvers. The deterministic solvers include stiff and nonstiff ordinary differential equation (ODE) solvers. The stochastic solvers include a stochastic simulation algorithm with implicit and explicit tau variations. Perform multiple stochastic ensemble runs. For more information, see Simulation.

Analyse

Save data from a simulation and export that data to the MATLAB workspace. Compare simulation and experimental data, perform sensitivity analysis, parameter estimation, and search for conserved moieties. For more information, see Further Analysis with MATLAB.

What Systems Biology Markup Language (SBML) 

It is an information standard for sharing, evaluating, and developing systems biology models cooperatively.

Its purpose is to provide a structure for creating models and sharing those models among various modeling and simulation software tools.

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