BIOINFORMATICS

SimBiology

1 September 2006

The MathWorks

The MathWorks has launched SimBiology, a graphical systems-biology tool that uses its mathematical engine to enable biologists to simulate, model, and analyse biochemical pathways in one integrated environment. Built on The MathWorks MATLAB engine, SimBiology improves communication among modellers and biologists and eliminates the need for computational biologists to apply specific tools at each phase of systems biology.

Biochemical pathway analysis studies organisms as systems comprised of elements that interact with one another through chemical reactions. Because of the complexity associated with examining pathways, computational systems biologists require model-based tools to graphically depict the pathways and a mathematical engine to accurately analyse experiment and simulation data.

SimBiology provides a complete modelling environment that includes both a graphical front end and a proven mathematical engine. SimBiology features a drag-and-drop interface, so that biologists who are non-programmers can create, edit, and view models of pathways. Biologists can simulate the modelled reactions with deterministic and stochastic simulation solvers, and then analyse the resulting data in SimBiology or perform custom analysis with MATLAB.

SimBiology automates many of the time-consuming tasks associated with systems biology, including sensitivity analysis, which assesses the impact of parameter changes on pathways and helps highlight likely drug targets within pathways. The parameter estimation functionality in SimBiology automatically generates estimates for unknown parameters within an existing model, so that biologists can use experimental data to refine a model and spend less time researching all facets of the parameters. Both types of automation reduce the need for time-consuming and costly wet-bench experiments.

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