Maths software turns to biological systems

Edited by the Engineeringtalk editorial team Jul 3, 2006

SimBiology is a graphical systems-biology tool that leverages an industry-proven mathematical engine to enable biologists to simulate, model and analyse biochemical pathways.

The MathWorks has announced the introduction of SimBiology, the first graphical systems-biology tool that leverages an industry-proven 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 nonprogrammers 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.

"Systems biology is a rapidly growing discipline that requires technology to help researchers and computational biologists overcome the complexity inherent with examining the interaction of genes and proteins".

"Until now, the tools available for systems biology have fallen short in addressing the challenges of this relatively new segment, featuring either strong mathematics or a graphical front end", said Kristen Amuzzini, Marketing Manager for Biotech, Pharmaceutical and Medical, The MathWorks.

"SimBiology was created in response to demand from our customers for a tool that addresses both areas, and by coupling the power of Matlab with an intuitive drag-and-drop user interface, we're able to provide those customers with the most comprehensive and proven systems-biology tool to help them improve the quality and speed of drug discovery".

SimBiology extends The MathWorks leadership in computational biology, complementing the Matlab and Simulink applications for the life sciences that customers already rely on to import data, analyse and visualise data; model biological systems; communicate results; deploy applications; and increase computing performance.

SimBiology is available immediately.

Commercial US pricing starts at $3000 per seat.