July | August 2006 | MathWorks, maker of the popular MATLAB programming environment, recently launched a modeling product, SimBiology, aimed at systems biology and synthetic biology markets. SimBiology includes a graphical front end and a drag-and-drop interface to help nonprogrammer biologists create, edit, and view models of biochemical pathways and run simulations.
“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 have fallen short in addressing this relatively new segment, featuring either strong mathematics or a graphical front end,” says Kristen Amuzzini, marketing manager for biotech, pharmaceutical, and medical markets.
MATLAB has long been used by researchers to model biological systems; but doing so isn’t a trivial task. The company hopes its biologist-friendly offering will ease the effort and speed adoption. This first release models biochemical reactions and can’t directly incorporate “omic” data. The models use both deterministic and stochastic simulation. Results can be analyzed in SimBiology or MATLAB. SBML models can be imported.
Amuzzi says SimBiology will automate time-consuming tasks such as sensitivity analysis and parameter estimation. The latter function should help researchers use experimental data to refine a model and spend less time researching all facets of the parameters. The models will also act as knowledge repositories, she says, and facilitate collaboration between researchers.
“At some beta sites, we are already starting to see modelers and programmers using [SimBiology] to communicate their pathways with biologists. One of the painful things we saw at pharmas is that modelers would work in one environment and then convert it to a PowerPoint slide to send to biologists, rather than being able to use something like this,” Amuzzini says.
Recently, systems biology has experienced a modest resurgence as modeling and simulation gain a firmer foothold in biopharma. One MathWorks customer, Novartis, recently elevated its modeling group to departmental status and expanded the department’s headcount to 35.
MathWorks had 2005 revenues of roughly $350 million and claims a million users across 175 countries. Besides Novartis, MathWorks products are used at Infinity Pharmaceuticals and selectively at MIT. Combining a tabular interface and a diagrammatic language should strengthen SimBiology’s appeal to the biologist community, though its inability to immediately incorporate genomics data may limit its early use to PD/PK kinds of activities.
SimBiology pricing is $3,000 for a single user, with the usual academic discounts.