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Merrimack Adopts the MathWorks' SimBiology To Drive In-House Network Biology Platform

Merrimack Pharmaceuticals has incorporated the MathWorks’ SimBiology simulation software into its in-house computational discovery platform, Network Biology, the MathWorks said this week.
Merrimack was one of the first beta testers for SimBiology, which the MathWorks launched last year. The product is built upon its Matlab numerical computing environment and allows modelers and biologists to model, simulate, analyze, and share biochemical pathways [BioInform 07-07-06].
Now Merrimack has cemented an agreement with the MathWorks that places SimBiology at the heart of its Network Biology platform, which was developed to analyze the system dynamics of protein networks.
A MathWorks spokesperson said that the agreement makes Merrimack “one of the first” commercial users of SimBiology, and is the first such agreement that the company has disclosed publicly.
Birgit Schoeberl, director of network biology at Merrimack, said in a statement that the company is already seeing a payoff from the software, noting that “a group of six researchers were able to create seven candidates in less than three years with SimBiology.”
That discovery, she said, “would’ve taken a lot more time without using modeling or by using multiple tools from other companies, and it would have required that we learn three or four different software packages.”
SimBiology includes graphical elements that researchers can use to build biological pathways in a drag-and-drop environment. That interface sits above the Matlab programming language to enable complex simulations using both stochastic and deterministic solvers.  The system also enables sensitivity analysis to predict the effect of specific parameters on the system and parameter estimation to help fit the model to experimental data.
SimBiology’s “point-and-click” simulation environment is suitable for both expert and non-expert users, Kristen Zannella, marketing manager for biotech, pharmaceutical, and medical at the MathWorks, told BioInform this week. “When tools are less user-friendly, they are more [oriented towards using] a command prompt and one needs to know the command … which is not what these scientists are trained for,” she said.
Schoeberl told BioInform last year that SimBiology offered a number of benefits over using Matlab alone, including a better user interface for graphically representing pathways and the ability to share models.
Zannella said this week that Merrimack wanted a more integrated approach for its Network Biology platform, which applies computational modeling to high-throughput quantitative biology.
“For different areas … like … simulation and analysis, a different tool is needed for each piece, and that was really the challenge they were faced with and why they were working so closely with MathWorks,” she said. “When we originally started working with them, they were using multiple tools.”

“For different areas … like … simulation and analysis, a different tool is needed for each piece, and that was really the challenge they were faced with and why they were working so closely with Mathworks.”

Schoeberl was unable for comment before press time, but said in a MathWorks “user story” that Merrimack chose SimBiology to “fuse our quantitative biology expertise with our modeling expertise.”
She said that the Network Biology system enables Merrimack to “analyze and simulate drug candidates using models, and streamlines the drug discovery process.”
Merrimack explains on its website that the system is based on quantitative modeling of cell signaling pathways. The company populates its models with experimental data derived from its proprietary antibody microarrays and other platforms. The company uses these network models for target discovery and validation.
Zanella said Merrimack’s platform is designed to examine protein networks in particular, such as protein-protein interactions and the pathways associated with certain diseases, as well as proteins within those pathways.
She added that the Mathworks is working with Merrimack to develop an efficient environment that is conducive to both modelers and scientists.
“One of the most unique things is [to] put computational models together with the scientists and put [the] Network Biology platform together so groups can work closely together,” she said.
Currently, only Merrimack’s computational modelers have access to Matlab and SimBiology, but the MathWorks said that Merrimack plans to roll out the tools to its experimentalists as well over the next year. 

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