Microsoft Makes Cloud-Based Biological Research Tool Open Source

Michael Stiefel | InfoQ | February 21, 2017

Bio Model Analyzer, a Microsoft cloud-based tool that biologists can use to model cell interactions and communications, is now available as open-source on GitHub under a MIT license. Researchers use Bio Model Analyzer (BMA) to create computer models that can compare the processes within healthy and diseased cells. Researchers drag and drop cells, their contents (such as DNA or proteins), and extracellular components onto a canvas. They can also draw the relationships between these components. These models can then be verified, revised, and re-verified in order to test and validate how living systems behave, or to examine how stable a biological system is.

BMA merges system biology and formal methods that were developed for the specification and verification of concurrent software systems. Much like CAD/CAM did for engineering development, the BMA uses human computer interaction and design to speed up research in areas such as drug interaction and resistance. “We are trying to change the way research is done on a daily basis in biology,” said Jasmin Fisher, a biologist by training who works in the programming principles and tools group in Microsoft’s Cambridge, U.K. lab.

A BMA model allows scientists to see the interactions between millions of genes and proteins.  Ben Hall is a Royal Society University Research Fellow in Cambridge, U.K. who works with Fisher. He said that BMA can be used to help figure out how to detect cancer earlier. It can also be used to understand how to better treat cancer by modelling which medicines will be most effective, and when a particular cancer might become resistant to them. The BMA is used to run experiments by comparing the information from a healthy patient with that of a cancer patient. It can simulate how a patient might respond to medications...