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. There are many variables, and many molecules, proteins, and genes in the human body. Only powerful computational models can sort through the combinations, looking for abnormalities, testing the possibilities, understanding how cancers develop and change within the body.
“I think it will accelerate research because we are able to test so many more possibilities than we possibly could in the laboratory,” said Jonathan Dry. He is a principal scientist at the pharmaceutical company AstraZeneca whose team collaborated with Fisher’s team. No longer will researchers have to make educated guesses, or be biased by their favored possibilities.
BMA makes it feasible to provide patients with more personalized cancer treatments. An individual might have other illnesses or might be taking other medications that might interfere with the treatments. These can be put into the model. “It really recognizes that every patient is an individual and there can be vast heterogeneity,” Dry said.
