Biology Foundation is seeking to build an open-source platform that biologists can download from the Web, and which has some common code most biologists need, Mercer says. Essentially, it’s meant to provide a template that individual researchers can build their custom applications on top of. It provides a range of algorithms for manipulating DNA, RNA, and protein sequences, and a set of connectors to publicly available resources on the Web, like the National Center for Biotechnology Information’s Basic Local Alignment Search (BLAST) tool. By providing some of this open-source code, it ought to save biologists some time and money on writing code to connect to things like BLAST, which can be better applied toward the killer experiments they want to do, Mercer says.
The Microsoft Biology Foundation “is like a Swiss Army knife of bioinformatics,” Mercer says.
The software platform is still in its beta form. Mercer was pretty pleased to note that Bellevue, WA-based Aditi Technologies had recently introduced a program for biologists called “DNA PReDUST” which was built on top of the platform. Collaborators at Cornell University, Queensland University of Technology, and the University of Texas are involved in helping build the platform, he says. His research group at Microsoft, of about 15 people, also has commercial partners that he couldn’t identify. But he wasn’t trying to make the platform out to be more than it is. There were about 1,300 downloads of the program by mid-April, after an initial round of researchers were invited to test-drive it, and it made a more public appearance at Microsoft’s annual TechFest in March.
“We’re not trying to run before we can walk here,” Mercer says.
There are plenty of other options for biologists if they want to seek out open-source platforms to take care of a lot of their bioinformatics grunt work needs. BioPerl, BioRuby, and Biopython are just a few. Not surprisingly, the Microsoft offering hopes to find an advantage by being easily hooked up to Excel, where a lot of biologists keep their data. And, naturally, Mercer and his team are thinking about ways to connect the Microsoft Biology Foundation with the proprietary program that Microsoft seeks to make money from—Amalga Life Sciences. I didn’t have time to ask about this is in great detail from the point person at Amalga Life Sciences, Jim Karkanias. But Karkanias did explain in a short note how his group should be able to work with the Microsoft Biology Foundation.
“Since MBF is positioned on the boundary between the world of predominantly academic small-scale, open-source software and the world of large-scale enterprise applications, it can act as one of our on-ramps for conducting life science research on the Amalga Life Sciences platform,” Karkanias says.
As much as Microsoft might like to one day dominate bioinformatics like Illumina does the world of sequencing instruments, it just doesn’t sound like a market that anybody can dominate—at least not yet.
“We understand it’s a heterogeneous community, and scientists should use the best software tools, not necessarily those that come from one software developer,” Mercer says. “We don’t know where the research will go next, so we don’t want to lock people in. You can’t lock people in.”
