Microsoft Builds Open-Source Tool for Biologists Drowning in Data, an ‘On-Ramp’ for Customers Who Pay

Xconomy Seattle — 

The boss at the world’s leading maker of high-speed gene sequencing instruments, Illumina CEO Jay Flatley, pulled no punches a couple weeks ago when asked about bioinformatics. This is the field in which people make software to help biologists store, analyze, and visualize vast piles of genomic data that are accumulating every day.

“If you look historically at bioinformatics companies, it’s road kill. There are almost no examples of very successful bioinformatics companies. People don’t want to pay for software,” Flatley said.

So while Illumina has built a company worth $5 billion on genetic analysis instruments, what does Microsoft want to do with software to manage data from those tools? The world’s biggest software maker (NASDAQ: MSFT) has been working for years to find an angle into biological research labs, without much to show for it. Labs around the world still use an aging spreadsheet program, Excel, to hold onto data the program was never meant to handle. Many individual labs cook up customized “home-brew” software programs on their own, figuring their experiments require something special. The customer base for each of those home-brew programs? About 15 to 20 people in an individual lab.

Obviously, this is a fragmented market that doesn’t lend itself to a one-size-fits-all program for the masses like Word or Excel. Yet Microsoft is well aware of the terabytes of genomic data piling up in labs, and the potential for IT to efficiently sift through this data in a way that could be useful for personalized medicine and making healthcare more efficient. About a year ago, it rolled out a program called Amalga Life Sciences which it hopes will get all the different IT programs talking to each other to help biologists start coping with their information overload.

But Microsoft has a lot more going on to serve biologists than just what’s being packaged into Amalga Life Sciences. So I was curious to hear from Simon Mercer, the director of health and well-being at Microsoft Research, a few weeks ago on a visit to his office in Redmond, WA.

Simon Mercer

Simon Mercer

I started off by telling him that I’m a biotech journalist who knows a lot more about cancer drugs than software development. Sure enough, when he said the term ALS, I immediately started thinking of amyetrophic lateral sclerosis, otherwise known as Lou Gehrig’s disease. To him, it means Amalga Life Sciences. Luckily, Mercer appears to have patience for the challenges of translating between biology jargon and computer jargon.

“If you have any questions about shrew chromosomes, I’m your man,” says Mercer. “I’m a biology refugee in a computer science company.”

Mercer, who has a doctorate in zoology, worked as director of software engineering at Ann Arbor, MI-based Gene Codes before moving to Microsoft Research in 2005. The vision he’s working on now is an open-source platform in early development called Microsoft Biology Foundation.

The idea is a pretty simple one. The average biology lab often has its own bioinformatics specialist, usually a postdoc who got interested after dabbling around in software code, Mercer says. This person has a small customer base, and their applications need to change a lot to keep up with the pace of different experiments, and capture data from a lot of instruments that go out of date fast.

This requires a lot of work, for what are essentially a hodgepodge of tiny, short-term markets. Even at a behemoth like Microsoft, “we couldn’t possibly build all the applications,” Mercer says.

So how can Microsoft get a foothold in the biology lab? The Microsoft … Next Page »

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