Whodat leading the open source bioinformatics movement?

Whodat leading the open source bioinformatics movement?

Summary: Bioinformatics is an area of growing need no one has managed to get their arms around. No one wants to pay for the software. So Microsoft is making the initial investment, open source.

TOPICS: Health, Open Source

It's Microsoft, that's whodat.

The Microsoft Biology Foundation, now available at Codeplex, is a toolkit under .NET coordinated through a team at Microsoft Research which aims to bring software into the business of evaluating DNA.

This is important, because bioinformatics is an area of growing need no one in the software business has yet managed to get their arms around.

No one wants to pay for the software, noted Illumina CEO Jay Flatley, yet the volume of genetic data coming available is overwhelming the kludged-together tools available for analyzing it.

It's a bit like the field of business intelligence was a decade ago, only it's too small to have created the proprietary giants open source companies reacted to. It costs too much for a company to build something of value, and there aren't enough companies willing to pay big bucks for the result.

So open source in this case becomes a necessity. But even here someone has to be the lead dog. Someone needs to make the central investment necessary for a community to form around. Or the business doesn't get started.

That's what Microsoft is doing here. You can question their motives (and some do) but they are stepping up to the plate, building the heart of the tools, making them available for download, and building a centralized community that can drive progress.

So when genetic companies finally decide that they need these tools, they can enter into the field at a price point they need, gradually see the value, and start paying on their own schedule.

This is how open source is supposed to work.

It's the sort of thing one would normally associate with Google, not Microsoft. But Microsoft has a big stake in the biology and health industries through its Amalga software, and its Healthvault PHR has made many more friends in the industry than Google Health. They are the natural firm to lead this.

As to why I led  with a New Orleans Saints chant, well it's a punny thing...the Saints are a business, not a religious movement, yet they are the center of a large voluntary community. That's what Microsoft wants to be here.

And there is a prize at the end.

Topics: Health, Open Source

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  • Actually, MS is quite the latecomer.

    Dear Dana, while I hope not to be classified as the typical MS basher, in this case I have to say that MS is quite late in the open source bioinformatics arena. We evaluated several OSS bioinfo tools in the SPIRIT project since 2000, and there are a few hundreds substantial projects that are used throughout academia, the private research world and industry that are quite more substantial than this first (respectable) entry. I would point our something like BioClipse as a general workbench system, BioJava and BioPython, BioConductor for the R statistical language (and R itself, now the de facto standard language for statistical analysis), many parsers for the various format and database used, BioSQL, EMBOSS, and on and on. Just parse through the presentation of the BOSC conference of the past (starting from 2000...) and you will get quite an idea of the activity and interest of this scientific community on open source. I welcome microsoft, of course, but to claim them a leader is a little bit of exaggeration.
    Carlo Daffara
    • RE: Whodat leading the open source bioinformatics movement?

      @cdaffara@... The problem isn't the level of activity in Bioinformatics - its the fact that everyone is taking potshots at their specific area of interest. Nobody is thinking about the problem holistically and designing a platform upon which an ecosystem can be supported. Further, many vendors of specific tools propse theirs as a one-language-fits-all solution which they never are.

      THAT is what Microsoft does so very well and what they're bringing to the field via the new framework: "a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework. Currently it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological Web services such as NCBI BLAST."
      • RE: Whodat leading the open source bioinformatics movement?

        @de-void Actually, the bioinfo field is one of the few in which there is a strong effort at integration. BioClipse is a good example - not only integrating parsers and connectors (all that there is in the MBF) but integrating display, query, job management (if you use grids and external schedulers) and much more. The people working in the field are usually quite happy to share and use the best tools available, making them similar to the statistical research community in this sense.
        If, on the other hand, you are implying that .net is multiplatform, then Bioconductor (based on R) has connectors and adaptors for basically every language that is in use by the scientific community.

        Having followed the field (with a stronger emphasis on the medical area, but with many bioinfo activities as well) I am puzzled by the idea that microsoft by releasing a library that implements common parsers and connectors available in several other tools, magically becomes an holistic provider, but I may be overlooking something.
      • RE: Whodat leading the open source bioinformatics movement?

        [i]>> Further, many vendors of specific tools propse theirs as a one-language-fits-all solution which they never are. <<[/i]

        So Microsoft provides a one-platform-fits-all solution. Awesomeness. Just so long as you're using Windows and aren't accessing or making changes to any APIs restricted by the .NET framework. Unfortunately, a very large portion of bioinformatic work is done on *nix. I don't have specific numbers, but looking at the data center specs for the many of the largest institutions and companies that work in bioinformatics, they're all some flavor of *nix. Fedora Core is used a lot, for some reason.

        [i]>> "... a language-neutral bioinformatics toolkit built [b]exclusively for Windows on the x86 architecture.[/b]" <<[/i]

      • How noble. They want to take something open and tie it to Windows-only tech

        [b] [/b]
      • RE: Whodat leading the open source bioinformatics movement?

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  • Thanks to all

    This is one of the best discussion threads I have seen at ZDNet Open Source in quite some time. My thanks to everyone, even the critics, for leaving some things to think about and follow up on.
    • Can you please tell me how to subscribe for email notification of replies?

      [b] [/b]
  • RE: Whodat leading the open source bioinformatics movement?

    A couple of reasons a single platform is not needed.
    1.) *nix tools are great at piping output from one to another.
    2.) It is the plugins, stupid.
    3.) Initial Installation and patch management on *nix is so much easier (yum install) and (yum -y update) that neither sysadmins nor users often don't realize they are on a different system.

    The nightmare of installing software and patch management on a closed source platform is why MS will want you to think a single platform is needed.
    • Yum? Most modern Linux distros use point-and-click GUIs like Synaptic for..

      ..installing/uninstalling/updating stuff.
  • RE: Whodat leading the open source bioinformatics movement?

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