Agilent grant for Open Source Data-Integration tools

I’m not sure how much I like relaying things for corporate interests on my blog, but occasionally I’ll do it if I haven’t seen it posted anywhere else.  I’m actually thrilled to do it if it’s something I’m interested in – or if it’s something I think is a great idea or well executed.  In this case, I’m kind of torn.  The idea is fantastic, but the execution leaves me rather… unimpressed.

In any case, this once, I’ll relay an announcement from Agilent that was sent to me, announcing that they are:

Fostering integrated, whole-systems approaches to biological research with two $75K grants for open source data-integration tool development. – link

While it’s a great idea, $75k isn’t a great salary for doing the bidding of an industrial corporation, but it isn’t a bad salary for an academic developing open source software. As with all salaries, it’s better than what I make as a grad student, so it has that appeal. (-;

However, I do need to point out that they’ve put a little asterisk beside “Open Source” on their web page, which takes you to this:

“All free or open-source licenses are acceptable except “any license requiring, as a condition of use, modification and/or distribution of the software subject to the license, that the software or other software combined and/or distributed with it be (i) disclosed or distributed in source code form; (ii) licensed for the purpose of making derivative works; or (iii) redistributable at no charge. Excluded Licenses include, but are not limited to the GPLv3 Licenses.“

That, to me, reads as though they’re fine with open source, as long as it’s not really open source.  I wouldn’t expect much else from any company sponsoring software that they plan to appropriate at the end of the grant (and likely improve upon and re-sell), but it is still somewhat disturbing to me.  At least, disturbing enough that I wouldn’t want to take them up on this offer.  Your millage may vary.  (I’ll also note that the application form for the competition is a Microsoft .doc file – which is about as anti-open source as you can get.  A company really dabbling in open source would use a PDF or ODF, no?)

The two grants are quite different:

Grant 1: “Specifically, we are looking for proposals that focus on automation of targeted mass spectrometry-based proteomics experiments (e.g., SRM, exact mass) aimed at hypothesis testing or validation of protein pathways and/or interaction networks generated by integrating existing transcriptomic and/or metabolomic data sets.”

Grant 2: “Specifically, we are looking for proposals that focus on the correlation of copy number events and whole transcriptome measurements aimed at hypothesis testing/validation of disease progression models.”

It’s worth noting that Agilent may decide not to award these grants at all – they’ll only do it if they find something they like, which is fair enough.  (I can’t see any company giving away a grant to a sub-par idea, anyhow.)

Frankly, I’m not sure why Agilent doesn’t just hire someone to work on this project – it’s a neat project that I’d be happy to work on anyways –  and that way Agilent gets control of the final project without the added hassle of the “open source” phase.  To each their own, however!

To all those who apply, good luck!

3 thoughts on “Agilent grant for Open Source Data-Integration tools

  1. I applaud your skepticism about our grant program and wanted to answer your question – what do we mean by open source and, really, what are we doing with these grants? Our goal is simply to enable multi-omic research among a wider body of researchers. A key barrier to adoption is a lack of tools for data integration, and by awarding these grants, we hope to get some of these tools built. We believe this will be a great benefit to users of Agilent’s proteomics, metabolomics, and genomics tools, as well as the scientific community at large.

    By specifying open source, our aim is to get tools that are freely available to any researcher. What we want to ensure with an open source license is that we will not be prevented from incorporating that tool into a larger set of data integration tools that are unified under a single user interface. When we say “open source” we want to ensure that it is truly open, not just for academia.

    • Thanks Leo,

      First, sorry about the slow reply – I’ve been unable to reply at length any earlier, due to a laptop failure while travelling. However, I did want to say thank you for your comment and to give you a quick response.

      I absolutely understand your point of view, it’s difficult for any corporation to juggle the open source versus closed source paradigms and it can be a dangerous legal edge to walk upon. That said, I’m not sure I agree with your comment that only academia can use open source licenses with GPL-like clauses. For instance, the Linux kernel is one of the most widely used GPL licenced codebases in the world, and it’s hardly limited to academia.

      The big difference to me is how the licence is interpreted. If you have a GPL style clause, then what you ensure is that all changes remain open to the community and that corporations must share any changes they make to the code. Yes, it does require a different business model (eg, not selling the code), but, again, that certainly does not limit it to academia.

      In this case, the selection of a non-GPL clause requirement sounds more like an announcement that you intent to revoke the “open source” status of the code in the future – which is anything but ensuring that it is truly open. Would you back up your grant with a promise that all changes made by agilent and it’s developers in the future would be contributed back to the open source code base, and not closed to those who are not your customers?

  2. Per Leo’s comment, in this case Agilent is saying open-source sans GPL style requirements. Berkley, Apache, Perl, MIT-style open-source licenses, IMHO, be acceptable. To me this true open-source, absolutely no restrictions on how the resulting source code may be used by others.

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