The Seven stones wondered what to do with a petaflop in science,\nin response to Declan’s The petaflop challenge in Nature.\nDeclan discusses in this commentary the increase in computing power and the necessity of parallel programming to make use of it.\nNow, I do have some ideas (e.g. enumerating metabolomic space, mining the RDF graph of our collective biological and chemical\nknowledge base for the one hundred most supported contradictions), but that is not what I want to talk about. It is this fragment\nfrom Declan’s piece:
\n\n\n\n\n“I’m amazed at what he can do just using open-source libraries,” [Horst Simon] says. Although there are exceptions, such as\nhigh-energy physics and bioinformatics, many labs keep their software development close to their chests, for fear that their\ncompetitors will put it to better use and get the credit for the academic application of the program. There is little\nincentive to get the software out there, says Simon, and such attitudes plague development.
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This is something that is very familiar to many of us: developing algorithms for scientific problems is not appreciated.\nIt worries me very much the way the scientific community currently deals with algorithms and data; it seems the community\ndoes not care about correctness or improvement at all, as long as the result illustrates what they think the (bio)chemical\nreality has to offer. At least, that is what effectively happens if they do no give proper credit to the scientific\nimportance of software development.
\n\nOf course, scientific credibility of software depends on the open source nature of the software:\n“Given enough eyeballs, all bugs are shallow”, The Cathedral and the Bazaar,\nE.S. Raymond. Or, in more traditional wording: science, and scientific software, must be reproducible and/or\nfalsifiable. The Blue Obelisk Movement is trying to achieve this\n(DOI:10.1021/ci050400b).
\n\nTherefore, I hereby challenge all experimental chemists in biologists to acknowledge the amount of scientific software\nthey already use, and give credit where credit is due. I challenge them to stand up and say that chemo- and\nbioinformaticians provide the methods they rely on daily to achieve there goals. I challenge them to say that\nthey stand of the shoulders of scientific software developers.
\n\nThe article should not have been called The petaflop challenge, but The open source challenge.
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