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August 29, 2007

Open Access Publishing

The question of where to publish the results of research (especially publically-funded research) has been steadily coming to prominence this year, particularly following a Nature news article revealing that a consortium of scientific publishers has hired a “pit bull” (Nature’s term, not mine) of Public Relations to fight their corner. The result seems to be PRISM, a lobby group opposed to open-access publishing.

A lot of electrons have been spilled over this issue, and, sadly, it is apparant that the debate is far from well-tempered. Scientists in favour of open access publishing are angered by claims that open access would mean the end of peer review. Those claims, it seems to me, are almost entirely unfounded; it seems to me that this is a claim being put around in the knowledge that it is false, to try and scare people off open access publishing. Open access journals such as BioMed Central and The Public Library of Science Journals are peer-reviewed by scientists in the relevant field (who do so for free) in the same way that pay-to-read journals are.

The case for public access to research the public is funding (through taxation) has been made elsewhere, and debated at length, so I won’t go into that here. I think there’s a slightly different point to be made from the point of view of advancing science, though. As a scientist, it’s very frustrating to find an interesting article referenced in a piece of research I read, or that crops up when doing a literature search, only to find that my institution doesn’t subscribe to the relevant journal. It’s obvious that making my research freely available is more useful to the scientific community at large than publishing it in a journal that requires other scientists (or their employers) to pay to read it. I’m aware of the parallel here to some of the things I said about free software a while back!

For junior scientists, there’s another issue, too. The next job (particularly if it’s a faculty/tenured post) will largely depend upon your publication record. The impact factors of open access journals are often not that high (partly because they’re relatively new), which may mean that potential employers who are too focussed on bibliometrics will rate papers therein less highly. Nailing your colours to either side of such debates can be dangerous, too, if you’re un-tenured. I’m evidently not entirely risk-averse!


July 05, 2007

Free software and science

Writing about web page http://www.gnu.org/philosophy/

This might sound like a rather unpromising title for a blog post by a veterinary epidemiologist, but I think the issues surrounding free software are relevant for all of us who use computers to do science. The question of whether to use free software or proprietary software is particularly acute for modellers, and other people whose published work contains the output of computer programs.

Free software means more than just software you don’t pay for. The classic analogy is that it’s free as in “free speech”, rather than just as in “free beer”. Specifically, free software gives its users four key freedoms:

  1. The freedom to use the software for any purpose
  2. The freedom to share the software with others
  3. The freedom to study the workings of the software
  4. The freedom to improve the software, and share those improvements with others

The latter two are particularly relevant to science. If I want to validate the results of your study, a good way would be to inspect the software you used to generate those results; not simply that given the same inputs, it produces the same outputs, but that the methods it uses to generate those outputs are correct. It’s very easy to get odd corner-cases wrong, and those mistakes might go otherwise un-noticed. Even if they don’t affect the study’s findings, they might be worth fixing before doing any further work!

Science is, at its best, about a community of scholars working to improve our understanding of the world. If scientists use free software, and make it available along with their research findings, then other scientists can build upon their work, avoid unnecessary reduplication of effort, and collaborate more effectively. It seems to me that free software should be the gold standard for scientific computing. If you write software as part of your research, please consider releasing it to the scientific community under a free licence such as the GNU GPL; if you are considering what software to use for a particular research project, consider carefully if there is a piece of free software you could use (with modifications if necessary). Not because you’ll spend less of your grant on software costs, but because it’s the moral and socially responsible thing to do!


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