No-one cares about your bioinformatics software

/ nsaunders

Here’s a tip. When you write an article about your software, the title of which indicates that open-source is important:

A universal open-source Electronic Laboratory Notebook

but you then:

  • provide almost no details in the abstract
  • do not provide a link to a website or repository from which your “free” software can be obtained
  • choose not to make the article open access
  • and put the installation instructions in a supplementary data file which is also not open access

Don’t be surprised when no-one uses your software.

Or is the publication more important to you than the product?

10 thoughts on “No-one cares about your bioinformatics software”

  2. Syst req:
    – WordPress, running on
    – Linux Ubuntu 8.04.4 LTS
    – Apache 2.2.8
    – MySQL 5.0.51a
    – PHP 5.2.4

    Communicated in an MS Word file. Mme. Voegele et al. seem to keen on free software. ;)

    I wonder: the authors included the WP customization templates in the appendix of a paywalled journal. Usually, journals get the copyright for all contents of the paper, including supplemental material. Would I infringe the journal’s copyright now if I put this code, freely available for anyone to review, on github?

  3. I see this very often now: “open source” gained currency as a positive thing, so many will use it without knowing what it means. Apparently, in this case, none of the reviewers (nor the editor) knew or took the time to care either.

    Seeing source code in Word file is a first for me, though.

    • I had not bothered to read further, but I’m learning interesting things via comments and Twitter. Installation is basically WordPress? Source code in a Word file…unfortunately, I’ve seen that before. Beginning to wonder why this one was not rejected by the editors.

  5. Yes, the publication in many cases is, unfortunately, more important than the product. Her’es the deal: publications are currency that can help buy you grants, promotion, tenure. Software — not so much. Software is of much lesser value for the first, and depending on your institute somewhere in the range of [0,0+epsilon) on the latter two. Academia judges primarily by publications, and takes mostly two indices into account: number of publications and impact factors. Because it’s easy. Is this a warped situation? Yes. Should it be changed? Absolutely. But until this changes, the publication does count more than the product. Actually, the P&T committee in many cases does not know that the publication itself is hollow, and does not care.

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  8. From the supplementary material, the section on free ELNs available, paragraph describing MyLabBook (built with Drupal): “Drupal and WordPress are similar, but the wiser choice was to opt for the CMS we already knew at IARC: WordPress.”. Indeed, wiser.

    Editors are people, people make mistakes, mistakes get propagated and amplified. Kind of lost hope in self-correcting mechanisms of science. Now, off to write that paper on using Twitter as a “Novel cloud based ELN platform with an embedded microcitation support”. Bioinformatics Journal! Here I come!

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