Skip to main content

Advertisement

Being open: our policy on source code

Article metrics

Fifteen years ago Genome Biology published its first Software article [1]. It described a suite of programs for the analysis of microarray data. The tool was deposited on the authors’ website (now defunct) and was “copyrighted against commercial gain”. The conditions of deposition and release reflected the understanding of and the reservations about open source that the scientific community had at the beginning of this century.

Many readers will be aware that this would not stand today: the times have changed, the field has matured, and the definition of open science has crystallized. Many researchers now acknowledge that openness and transparency foster better, reproducible research. A Comment published in our journal last year argued that all research should be carried out openly, so that what we today call ‘open science’ should just become ‘science’ [2]. One recent study also showed that, despite common misconceptions, open science can actually aid researchers’ careers [3].

With all the benefits that open science brings, our authors and readers could not have been surprised in the past several years to see us require that any source code published as a part of an article is deposited in a recognized public source code repository [4]. Since the beginning of 2016 we have also started requesting that the authors of Method and Software articles describing new computational tools archive the version used in the manuscript in a DOI-assigning repository, such as Figshare [5] or Zenodo [6]. This way the researchers trying to reproduce analyses described in the article can use the exactly same code as the authors - inoculating those analyses against the inevitable evolution of code.

We consider source code availability and accessibility to be important to ensure that computational analyses can be easily repeated and research shown to be reproducible. It is, however, no less critical that the source code can be utilized by others to further their own research: that other people can use it, and develop it, and build on it (and cite it [7]), and create new and wonderful tools that the authors of the original may not have even dreamed of. And an important factor affecting the ability to do this is the source code license.

This is why Genome Biology requires that the source code published as a part of an article is released under a license complying with an Open Source Definition, as defined by the Open Source Initiative [8]. This means that the source code can be used, modified, and distributed by anyone (importantly, the definition assures no discrimination against fields of endeavor; for more see Box). We believe that, together with a robust source code archiving strategy, employing open source licenses serves to preserve the source code long-term — through its re-use, re-purposing, and further evolution. And thus it really helps it become a foundation of research not yet imagined.

References

  1. 1.

    Breitkreutz BJ, Jorgensen P, Breitkreutz A, Tyers M. AFM 4.0: a toolbox for DNA microarray analysis. Genome Biol. 2001;2(8):software0001.1–3.

  2. 2.

    Watson M. When will ‘open science’ become simply ‘science’? Genome Biol. 2015;16:101.

  3. 3.

    McKiernan EC, Bourne PE, Brown CT, Buck S, Kenall A, Lin J, et al. How open science helps researchers succeed. eLife. 2016;5:e16800.

  4. 4.

    Genome Biology’s guidelines on source code deposition. http://genomebiology.biomedcentral.com/submission-guidelines/preparing-your-manuscript/software. Accessed 05 Aug 2016.

  5. 5.

    Figshare. http://figshare.com. Accessed 04 Aug 2016.

  6. 6.

    Zenodo. http://zenodo.org. Accessed 04 Aug 2016.

  7. 7.

    Smith AM, Katz DS, Niemeyer KE, FORCE11 Software Citation Working Group. Software Citation Principles. PeerJ Preprints. 2016;4:e2169v1.

  8. 8.

    Open Source Initiative. http://opensource.org. Accessed 04 Aug 2016.

  9. 9.

    Pachter L. The myths of bioinformatics software. http://liorpachter.wordpress.com/2015/07/10/the-myths-of-bioinformatics-software. Accessed 04 Aug 2016.

  10. 10.

    Choose an open source license. http://choosealicense.com. Accessed 04 Aug 2016.

  11. 11.

    Brown CT. On licensing bioinformatics software: use the BSD, Luke. http://ivory.idyll.org/blog/2015-on-licensing-in-bioinformatics.html. Accessed 04 Aug 2016.

  12. 12.

    Wheeler DW. Make Your Open Source Software GPL-Compatible. Or Else. http://www.dwheeler.com/essays/gpl-compatible.html. Accessed 04 Aug 2016.

  13. 13.

    Morin A, Urban J, Sliz P. A quick guide to software licensing for the scientist-programmer. PLoS Comput Biol. 2012;8(7):e1002598.

Download references

Acknowledgements

We would like to acknowledge Hilmar Lapp for his thoughtful advice, and Amye Kenall and Dominique Morneau for their helpful comments.

Authors’ contributions

RTM and LF conceived and wrote the manuscript. Both authors read and approved the final manuscript.

Competing interests

Both authors are employees of BioMed Central, the publisher of Genome Biology.

Author information

Correspondence to Rafal T. Marszalek.

Rights and permissions

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Marszalek, R.T., Flintoft, L. Being open: our policy on source code. Genome Biol 17, 172 (2016) doi:10.1186/s13059-016-1040-y

Download citation