New PLOS Open data policy

PLOS one logoPLOS has announced some changes to their publishing policies, and these changes are great news.  The new PLOS policies will go a significant way towards encouraging open data and open source.  Although the announcement itself is somewhat vague on the subject of source code, the actual PLOS One Sharing Policy is excellent:

…if new software or a new algorithm is central to a PLOS paper, the authors must confirm that the software conforms to the Open Source Definition, have deposited the following three items in an open software archive, and included in the submission as Supporting Information:

  • The associated source code of the software described by the paper. This should, as far as possible, follow accepted community standards and be licensed under a suitable license such as BSD, LGPL, or MIT (see for a full list). Dependency on commercial software such as Mathematica and MATLAB does not preclude a paper from consideration, although complete open source solutions are preferred.
  • Documentation for running and installing the software. For end-user applications, instructions for installing and using the software are prerequisite; for software libraries, instructions for using the application program interface are prerequisite.
  • A test dataset with associated control parameter settings. Where feasible, results from standard test sets should be included. Where possible, test data should not have any dependencies — for example, a database dump.

However, the one loophole is that they allow for code that runs on closed source platforms in “common use by the readership”  (e.g. MATLAB), although it must run without dependencies on proprietary or otherwise unobtainable ancillary software.  That “common use” loophole could potentially be a mile wide in some fields.  Is Gaussian a common use platform in computational chemistry and therefore exempt from this new policy?   If so, the policy is a bit toothless.  I’d like to see the limits and bounds of the “common use” loophole more clearly stated.

The announcement makes PLOS ONE a much more attractive place to send our next paper.

Do you want to know you can measure DNA contour lengths using ImageJ?  Perhaps you want to stain a C. Elegans embryo for imaging?  Or possibly, you might want to test whether or not you have gotten an immune response using ELISA?

Martin Fitzpatrick sends word of a cool collection of open access scientific protocols called  For the uninitiated, protocols are the recipes that scientists use to carry out experiments in a reproducible way.  The list of protocols posted to to date has a number of interesting and important biochemistry and biology experiments.

There’s also a neat companion site called which concentrates on many of the same things we do – the use of open source software in the sciences.