PLoS ONE – How Biologists Beat Engineers…

April 26, 2011


One of the most progressive Scientific Journals available today,
is bringing shame to many engineering Conferences and Journals,
by taking the initiative and showing them how is that real scientific
publishing is done
when computation (software) is involved.

PLoS ONE goes to the core of Openness and Reproducibility.

Here are the instructions for authors,
They are so perfect, that there is few we could add to them, except
to express our admiration for a publisher that understand its role in
the scientific community:  “Effective Dissemination of Usable Information”.

The following text has been taken from:
and only formatting and emphasis has been added.

Reporting Software Articles

PLoS ONE supports the development of Open Source software and believes
that for submissions in which software is the central part of the paper,
then adherence to appropriate Open Source standards will ensure that the
submission will conform to our requirements which state that


“methods must be described in sufficient detail so that another
researcher is able to reproduce the experiments described


as well as our


“aim to promote openness in research and intention that all work
published in PLoS ONE can be built on by future researchers.”


Therefore, if new software or a new algorithm is central to a paper,
authors must confirm that the software conforms to the definition of
Open Source
as defined by the ten rules of the Open Source initiative
and have deposited the following in an open software archive as well as
included as supplemental information with the article:

  1. 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 Mathmatica and Matlab
    does not preclude a paper from consideration, although complete
    Open Source solutions are preferred.
  2. Documentation for running and installing the software: For end user
    applications instructions for installation and using the software are prerequisite;
    for software libraries instructions for using the API are prerequisite.
  3. 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.


Acceptable archives are: SourceForge, Bioinformatics.Org, Open Bioinformatics Foundation (O|B|F),
Google Code, BerliOS Developer, Savannah, and the Codehaus. Authors should provide a direct
link to the deposited software from within the paper.

Deposition with the journal as well as an Open Source archive ensures that the original source
associated with the paper is available as well as any enhancements made after the paper is published.
If the article covers a well established project that has been providing an open source code
repository for an extended amount of time, it can also be considered.

A condition of acceptance is that

          the software can be run by reviewers accessing the public software

and that

          results presented in the paper are reproducible.


The software only need run on one hardware/software platform in common use
by the readership (including Matlab), although it must run without dependencies
on proprietary or otherwise unobtainable ancillary software


Articles describing software that requires access to databases and other resources
whose persistence is not guaranteed (e.g., individual laboratory databases without
funding support) will not be considered.


In addition, the results described in the paper must be reproducible when peer reviewers,
editors, or readers run the software on the deposited dataset and with the provided control


In cases where the software/algorithm is not central to the paper, we nevertheless
encourage authors to make all relevant materials freely available.


The text above was taken from:
and only formatting and emphasis has been added.



If only the Engineering Conferences and Journal
could learn from Biologists…



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