Nature Methods | Methagora

Social software

Don’t be mistaken, Nature Methods’ material sharing policy includes the requirement to make custom-developed software available upon publication. But there are several ways of making software available. We examine the various degrees of disclosure and the choice of formats and try to clarify our position. Let us know if we are heading in the right direction!


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    Stew said:

    What’s meant by ‘made available’, though? If an author puts up some code on their own website there’s no guarantee that it’ll still be there after a year or two.

    When you make a sequence available you have to submit it to GenBank. When you make software available should you have to submit it to SourceForge, Google Code or some other semi-permanent repository?

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    Roland Krause said:

    One year might even be an optimistic estimate. I know several cases where the code never went public before the postdoc left the building.

    Depositing the complete code with SourceForge should be a requirement for any work without hard experimental results.

    For simple computations, pseudo code in the paper would be more useful than the Perl script. The aspect should be highlighted in the review process more than already is with many journals.

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    Daniel Evanko said:

    Custom software is considered to be no different than other materials and protocols developed by authors and reported in a paper. There are no restrictions on authors patenting such materials and protocols and then selling or licensing them. Requiring the authors to place their software in an open depository would prevent them from exercising these rights.

    This does not mean though that there isn’t a problem with software becoming unavailable when responsibility rests with the authors to provide it upon request. This is the reason we decided to explicitly state that software falls under our materials and data availability rules as detailed in the Guide to Authors. Since authors must agree to abide by these rules as a condition of publication, it provides us with the legal means to enforce this policy if at some point the authors refuse to provide the software to people who request it. Thus, they can make the software available in whatever form they like but it must remain available for the foreseeable future.

    Of course, if authors do decide to release their software under an open source license it simplifies things enormously if they take the time to submit the code to one of the repositories you mention.

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    c e carter said:

    Hello, I am new here. Just put down last months issue of nature/methods editorial segment that this blog existed. So, I came here to check it out. I’m mainly interested in stem cell research. But, couldn’t find anything like that. Nor did I see anything around here like that yet. So, I’ll just be an observer for now. Thanx.

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    Dinesh said:

    Hi, It seems to be a nice move by Nature Methods to ask scientists to put their software online for public use.However, it looks far from been achievable.In my own experience, I have asked a few scientists (who have published interesting papers in Nature Methods)if they can provide a few plasmids (e.g, redox sensing GFP), but they never replied, what to talk of accepting or denying.Who should be held responsible for such things? I had this notion that people publishing in Nature group journals are more committed to science and sharing scientific resources, are ethically more responsible.But, am sorry to say, it was all illusion. So, I agree to Ronald Krause that authors should be made/persuaded to put their software on free sources.Afterall, its the public money which has been used for the work and so the people in general should have access to it.Thanks.

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    Veronique Kiermer said:

    When publishing their work in a Nature title, authors agree to respect our publication policies. As stated in the editorial, sharing material is a condition of publication.

    So, if you request a plasmid and get no response, you should start by insisting. (Many of us have been guilty of loosing an email in a pile of ‘to do’ things). But if some gentle reminding does not get you anywhere, or leads to refusal to send the requested reagents, by all means do contact the journal’s Editor. Refusing to send reagents is a breach of Nature policies and the Editor will contact the authors to have this resolved. If the situation cannot be resolved promptly and the reagents remain unavailable, the Editors will publish an addendum to the paper, which becomes a permanent part of the publication and the PDF of the paper, stating that the authors are not complying with the policy.

    More information on Nature policies can be found on the new authors and referees website.

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    Alan Coelho said:

    I am quite stunned to learn that Mature Materials has gone down this path. I publish mainly algorithms that are placed in a commercial package. The package is used by over 2000 scientists and if all journals were to adopt Nature Materials policy then those users would be deprived of peer reviewed articles. This is a shameful act especially as institutes do not in general fund the development of such software. This is the classic act of locking the doors to the ivory tower. It seems that the “arrogance of physics” is alive and kicking.

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    Martin Hafner said:

    Sharing materials is easy as long as it is about plasmids, cell lines or programs. However, some materials require quite some effort for their production and are thus limited. E.g., production of recombinant proteins can be time consuming and expensive. In addition, in some cases it is impossible to share the cells or vectors that have been used to produce these proteins because of IP issues or because MTAs from third parties are required.

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    software developer said:

    Actually I do not understand how you make software available. And what are your several ways? And does it mean that we will not pay for using someone else’s software?