Thursday, May 11, 2006

New open access journal Source Code for Biology and Medicine

BioMed Central is setting up a new peer-reviewed, open access journal Source Code for Biology and Medicine. It will "encompass all aspects of workflow for information systems, decision support systems, client user networks, database management, and data mining". Basically, anything that fits into chem-bla-ics. (Thanx to Werner, for pointing me to the website!)

The 'source code' aspect is the interesting thing of this new journal. The editorial board set the aim to publish source code for distribution and use in the public domain in order to advance biological and medical research. And, in a bit more detail, they list the following goals:

  • increase productivity

  • reduce discovery times

  • reduce search times for source code

  • provide a historical reflection of source code applied

  • serve as a repository

This comes close to what open source is trying to achieve too, but I do not differences. For example, the announcement mentions the public domain (see the WikiPedia entry). I tend to be a bit confused by the use of this term: to me the public domain is where things end up after copyright claims have ended, and everyone is free to do with it whatever he wants, and, very important in this case, that open source software is not in the public domain. Do they mean that they will not allow open source in the new journal?

I also wonder wether we need a journal like this? Open source projects often have other resources available that serve as repository (e.g. SourceForge), and the use version control systems as repositories (like CVS, Subversion) is widespread too, which takes care of the historical reflection. Indeed, many open source software is already published in other journals.

The process of picking the journal to submit to, often involves looking up the journals impact factor. Is this new journal expected to get a high impact factor? How many people will regularly read the journal? Will it be read by the right audience, or just by fellow bioinformaticians?

Though I have my doubts about the success of this journal, I am looking forward to the first issue!

Update: Pedro pointed me to the About page of the SCFBM, giving details on the types of articles taken into consideration.


  1. Thanks for the info ! :)
    Unlike sourceforge, submiting a paper this journal will allow scientists to get a publication in a peer reviewed paper and as you know, a publication list may be critical for a carreer. Moreover, I hope this journal will allow programmers/me(!) (not pure theorists) to get a publication.


  2. I know nothing about the intent of this new journal's editorial board or their intent, so this isn't intended to necessarily respond directly to that, just to resolve some common misconceptions about "public domain"

    "public domain" does not necessarily mean "copyright relinquished" or "copyright expired". One common (though some pedants will argue that it is incorrect) use of "public domain" is to mean one of those two things, but in general the concept of public domain is much wider. Remember that copyright and license are different concepts, and open source is about license, not copyright. All true open source licenses are public domain licenses, regardless of who owns the copyright.

  3. Hi anonymous,

    First, thanx your insights.

    Indeed copyright and licenses is not the same. OK, so 'public domain' does not mean it has no copyright anymore. But what *does* it mean then? I also do not understand your statement about true open source licenses: what's an example of a false open source license? And why are open source licenses supposed to be public domain licenses?

    For example, Wikipedia states that things from the public domain may be used by anyone for anything. This is certainly not the case for open source licenses like GPL or many of the Creative Commons licenses. Would you consider something like BSD to be one of the few true open source licenses?

  4. I disagree with the anonymous comment. Legally, public domain specifically refers to creative works for which the copyright has expired (at the present moment anything created/published before 1910 or something). Public domain material can be used for any purpose whatsoever (ie you can take it and recommercialize it).

    The reason the open source licence works is that copyright specifically prohibits modification, duplication or distribution by default. Open source licences relax that restriction, allowing anyone to modify or distribute the copyrighted material IF they agree to the stipulations in the licence; ie all modifications are also covered by the same license, and if you distribute the program you must also make available the source code. But once the copyright expires on a piece of open source code (or any code for that matter, even proprietary) then anybody can take it and do with it anything that they like.

    Anonymous cause I don't have a blogger account.