(Via chem-bla-ics and Yakafon)
BioMed Central will be hosting a new journal entitled "Source Code for Biology and Medicine". According to journal description:
Source Code for Biology and Medicine aims to publish source code for distribution and use in the public domain in order to advance biological and medical research. Through this dissemination, it may be possible to shorten the time required for solving certain computational problems for which there is limited source code availability or resources.
Looking around I fount the about page where you can see the type of papers that they expect:
* Original research: reports of data from original research. Describe novel implementation of source code used for acquiring new results, not previously published elsewhere. Research articles require complete source code files with compiled executables, libraries, or class modules (object-oriented programming with use of class libraries is the recommended programming style)..
* Methodology articles: discuss first-time publication of source code for a commonly used approach, for which code is not widely available in peer-reviewed biomedical literature. Methodology articles require complete source code files with compiled executables, libraries, or class modules (object-oriented programming with use of class libraries is the recommended programming style).
* Brief reports:short synopsis of applied algorithm without publication of the source code.
* Software reviews:discuss the application of published workflow or algorithm source code.
This journal could serve as an extra incentive for people to deposit their code for open access. Maybe all that code that we use but we don't really ever tide up into a nice package can know be sent to this journal. I am not sure if there is space for this with already three well known journals (Bioinformatics, BMC Bioinformatics and PLoS Comp Biology).
Comments
A great initiative
This is great - I hope very much that it succeeds. There must be many bioinformatics hackers who have useful bits of code sitting in cvs repositories and as Pedro says, perhaps this will provide incentive to clean it up and get it out there.
I think it's also recognition that what we do is worthy. Lately I've been concerned that in research, it can be difficult for people whose main focus is programming to convert their daily labour into something that other scientists take seriously (i.e. publications). Perhaps this is an avenue for more recognition of those efforts.
Documentation
And as a side effect, we might get decent docs on more code...
about time
I've always felt that providing source code should be a requirement of publication in existing biomedical journals ... after all, 'wet' lab scientists are typically required by most respectable journals to lodge all new sequences or structure coordinates in the relevant public database prior to publication. Many also require authors to send any vector (eg plasmid) used in the publication to others who request it (although it is amazing how often plasmids are 'lost'). Why has this never been the case for source code ?