[Biojava-l] How to share code while protecting copyrights?

Andreas Prlic andreas at sdsc.edu
Wed Oct 13 18:48:32 UTC 2010

> Forgive me for being pessimistic, but I do not believe you can
> publically distribute your code without running the risk of being
> scooped.  Mark's suggestions are very good; however, the safest route
> would be to withhold distribution of your code until your work is
> published (or at very least accepted).

I think that is too conservative - if getting scooped is an issue, I would
release the code shortly before submission of the first manuscript to a
journal. That way the source code can form part of the publication and the
referees can view the code during the review process.  Many views/downloads
of articles happen in the first few weeks after publication. Having a link
to the source code in the paper can be a great advertisement for the open
source project and help in community-building.


> Also, I would suggest this argument for convincing your group to use
> BioJava (disclaimer - I am not a lawyer).
> Under the LGPL, you are not obligated to release your source code if:
> (1) you create a "work based on the library" (e.g. direct modifications
> or additions to the licensed work) but do not distribute it, and
> (2) you create a "work that uses the library" by dynamically linking
> your work to the licensed work (see distribution clause #5 of the LGPL:
> http://www.gnu.org/licenses/lgpl-2.1.html)
> If you follow choice #2, you can license and distribute your work under
> terms of your group's choosing (open or closed, submit it to the BioJava
> developers for inclusion or not) while gaining the benefit of reusing
> BioJava.
> ~Steve
> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org
> [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Mark
> Schreiber
> Sent: Wednesday, October 13, 2010 4:26 AM
> To: McSweeny, Andrew J
> Cc: biojava-l at biojava.org
> Subject: Re: [Biojava-l] How to share code while protecting copyrights?
> Hi -
> My understanding of copyright is that it is yours as soon as you assert
> that
> it is your creation. You can simply add a copyright statement to each
> file
> containing the code (in the header for example). The reality is that
> defending copyright is your responsibility. If someone violates it, you
> have
> to take them to court or issue a legal letter.
> You can also put an appropriate license on the code specifying how it
> can be
> used. Examples include GPL, LGPL, BSD, Apache License etc. You can pick
> one
> of these that best matches your needs. BioJava code is LGPL so if you
> want
> your code to go into the BioJava code base you will need to make your
> code
> It's always a good idea to add @author tags to Java code to ensure
> appropriate attribution.
> Finally, if someone steals your code and publishes results before you
> then
> you can always make a complaint to the journal editors. If it is a
> reputable
> journal, and you have reasonable proof the editor should take some
> action
> such as forcing a retraction.  You can also make a distribution
> agreement
> saying that if someone uses this code they agree not to publish without
> first consulting you.
> If you want to make it really water tight, get a lawyer and explain
> specifically what you want to share and what you want to protect or
> prevent.
> - Mark
> On Tue, Oct 12, 2010 at 11:41 PM, McSweeny, Andrew J <
> andrew.mcsweeny at rockets.utoledo.edu> wrote:
> > Hi,
> >
> > I am working on a project which simulates sexual reproduction in a
> > population of digital organisms.  Their genome is just a contig from
> hg18.
> >  It's pretty interesting and I can talk more about it in the
> future....
> >
> > Anyways, how can I share my code for this project without having to
> worry
> > that someone else will use it to publish a paper before my group does?
> >
> > I'm certain nobody in the open source community would do that, but how
> do I
> > convince my group that opening our project to BioJava is a good idea?
> >
> > -Andrew
> >
> > _______________________________________________
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> >
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526

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