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

Hilmar Lapp hlapp at drycafe.net
Wed Oct 13 21:44:36 UTC 2010

How and when you want to be attributed in publications, and what you  
want someone else not to publish on, is an ethical matter. Licenses  
are legal instruments and not suited for ethical questions or social  
conventions. Rather, this is addressed by ethical and social  
conventions and requests.

A good example is the Ft Lauderdale agreement, which is not a legal  
instrument but an ethical request of those who peruse immediate- 
release sequencing data. If you have ethical or social requests to  
make of those who peruse your code, state them explicitly in a README  
and in the code.

By their nature, you can't legally enforce them. However, ethical  
behavior is policed - by all of us as a scientific community, not in  
the courts.


On Oct 13, 2010, at 1:21 PM, Steve Darnell wrote:

> Andrew,
> 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).
> 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  
> 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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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :

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