> 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. Andreas > > 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: [email protected] > [mailto:[email protected]] On Behalf Of Mark > Schreiber > Sent: Wednesday, October 13, 2010 4:26 AM > To: McSweeny, Andrew J > Cc: [email protected] > 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 > LGPL. > > 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 < > [email protected]> 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 > > > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
