Comments (Score 4, Informative)

I am the researcher mentioned at the beginning of the article, and I hope to address some of the questions that have arisen here. Please note that while the quotes in the article are accurate, the views ascribed to me are sometimes misleading

What exactly is the agreement I have with the University?
Briefly, my agreement with the University allows me, as well as members of my group, to produce open source software so long as:
(1) all authors agree for the software to be open source,
(2) the funding source agrees with the code being open source, and
(3) no laws are broken (including aspects of patent law embodied in the Bayh-Dole act).

Note that while this agreement permits my group to produce open source software, it does not require that we produce open source software. This is a blanket agreement covering all of my software written at the University.

Who funded this research?
The agreement covers all of my software development, regardless of source (though, as noted above, each source must be consulted). It was drawn up before I had any funding, as part of my employment agreement. Since then, my research has been funded from public sources (NIH, NSF, DOE, LBNL, and the University of California), and from a private charity (a Searle Scholarship).

Some clarifications of my views, where the article was imprecise

1. I believe it is desirable for authors to be allowed to produce open source software. At this point, I think it would be inappropriate for it to be required, as others have proposed. I currently have no problem with other scientists who readily distribute their software but not use open source licenses.
   
2. I believe that prospective authors of open source should approach their Universities with a standard contract similar to mine. I do not presently support a movement to "force universities to allow 'open source' publishing," as the article states.
   
3. I am not opposed to the Novartis/Syngenta agreement at Berkeley, as the article suggests. In fact, I have not studied that agreement carefully, and so I have no considered view of it. My impression is that much being said here about the agreement is incorrect.
   
4. I feel that fixing bugs is only one of many benefits of open source, and probably not the primary benefit (as the article suggests)
   
5. My agreement does not run counter to laws that allow the University to enter exclusive licensing agreements. The primary law governing such agreements is Bayh-Dole, which covers patents. My agreement only covers copyright. Moreover, my agreement has as a prerequisite permission from the funding source.
   
6. I agree with Phil Green that many individuals have greater respect for software that they've paid for. No problem: have both an Open Source and a commercial license for the code (as is the case for important programs like HMMER).

Some closing notes...

1. The University's default licensing agreement allows anyone to use the source code for non-commercial, research purposes. It's not nearly as bad as most posters here suggest. See it here (note: the original site is down; this is the google cache).
   
2. It is instructive to actually read the U.S. patent code as modified by the Bayh-Dole act. As I understand it, the main point of this act is encourage intellectual property from federal funding to be developed, rather than left to sit on in the dust on a shelf.
   
3. The University of California, Berkeley was quite helpful in arranging my open source agreement. I understand why their default license is different, and I appreciate their assistance in modifying their standard terms to accommodate my scientific goals. I was very happy with the University's response, and I think the agreement is eminently reasonable.

I welcome follow-up postings here and will try to answer further questions that arise.

Steven E. Brenner
http://compbio.berkeley.edu