Because HMMER has commercial value, I spend an inordinate amount of time explaining the choice of the GPL. Open source licenses are widely misunderstood.
Most of my funding comes from the National Human Genome Research Insitute at the National Institutes of Health (NIH). NIH grants policy states that the results of NIH-funded research must be made available to qualified scientists upon request. The free exchange of information is also a fundamental tenet of publicly funded science. The simplest means of disseminating information about how HMMER works is to distribute documented source code. I take this responsibility seriously. While I am in academia, my software will be freely available in source code form.
At the same time, I'm not going to put HMMER in the public domain. If I did, someone could incorporate HMMER into a proprietary software package without my permission or knowledge. I couldn't see the improvements they were making to my work. They might sell the proprietary software and not contribute a fair share of the profits to Washington University or my research lab. So I need a distribution license that lets me distribute it freely, while at the same time trying to make sure that I don't get taken advantage of.
Some developers license their software under restricted ``academic only'' licenses, such that ``commercial'' users have to pay license fees. Having worked in a biotech startup, I strongly oppose this sort of license. Most industry scientists contribute to basic research, and they consider themselves no different from their counterparts in academia. The line I want to draw is between open and proprietary, not academic and commercial. Commercial scientists can be open, and academic scientists can be proprietary. (And NIH's free resource distribution policy does not distinguish between academic and industrial peers.)
Open Source licenses (aka ``free'' software licenses) like the BSD license, the Perl Artistic License, the Netscape Public License, and the GNU Public License do what I need. The GNU Public License is the best known of these licenses. So long as you play the game - that you are working in a nonproprietary manner, accepting that any of your modifications to my code must also be GPL'ed and made freely available as open source code - you get free, open access to HMMER source code. But if you want to use HMMER in a proprietary way, the GPL does not grant you that right, so you must contact the Washington University tech transfer people to arrange a special proprietary license (and, unsurprisingly, we'll charge you fair license fees).
The GPL is often misinterpreted as a socialist license, and I sometimes field questions about why I'm so determined to oppose commercial development, or even undermine it (by distributing free software). This is a misunderstanding. American universities have a responsibility, under the 1980 Bayh/Dole act, to transfer technology to the private sector. I respect the economic goals of Bayh/Dole. In my view, there is a productive tension between Bayh/Dole and scientific ethics. The purpose of the HMMER GPL is not to impede commercial development, but rather to maintain this tension. As an academic, my primary responsibility is to make my work available. As an American research university, the job of Washington University and our technology transfer office is to make HMMER available for proprietary use under appropriate terms. We can and do license HMMER for proprietary use. We're just not going to give it away for proprietary use, that's all. If you want to make a profit from HMMER, we want a fair share so we can put it towards the research that develops HMMER.
Whew. You think that was long-winded? That's nothing; the full text of the GNU GPL follows:
The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software-to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it.
For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.
We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software.
Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations.
Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all.
The precise terms and conditions for copying, distribution and modification follow.
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You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee.
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