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User's Guide
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HMMER
User's Guide |
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.
Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does.
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.
These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program.
In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License.
The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable.
If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code.
If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances.
It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice.
This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.
Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and ``any later version'', you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation.