FYI: [Bioinformatics] Open Source Petition FAQ (fwd)

---------- Forwarded message ----------
 Date: Tue, 04 Dec 2001 13:51:37 -0800
 From: Harry Mangalam <mangalam |-at-|>
 To: bioinformatics |-at-|
 Cc: Andrew Dalke <dalke |-at-|>
 Subject: [Bioinformatics] Open Source Petition FAQ
 Q   What is this petition about?
 A   The aim of this petition is to educate researchers and the agencies that
     fund them about the advantages of using Open Source Software (see below).
     We think that software developed under the grants from public agencies -
     those funded by your tax dollars - should be made Open Source in order to
     accelerate the process of science while reducing the cost of further
     investigation as well as making the software assisting such investigations
     more robust and widely useful.  Software developed under grants from private
     agencies would of course be exempt from such a requirement, but they might
     also consider requiring or advocating this for the reasons we provide below.
 Q:  Why even consider Open Source?  And why is Open Source for Scientific
     applications any different than for anything else?
 A:  We liken Open Source as peer review.  In a scientific endeavor, we make a
     hypothesis and provide evidence to support or discredit the hypothesis.  In
     reporting the evidence, we publish the data in as raw a form as possible so
     that others can examine and critique it.  This is how Science tends to move
     forward. We submit that like other forms of materials and methods, the
     source code of software involved in arriving at a decision should also be
   - This peer review of software allows bugs or exceptions that the original
     authors did not account for to be found and fixed by others.
   - It provides for a mechanism by which original features can be incrementally
     improved and additional features can be added without the underlying
     infrastructure (initialization, input/output, data structures, help &
     documentation files) being rebuilt from scratch.
   - Because of the wider use, it encourages more standardization of more
     efficient file or exchange formats, decreasing the time spent on converting
     one format to another.
   - It increases the speed of code development thru the methods noted above,
     can make research cheaper, and therefore increase the return on investment
     in  research, especially important these days as public support for
     research is  under pressure.
 Q   Why Open Source, why not Free Software?
 A   Open Source Software is a generic term for software that is available
     in source code form.  There is an organization that advocates Open Source
     Software in various forms and makes various cases for its use at:
     Free Software (in its capitalized form anyway) is software that is
     distributed under the Free Software Foundation's General Public License
     (, which is one form of
 Open Source.
     The GPL is a relatively strict form of Open Source which, while
     guaranteeing your freedom to modify and redistribute code, also has
     restrictions which decrease some freedoms to do other things with the
     code.  These restrictions bother some people more than others.
        We are not fanatic about which kind of licensing under which  the code is
     made available; only that the code is made available without restraint for
     examination and use by the public.  We also suggest a licensing mechanism
     that we believe addresses the concerns of the inventor, copyright holder,
     technology transfer office, and private companies that wish to
     substantially increase the utility of such code and charge money for such
     proprietary extensions.
 Q   Doesn't OSS/FS require me to give my code away for free?
 A   OK - this is where the rubber meets road.  It is our opinion that if you
     take Public taxpayer money to develop an idea at an academic or
     non-profit institution, you have a responsibility to allow the Public to use
     it.  'The Public' includes both for-profit companies (which also pay taxes)
     as well as individuals who might be interested in the results of the
     research.  Note that we are strongly against the privatization of public
     resources.  If a private corporation wants to use the code, they are bound
     by the same requirements as an individual.  The company should be able to
     use and modify the code for internal purposes as would an individual.
     beyond this, things get less clear.  Whether and how the company should
     be able to redistribute the code is debatable although it is our contention
     that the best way of addressing the competing claims and requirements
     (especially the Bayh-Dole Act - see below) is a DUAL LICENSE, defined below:
     The DUAL LICENSE approach.
     We suggest that the best way to satisfy both our request for release of the
     software for public use and the requirement for institutions to be able to
     license their IP (a la Bayh-Dole) is to use a DUAL license approach. In
     this scheme, the code would be available to all for Open Source use and
     iterative development, but companies who required exemption from the
     covering Open Source license could be granted it from the copyright holder
     or their institution.
       This arrangement would not only allow the code to be examined, stressed,
     and debugged by the user community who would be getting a return on their
     tax dollar, but that *improved* code could also be licensed to external
     companies who needed to incorporate it into their products without the
     requirement to make their changes or adjunct code Open Source in return -
     essentially paying for permission to privatize code developed with public
     funds.  The idea is that the code base itself would improve over time and
     become more valuable to more companies.
       This arangement would require that developers who contributed to this
     effort were aware of and agreed to the provision that their efforts
     were being 'harvested' by the copyright holder.
 Q   Doesn't OSS/FS violate Bayh-Dole?
 A   The Bayh-Dole act of 1984 (more precisely, P.L. 96-517, The Patent and
     Trademark Law Amendments Act, with further amendments described in  P.L.
     98-620) was a landmark law that dramatically changed the way Intellectual
     Property was handled.  Rather than try to squeeze it into this FAQ, I refer
     you to the Universities' POV: [ ]
     a generally supportive series of articles from Columbia University (one of
     the largest beneficiaries of the Law):
     [ ],
     as well as an extremely harsh criticism of the Law:
     [ ], and a
     piece in the Atlantic describing the implications and history of it:
     [ ]
     We contend that our suggestion does not violate the Bayh-Dole Act, and in
     fact may make it MORE remunerative to the licensing agencies rather than
     less.  We are not asking that the Universities give away their Intellectual
     Property, but that they make it available under different processes than
     they do now.  Remember 2 things: 1) we are talking only about software and
     2) software is an implementation of an idea or algorithm.  Once an
     algorithm is published, the implementation of the algorithm as running code
     is less of an issue than the original research leaading up to the
 Q   Why do some researchers oppose this petition?
 A   There have been several objections to this petition by people who are
     in the position to be impacted by it.
       Phil Green (Washington University) has indicated that while he thinks all
     research results should be open, he objects to software being specifically
     singled out because of the perception that when things are freely
     available, they are deemed to be worth less or valued less.  There are
     certainly several stories about how a low priced but competetive product
     did not begin to sell well until its price was RAISED to be more in line
     with the competition.
       Steve Brenner (UC Berkeley) has objected to the REQUIREMENT that the code
 be made
     available as Open Source, indicating that his feeling is that investigators
     should have the option to do so and come to an amicable agreement with
     their home institution and funding agencies.  He also supports the dual
     licensing approach.  Here we have no problem with this except if the grant
     was performed with public funds, the public has a right to be able to use
     the results of that funding.  If the funding was private, then the funding
     agency has the right to insist on whatever they consider correct.
       Andrew Dalke has argued that forcing Open Source may in fact harm the
     scientific process in the following ways:
     - it will decrease the heterogeneity and quality of research by preventing
       researchers from taking advantage of more advanced proprietary software
       or databases. Since proprietary code is often better maintained and
       readable, requiring OSS is a serious detriment to good research.
     - relatedly, it will harm those doing current research with proprietary
     - source code is not required to validate an algorithm or computational
       approach as long as it is well-described in a publication and therefore
       may in fact decrease the quality of publication and research.
     - even if source code is made available, there is so much variability in
       hardware, compilers, libraries and non-deterministic variables
       (especially in network operations) that source code will not help that
       much anyway.
     - much of academic source code is so poorly written that it's not worth
       looking at anyway.  It's easier to write from scratch.
     - much current academic software is a conglomeration of bits from so many
       sources that it would be impossible to unravel the ownership and
       enforce distribution under a particular license.
     - seeing the source code will 'taint' researchers and decrease innovation
       by encouraging tunnel vision. 'The way that was is the only way.'  Also,
       easy access to source code will lead to lawsuits over re-implementations
       (at what point does re-implementation/reverse engineering meld with
       copyright infringement?)
     - making source code available without redistribution rights (you can view,
       modify, and use the source code but you can't redistribute the source
       code), addresses all valid concerns.  Why go further?
     - the definition of public funding is fuzzy. Who decides what proportion of
       public funding triggers your requirement?
     - if your petition succeeds, who will verify that recipients are complying
       with its requirements?  And how?  A law without teeth hardly better than
       law at all.
     - even supposedly OSS can come with such silly or onerous requirements that
       it effectively ceases to be Open Source (required notifications, pages of
       required header comments or attribution, etc).
     - why Open Source?  Why not require release of such software into the
       Public Domain such as many government agencies already do?
     - changing the 'funding ecology' this drastically will hurt science.  We
       should take more time adn smaller steps.
     - the goverment already has too much influence on our lives; this is yet
       another potentially intrusive and onerous requirement to do research.
       [Andrew - what did I miss?]
       While there has been no official statement on this from any of the
     federal funding agencies, many have unofficially been enthusiastic about
     making more more research software Open Source.
 Q   How can I add resources to the site?
 A   If you have an Open Source resource, or a resource that's useful
     for developers of Open Source software (such as a WWW site or an
     article), then you can add it to the list of resources
     ( You must
     first register as a user
     ( If
     you've already signed the petition, you are already registered.
 Q's currently without A's
 Q:  What are some of the downsides of this petition if it succeeds?
 Q:  What about existing software that has multiple sources including some that
     are non-OSS? For example, SW that includes commercial libraries (Rogue
     Wave's 'tools.h', Numerical Recipe's implementation of standard algorithms?)
 Q:  If it succeeds, who will oversee that the requirements are met?   Who will
     ensure that groups so funded do in fact make their source code available?
 Q:  Does this require that certain coding standards are met?  Who ensures that
     the code is readable and not the result of running it through an obfuscator?
 Q:  Does the Scientific method really require making the source code available?
     Aren't there other ways to verify an algorithm or claim?
 Q:  I'm funded by a variety of grants, some public, some private.  What is the
     percentage cutoff for the definition of 'Public Funding'?
 Q:  I'm currently funded by a private foundation that has no such OSS
     requirement, but I want to publich in a reputable journal.  Will this
     petition reflect badly on my NOT publishing the Source Code?
 Q:  What if my research currently is based on or depends on Proprietary
     software which cannot be made Open Source?
 Q:  I'm currently using OSS for my project but the license under which it is
     distributed is incompatible with other (also acceptable) OSS licenses.  How
     will this be resolved?
 Q:  Which Open Source license do you require?  I don't like that one.  Why don't
     you use ___________, which is much more intelligently phrased and
     acceptable to all clear-thinking people?
 Q:  Why Open Source as opposed to Source Code Availability ('Source Under
     Glass') where I will will allow you to view and modify the source code but
     not redistribute it?  Wouldn't this enable people to evaluate the code to
     the extent required for scientific validation without the overbearing
     requirement for Open Source release?
 Q:  Why not require something like a Government 'SourceForge' an 'active
     repository' of publicly funded codes?
 Q:  Will such software be OSS in perpetuity or will it 'lapse' to Public Domain
     in X years?  Define and justify X.
 Cheers, Harry
 Harry J Mangalam  --  (949) 856 2847 (v&f)  --  mangalam |-at-|
 hjmangalam |-at-|, harrymangalam |-at-| (if  |-at-| home
 service ends)
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