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

From: Eugene Leitl <[email-masked]>
Date: Tue, 4 Dec 2001 23:34:25 +0100 (MET)

---------- Forwarded message ----------
Date: Tue, 04 Dec 2001 13:51:37 -0800
From: Harry Mangalam <[email-masked]>
To: [email-masked]
Cc: Andrew Dalke <[email-masked]>
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
    published.

  - 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:
    http://www.opensource.org
    Free Software (in its capitalized form anyway) is software that is
    distributed under the Free Software Foundation's General Public License
    (http://www.gnu.org/copyleft/gpl.html), 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: [ http://www.ucop.edu/ott/bayh.html ]
    a generally supportive series of articles from Columbia University (one of
    the largest beneficiaries of the Law):
    [ http://www.columbia.edu/cu/21stC/issue-3.1 ],
    as well as an extremely harsh criticism of the Law:
    [ http://www.alternet.org/story.html?StoryID=9290 ], and a critical
    piece in the Atlantic describing the implications and history of it:
    [ http://www.theatlantic.com/issues/2000/03/press.htm ]

    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
    publication.

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
      software.
    - 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 no
      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
    (http://www.openinformatics.org/dsp_ResListing.php). You must
    first register as a user
    (http://www.openinformatics.org/frm_EditUserAccount.php). 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)  --  [email-masked] (primary)
[email-masked], [email-masked] (if @home service ends)
                    <<plain text appreciated>>
_______________________________________________
bioinformatics mailing list
[email-masked]
http://labs.oreilly.com/mailman/listinfo/bioinformatics