Bioperl: UCSF Discussion, Public V. Private Genome Efforts
BobbyO
BobbyO@cgl.ucsf.EDU
Thu, 21 Jan 1999 17:15:55 -0800
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Hi Richard,
I enjoyed talking with you over lunch & after your UCSF seminar.
Like yourself,
I am quite concerned about the potential damage to scientific progress
from private
sequencing/annotation/patents at the genomic scale. Intellectual
property law which safeguards investment and rewards
risk is an essential protection for creativity and innovation. This
morality behind this logic does not extend to the use of publicly
developed tools which allow rapid legal-rights mining on genomic data,
and subsequent long-term loss of incentive for labor-intensive
biological and medical research.
As mentioned, I believe that an effort to leverage mass-sequencing
firms' obligate dependence
on publicly funded, academically created tools, could be used to insure
both fair use and reasnable profit
from genomic data. For example, I believe that informatics software
including Phred, Phrap, BLAST,
MOST, and SAM are all supported by public funds. Without these tools,
the assembly of contigs, the functional or homological annotation of
genes, and their associated patents would be quite difficult to achieve.
A license attached to these tools which restricted their use in
producing patentable results, would bring much force to the academics'
requests at the information-exchange bargaining table.
Legal tools which protect fair use and open distribution of
software have been pioneered for some time, and provide a ready model
for developing a license for publicly funded bioinformatics software.
For example, the widely-known GNU copyleft is a document which need
merely be attached to the sourcecode of any program to insure that
software's free & open-code distribution forever. Any further
distribution of that sofware is then legally required to include
sourcecode, credit to all authors, etc. Using this model, a document
(the Open Academic Sofware Use License, OASUL) could be devised which,
when attached to scientific software, provided desirable restrictions or
bargaining rights for the authors on commercial use of the software. Key
points here are:
0) Proceed quickly, with completion of this effort within months, as
the 2-year timeframe for significant completion of private human genome
sequencing efforts is very short.
1) Develop a OASUL license-document which guarantees academics'
rights on commercial
use of their software. This license must be publicly and widely
available, legally sound, and activated simply by
attaching the license to the software before distribuiting it.
2) Request a mandate from one or more major funding sources that the
OASUL license be attached to sofware developed
with public funds.
Also useful would be:
3) Allow optional appendices to the OASUL which, on attachment to
the software below the primary OASUL document, would remit certain
rights for each software tool to be remanded by proxy to academic
negotiating groups such as the NIH, International Human Genome Project
Board of directors, or relevant University System housing the software
developers' laboratories.
4) A version of the license which applies to bioinformatics
algorithms, in addition to software, which are
coverable by US &/ international intellectual property law.
5) Crafting of these licenses such that they obligately guarantee
free distribution & use of software for any non-profit use.
As a student, my voice & position are below the notice of leaders
who could apply these ideas for the benefit of our
community. If yours is not, and you still agree with this proposition
now that it is more carefully stated, then I hope this letter is of use.
Thank you for your time and consideration,
Bobby Otillar
UCSF
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<html>
Hi Richard,
<br> I enjoyed talking with you over lunch & after
your UCSF seminar. Like yourself,
<br>I am quite concerned about the potential damage to scientific progress
from private
<br>sequencing/annotation/patents at the genomic scale. Intellectual property
law which safeguards investment and rewards
<br>risk is an essential protection for creativity and innovation.
This morality behind this logic does not extend to the use of publicly
developed tools which allow rapid legal-rights mining on genomic data,
and subsequent long-term loss of incentive for labor-intensive biological
and medical research.
<br> As mentioned, I believe that an effort to leverage
mass-sequencing firms' obligate dependence
<br>on publicly funded, academically created tools, could be used to insure
both fair use and reasnable profit
<br>from genomic data. For example, I believe that informatics software
including Phred, Phrap, BLAST,
<br>MOST, and SAM are all supported by public funds. Without these tools,
the assembly of contigs, the functional or homological annotation of genes,
and their associated patents would be quite difficult to achieve. A license
attached to these tools which restricted their use in producing patentable
results, would bring much force to the academics' requests at the information-exchange
bargaining table.
<br> Legal tools which protect fair
use and open distribution of software have been pioneered for some time,
and provide a ready model for developing a license for publicly funded
bioinformatics software. For example, the widely-known <a href="http://www.fsf.org/copyleft/copyleft.html">GNU
copyleft</a> is a document which need merely be attached to the sourcecode
of any program to insure that software's free & open-code distribution
forever. Any further distribution of that sofware is then legally required
to include sourcecode, credit to all authors, etc. Using this model, a
document (the Open Academic Sofware Use License, OASUL) could be devised
which, when attached to scientific software, provided desirable restrictions
or bargaining rights for the authors on commercial use of the software.
Key points here are:
<br> 0) Proceed quickly, with completion of this effort
within months, as the 2-year timeframe for significant completion of private
human genome sequencing efforts is very short.
<br> 1) Develop a OASUL license-document which guarantees
academics' rights on commercial
<br>use of their software. This license must be publicly and widely available,
legally sound, and activated simply by
<br>attaching the license to the software before distribuiting it.
<br> 2) Request a mandate from one or more major funding
sources that the OASUL license be attached to sofware developed
<br>with public funds.
<br>Also useful would be:
<br> 3) Allow optional appendices to the OASUL which,
on attachment to the software below the primary OASUL document, would remit
certain rights for each software tool to be remanded by proxy to academic
negotiating groups such as the NIH, International Human Genome Project
Board of directors, or relevant University System housing the software
developers' laboratories.
<br> 4) A version of the license which applies to bioinformatics
algorithms, in addition to software, which are
<br>coverable by US &/ international intellectual property law.
<br> 5) Crafting of these licenses such that they obligately
guarantee free distribution & use of software for any non-profit use.
<p> As a student, my voice & position are below the
notice of leaders who could apply these ideas for the benefit of our
<br>community. If yours is not, and you still agree with this proposition
now that it is more carefully stated, then I hope this letter is of use.
<p> Thank you for your time and consideration,
<p> Bobby Otillar
<br> UCSF
<p>
<p> </html>
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