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			[[Category:Software]]
			[[Category:Free]]

Frodo at 23:27, 10 March 2014

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	A number of you asked to see the final list. Below is the list of		A number of you asked to see the final list. Below is the list of
	software, followed by a summary of people's comments.		software, followed by a summary of people's comments.
			<pre>
	Application Contributing Company Author Availability		Application Contributing Company Author Availability
	URL		URL
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	<http://www.chemaxon.com/forum/ftopic193.html>		<http://www.chemaxon.com/forum/ftopic193.html>
	http://www.chemaxon.com/forum/ftopic193.html		http://www.chemaxon.com/forum/ftopic193.html
			</pre>

	Programs available for a "nominal" fee from the Quantum Chemistry		Programs available for a "nominal" fee from the Quantum Chemistry

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2012-10-08T20:31:13Z

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JohnIrwin at 19:03, 27 September 2007

2007-09-27T19:03:35Z

New page

Many thanks to those who sent examples of software contributed by
pharma, and for the many thoughtful comments on the issue.

A number of you asked to see the final list. Below is the list of
software, followed by a summary of people's comments.

Application Contributing Company Author Availability
URL
RasMol GlaxoWellcome Roger Sayle open source
<http://www.umass.edu/microbio/rasmol/index2.htm>
http://www.umass.edu/microbio/rasmol/index2.htm
OELib OpenEye, others Matt Stahl open source
<http://www.eyesopen.com/products/toolkits/oelib.html>
http://www.eyesopen.com/products/toolkits/oelib.html
JME Novartis Peter Ertl free
<http://www.molinspiration.com/jme/> http://www.molinspiration.com/jme/
tpsa.c Novartis Ertl et al. open source
<http://www.daylight.com/meetings/emug00/Ertl/>
http://www.daylight.com/meetings/emug00/Ertl/ NEWLEAD Novartis Vincenzo Tschinko free
<http://www.ccl.net/cca/software/SGI/newlead/README.shtml>
http://www.ccl.net/cca/software/SGI/newlead/README.shtml
Moloc Roche Paul Gerber fee (non-academics)
<http://www.moloc.ch> http://www.moloc.ch
MMFF94 Merck Thomas Halgren free
<http://ccl.net/cca/data/MMFF94/> http://ccl.net/cca/data/MMFF94/
Pgchem::tigress Bayer Ernst-Georg Schmid
<http://pgfoundry.org/projects/pgchem/>
http://pgfoundry.org/projects/pgchem/
OpenBabel Merck (provided financial support) open source
<http://sourceforge.net/mailarchive/forum.php?thread_id=8125020&forum_id
=3042>
http://sourceforge.net/mailarchive/forum.php?thread_id=8125020&forum_id=
3042
PyMOL Delano Scientific Warren DeLano open source
<http://pymol.sourceforge.net/> http://pymol.sourceforge.net/
various java programs ChemAxon, others open source
<http://www.chemaxon.com/forum/ftopic193.html>
http://www.chemaxon.com/forum/ftopic193.html

Programs available for a "nominal" fee from the Quantum Chemistry
Program Exchange ( http://qcpe.chem.indiana.edu), contributed form the
1970s through 2000s. Source code for 20 or so programs reportedly were
contributed by industry. PRODIS Abbott Low-Energy Conformations of Flexible Molecules MOLSV Merck Molecular Volume and Surface Area Calculation RNGCFM Merck Exploration of Medium-Size Ring Conformations BIGSTRN-3 Merck General-Purpose Empirical Force-Field Program SEA Merck Steric and Electrostatic Alignment Molecular
Superposition Program SEAL Merck An Alternate Method for the Alignment of
Molecular Structures SAMPLS Merck Sample Distance Partial Least Squares Program
("used to develop a structure-activity relationship (SAR) for any single
response (i.e., biological activity), based on the "distance" between
samples (e.g., chemical compounds) in a training set.") NEWLEAD Novartis Generation of Candidte Structures DGEOM DuPont,Chiron Distance Geomerty Program ("DGEOM is a distance
geometry program for molecular model-building, receptor modeling,
conformational analysis, and NMR solution structure determination") MOLAREA Lilly Calculation of the Surface Area of a
Non-Spherical Molecule or Molecular Cavity in a Fluid from the Van der
Waals Radii of Component Atoms USURF Upjohn Generation of Smooth Molecular Dot Surfaces TRIBL DuPont (no longer available) A Complete Molecular Modeling
Software System
It was also noted that:
- Many SPL scripts for Sybyl were developed/contributed by people in
industry. These may not be "open source" in the usual sense, but SPL
lends itself to reuse/translation into other languages.
- Pharma has also provided significant contributions to bioinformatics
open source projects.

To summarize (and plagiarize) people's comments:

Benefits of contributing to open source:

- External improvements on contributed code -- if the code remains
in-house, no external review or improvement is possible. This "piling
on" effect is significant.
- Control over product development -- does a particular software project
meet your needs? Contribution to open software allows you to better
address specific issues and target your projects.
- Benefits from external maintenance -- if you maintain your own
internal version, you will be constantly trying to keep up with the
external official version.
- Good publicity in the community, possible tax write-off benefits for
charitable contributions.
- Improved return on investment of resources: - Increased benefit to the company when code is contributed to the
community, since the company has use of the code, whether left in-house
or donated. Thus others' contributions add value. - It's easier to let an external group enhance and maintain it.
- Open source fixes bugs better than commercial vendors, so presumably
better than in-house code too. - Continuity: Very often the code is associated with an individual. - Maintenance can be continued when the developer leaves, benefitting
the originating company.
- This also benefits the developer, who can continue to use and
develop the code afterwards.
Possible concerns:

- reputation (the code could be seen to reflect on the company)
- liability
- maintenance (this is impossible to guarantee)
- distribution - it is not always easy to find a site where the material
can be mounted.
- license (supporting Open source might be seen to be undermining their
commercial vendors)
- loss of IP

Counter-arguments:

- Reputation: - The flip side is free advertising.
- Contributions can always come from an isolated individual rather
than being publicly blessed by the company. (However, initial software
development is often done on company time, so belongs to the company.) - Liability: - The open source license itself restricts liability -- because the
program is licensed free of charge, no warranty is express or implied. - A code repository could be established where it was made it clear
that there was no further implied commitment and that donation was
accepted as a final act. - Maintenance and distribution is handled by existing frameworks (i.e.,
the project you're contributing to). - License: If a commercial software vendor is concerned about being
undermined by an open source solution, then they have not made their
case to clients. A commercial solution should provide a clear advantage
over an open source solution. - IP: - Contributing software is no different from publishing scientific
papers describing syntheses and new techniques, which pharma does all
the time. - There's very little IP "loss" in open source contributions. You or
your company retains the original copyright. You can still sell
commercial versions of that code. - Many projects, while quite useful, don't make much use of
proprietary knowledge, so the value of the protected IP would likely not
be high.

-----Original Message-----
From: Peter Spiro Sent: Monday, September 26, 2005 8:15 PM
To: 'OpenBabel-discuss@lists.sourceforge.net';
'chminf-l@listserv.indiana.edu'; 'chemistry@server.ccl.net';
'qsar_society@accelrys.com'
Subject: Open source contributions by pharma.

Hello all,

Does anyone know examples of free or open source scientific software
contributed by pharmaceutical companies?

I ask because I'd like to contribute to certain open source projects,
which my co-workers would be more comfortable with if they knew it was
an acceptable practice in the pharma industry. (After all, the
industry's livelihood depends on protecting IP, so giving something away
can seem a bit strange to some, though they do understand the benefits
of open source.)

Examples I know of directly from pharma are RasMol (GlaxoWellcome), JME
molecular editor (Peter Ertl, Novartis; free though not open source),
and Ertl et al.'s polar surface area code. Other open source examples I
know of from cheminformatics companies include OELib and PyMOL.

Are there others?

Thanks!

Peter Spiro

Renovis, Inc.

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Open Source by Pharma - Revision history

Frodo at 23:28, 10 March 2014

Frodo at 23:27, 10 March 2014

Therese: 1 revision

JohnIrwin at 19:03, 27 September 2007