[Open Babel] RE: Open source contributions by pharma.

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[Open Babel] RE: Open source contributions by pharma.

Peter Spiro-2
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      
OELib       OpenEye, others      Matt Stahl          open source      http://www.eyesopen.com/products/toolkits/oelib.html
JME         Novartis             Peter Ertl          free             http://www.molinspiration.com/jme/
tpsa.c      Novartis             Ertl et al.         open source      http://www.daylight.com/meetings/emug00/Ertl/  
NEWLEAD     Novartis             Vincenzo Tschinko   free         
Moloc       Roche                Paul Gerber         fee (non-academics) http://www.moloc.ch
MMFF94      Merck                Thomas Halgren      free             http://ccl.net/cca/data/MMFF94/
Pgchem::tigress Bayer            Ernst-Georg Schmid                   http://pgfoundry.org/projects/pgchem/
OpenBabel   Merck (provided financial support)       open source      http://sourceforge.net/mailarchive/forum.php?thread_id=8125020&forum_id=3042
PyMOL       Delano Scientific    Warren DeLano       open source      http://pymol.sourceforge.net/
various java programs ChemAxon, others               open source      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
- 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: '[hidden email]'; '[hidden email]'; '[hidden email]'; '[hidden email]'
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?




Peter Spiro

Renovis, Inc.


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