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
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 http://www.ccl.net/cca/software/SGI/newlead/README.shtml
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.
- reputation (the code could be seen to reflect on the company)
- 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
- 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.)
- 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.
- 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.
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