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[Open Babel] Open source contributions by pharma.

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[Open Babel] Open source contributions by pharma.

Peter Spiro-2

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

peter murray-rust
[reply to OpenBabel only...]
At 04:14 27/09/2005, Peter Spiro wrote:

>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.)

This is a generous offer and I welcome it. I have some experience
having spent many years in Glaxo, including the time when Roger Sayle
was developing and RasMol. As far as I remember there was no
resistance to distribution, though the lack of license turned out to
be a problem.  When I left Glaxo they formally allowed me to take
some of the software I had written and some of this has found its way
into various Open contributions.

>
>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.

As announced on this list we have been grateful fro sponsorship from
Merck (UK) for Nick England (student) to add stereochemistry to OB
over the summer.  Although this is slightly different it is a useful
mechanism for creating Open code.

I suspect that companies may be less concerned about IP and more
concerned with:
- 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)

Very often the code is associated with an individual ...

I wonder whether there is a role for a repository (on sourceforge)
where contributions could be made where it is clear that the donor
made it clear that there was no further implied commitment and that
donation was accepted as a final act. I suspect that the author and
their organisation would need to be explicit (for license purposes).

P.

>
>

Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069



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

Geoffrey Hutchison
In reply to this post by Peter Spiro-2

On Sep 26, 2005, at 11:14 PM, Peter Spiro wrote:
> 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.)

There are many industries which protect their IP. I'd ask a different  
question. Does the pharma industry publish scientific papers  
describing syntheses and new techniques? Yes, of course. They're  
publishing implementations of their work. I do not see this as any  
different than software contributions.

I can think of many pharma contributions to computational modeling  
too. Merck opened the entire MMFF94 validation suite:
http://ccl.net/cca/data/ff_evaluation_suite/
http://ccl.net/cca/data/MMFF94/
http://ccl.net/cca/data/MMFF94s

Pharma has also provided significant contributions to bioinformatics  
open source projects. Among the benefits:
* Good publicity in the community, possible tax write-off benefits  
for charitable contributions.
* Benefits from external maintenance -- if you maintain your own  
internal version, you will be constantly trying to keep up with the  
external official version. (I've been there before and it's  
definitely much better to get code contributed to the "mainline"  
version.)
* 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.

I think many of us would be interested in a summary of responses to  
your request.

Replying to Peter:
> I suspect that companies may be less concerned about IP and more  
> concerned with:
> - 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)

Remember that most open source donations to existing projects are one-
time deals. Many, many OB contributors add one bit of code and  
disappear. The open source license itself restricts liability --  
because the program is licensed free of charge, no warranty is  
express or implied. Maintenance and distribution is handled by  
existing frameworks (i.e., the project you're contributing to). And  
of course if a company is worried about negative reputation (vs. free  
advertising), contributions can always come from an isolated  
individual rather than being publicly blessed by the company.

That leaves a commercial vendor vs. open source support. Honestly, if  
a commercial software vendor is concerned about being undermined by  
an open source solution, then they have not made their case to  
clients. If a commercial software product costs X dollars, as an  
academic with a budget or a pharma company (or whoever), I expect  
some ROI on that money. If someone is charging me money when a  
suitable free (cost) product is available, there had better be an  
excellent reason for the commercial solution.

Cheers,
-Geoff


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

peter murray-rust
At 16:44 27/09/2005, Geoffrey Hutchison wrote:

>Replying to Peter:

==PeterMR - I goofed elsewhere because I misread "Peter"

>>I suspect that companies may be less concerned about IP and more
>>concerned with:
>>- 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)
>
>Remember that most open source donations to existing projects are
>one- time deals. Many, many OB contributors add one bit of code and
>disappear. The open source license itself restricts liability --
>because the program is licensed free of charge, no warranty is
>express or implied. Maintenance and distribution is handled by
>existing frameworks (i.e., the project you're contributing to). And
>of course if a company is worried about negative reputation (vs. free
>advertising), contributions can always come from an isolated
>individual rather than being publicly blessed by the company.
>
>That leaves a commercial vendor vs. open source support. Honestly, if
>a commercial software vendor is concerned about being undermined by
>an open source solution, then they have not made their case to
>clients. If a commercial software product costs X dollars, as an
>academic with a budget or a pharma company (or whoever), I expect
>some ROI on that money. If someone is charging me money when a
>suitable free (cost) product is available, there had better be an
>excellent reason for the commercial solution.

These are really straw men - my point was not that I believe these
but that *pharma companies* might. Maybe they are unimportant - if
so, fine. If not, then we need to continue to argue against them.

P.


Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069



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