NONMEM Users Network Archive

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Re: NONMEM 7 Update

From: Nick Holford <n.holford>
Date: Sat, 04 Jul 2009 20:01:22 +0200

Hi,

I think some interesting issues have been raised about Icon's plan to
distribute encrypted source code. I would like to ask what does this really hide
and how can it benefit Icon and the user community?

First -- what is being hidden?

1. The 'old' estimation methods (METHOD=ZERO, METHOD=CONDITIONAL) with
their various options such as LAPLACE were revealed to previous licensees
of NONMEM. As far as I can tell these 'old' methods, in NONMEM7, function
very similarly to earlier versions but have been just been tweaked with some
changes in convergence options (NSIG, SIGL).

2. The 'new' ITS and MCPEM methods presumably came from the S-ADAPT package
(developed by Bob Bauer) whose licensing agreement says "No part of the sofware
may be repackaged into a non open-source version, and no part of the software
may be sold for profit.". It remains to be seen how these new methods will help
users but I am hopeful that incorporating these methods will give us new
opportunities to improve the science.

3. I cannot be sure about the origins of the NONMEM SAEM method in
Monolix but the SAEM code in Monolix is distributed under a Free Software
license agreement and it seems likely that this has been helpful for the NONMEM
implentation. I am hopeful that the pioneering efforts of the Monolix team will
benefit NONMEM users.

Thus the core methods of NONMEM, both old and new, are already available
to others who may want to compete with Icon so I wonder what the
encrypted source will really hide?

It is clear that the IMSL source code cannot be distributed to users
because that is the contract that Icon have with IMSL. Would it be
possible to distribute the licensed NONMEM source code with object code
libraries for the IMSL routines?

Serge asked " How many people took advantage from the fact Nonmem was
distributed as open source?". Under the earlier NONMEM license I was able to
make modifications to the code to fix minor problems with compilers, improve
the output formatting and compute interesting things like the determinant of the
information matrix. These changes could be made without understanding the whole
NONMEM system and no doubt others like me without formal training in fortran or
statistical software development were also able to personalise things.

After the major recoding effort of NONMEM into a modern fortran dialect
(thanks to Icon) it is likely that the code will no longer be
"functionally encrypted" and indeed might be usefully extended by others
developing new methods in this area. So even if only a few people have
been able to take advantage of the source code for NONMEM in the past it
is more likely that in the future more people will be able to contribute
to its development. Furthermore, inability to access the source code will also
make it harder for 3rd party developers to help users (e.g. NMQUAL) to fix known
bugs and to create qualified installations using different SIZES.

Second -- How does it aid Icon?
Hiding the source code might reduce the potential user base and thus license
fees for Icon because statistical algorithm development has frequently had its
roots outside of proprietary implementations. As Thierry pointed out (comparing
S-Plus with R) isn't there a risk that hiding NONMEM will encourage others to
develop an competing alternative?

Once again I want to congratulate Bob, Tom and Alison for their efforts
to modernize NONMEM and prepare us for a new and more powerful tool. But
hiding the source code seems against the community spirit of nmusers who give
freely of their experiences and expertise and the advantages, if any, to Icon
remain obscure.

Best wishes,

Nick

--
Nick Holford, Professor Clinical Pharmacology
Dept Pharmacology & Clinical Pharmacology
University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand
n.holford
mobile: +33 64 271-6369 (Apr 6-Jul 20 2009)
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Received on Sat Jul 04 2009 - 14:01:22 EDT

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