Dear Koen,
Depending on what type of work you want those add-ons to do (run
manager, graphing, reporting, etc...), different options are available
to you.
There a couple of free software packages that offer very nice wrapper
functions around NONMEM (for VPC, bootstrapping, simulation and more), e.g.:
- Wings for NONMEM developed by Nick Holford,
- Perl-speaks-NONMEM developed by many people at Uppsala (currently
maintained by Kajsa Harling)
With respect to pre- and post-run graphing tools, PsN is usually
associated with Xpose (also from the Uppsala group), which is a
collection of R packages designed to produce a whole variety of graphs
from PsN inputs and outputs. I am not sure how easy it is to interface
Wings with Xpose... Nick Holford can certainly comment on this point. I
know that some people have developed some post-processing scripts from
Wings outputs but I don't know about their public availability.
There are most likely other free tools out there, but I mostly familiar
with the Wings and Psn/Xpose. Google will give you the links to Wings,
PsN and Xpose websites.
Alternatively, some companies have developed complete interfaces to
integrate NONMEM in some sort of GUI. Most of them include a code
editor, run manager, and graphing tools. I will let those companies
present their products.
Sebastien
Jolling, Koen (Wavre) wrote:
Dear Nick and Juergen,
Thank you for our input.
So if I understood correctly, it seems that the best choice is either
NONMEM VI release 2 or wait for NONMEM 8. Would it still be possible
to buy NONMEM VI release 2?
Also interesting to know would be what the most useful add-ons are to
be use with NONMEM. Could some indicate?
Thanks,
Koen
------------------------------------------------------------------------
*From:* [email protected]
[mailto:[email protected]] *On Behalf Of *Jurgen Bulitta
*Sent:* zaterdag 23 oktober 2010 23:30
*To:* 'Nick Holford'; [email protected]
*Subject:* RE: [NMusers] New versus old NONMEM
Dear Koen,
I agree with Nick that I cannot see any good reason to use NONMEM V
anymore
for a new project. The FOCE+I algorithm in NONMEM VI was in several
cases a lot
more stable than FOCE+I (with the SLOW option) in NONMEM V.
However, if FOCE+I in NONMEM V ran fine, the results I got during
re-analysis of the same
datasets in NONMEM VI were either "identical" or very similar to the
results in NONMEM V.
I ran such a comparison over around 5-10 datasets and this was on
different compilers,
CPUs, and operating systems. Some complex models ran however more
robust in
NONMEM VI than in NONMEM V.
The Uppsala group probably has more experience on this than anybody
else, since they
used NONMEM VI beta for several years in parallel to NONMEM V, as far
as I know.
NONMEM VII of course offers you a series of EM-type algorithms that
are not
available in NONMEM VI and that do not require an approximation to the
likelihood
equation. If you are not in a hurry, you might wait for NONMEM VIII
which will offer
significant benefits for parallelization, for example.
I would select the operating system according to the recommendations
of NONMEM VIII,
since installing a parallelized version will probably be a bit more
tricky. I guess ICON
will support Win 2003 / 2008 Server 64 bit and a couple of
distributions of Linux and
it would be great to hear from our colleagues at ICON about this.
Please take care to
use a 64 bit OS to be able to use more than 3 GB of RAM.
Hope this helps.
Best wishes
Juergen
*From:* [email protected]
[mailto:[email protected]] *On Behalf Of *Nick Holford
*Sent:* Saturday, October 23, 2010 2:32 AM
*To:* [email protected]
*Subject:* Re: [NMusers] New versus old NONMEM
Koen,
What are the advantages of NONMEM7 with respect to older versions like
V and VI?
Automatic computation of eta and epsilon shrinkage.
The default objective function display format is easier for humans to
read (this can easily be implemented in NONMEM VI by changing the
source code).
Is it still "acceptable" to use versions V and VI nowadays?
I consider NONMEM V is obsolete and people still using it either are
using an unlicensed version or have terrible IT support.
NONMEM VI release 2 is the most reliable version. There are bugs in
NONMEM 7 that are not present in NONMEM VI (e.g. see recent email from
Paulo Denti).
In my experience NONMEM VI is generally faster and uses less memory
than NONMEM 7 which is a big advantage on multi-core machines. I can
only run 3 problems with NONMEM 7at the same time but I can run 8
problems with NONMEM VI on the same 8 core machine. The next version
of NONMEM 7 is expected to fix this memory problem but it remains to
be seen if it faster.
Is there an "optimal" combination of NONMEM, compiler and operating
system?
The fastest compiler I know of is Intel Visual Fortran for both NONMEM
VI and NONMEM 7. There are occasionally differences in results between
compilers but I don't know of any systemic study that would favour one
compiler over another in terms of accuracy and consistency of results.
I am not aware that the OS makes any difference to the way that NONMEM
runs if the same compiler and hardware are used. Some virtual machine
hosts may be slow down runs e.g. I find that intensive disk activity
e.g. creating simulation table files with Windows 2003 running as a
virtual machine on top of Xen server is much slower than a native
Windows 2003 installation.
The main thing is to use the fastest CPU you can find!
Nick
On 23/10/2010 4:00 a.m., Jolling, Koen (Wavre) wrote:
Dear,
I would greatly appreciate your opinion on the following questions:
What are the advantages of NONMEM7 with respect to older versions like
V and VI?
Is it still "acceptable" to use versions V and VI nowadays?
Is there an "optimal" combination of NONMEM, compiler and operating
system?
Thanks,
Koen
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