NONMEM Users Network Archive

Hosted by Cognigen

Re: Proposal to built an interface for SADAPT

From: Nick Holford <n.holford>
Date: Sun, 22 Mar 2009 10:04:12 +0200

Serge,

Thank you for your offer to put time and energy into making S-ADAPT more
usable. I have had limited experience with S-ADAPT but the nightmarish
complexity of having to write multiple subroutines in different files
and special data sets to describe covariates made me give up. I was
assisted by someone with quite a lot of S-ADAPT experience but after
some months of effort we could not get what seemed to me to be a simple
model to work. The same model and covariate structure was easily
expressed using NM-TRAN for NONMEM.

I was epecially interested in using S-ADAPT because of its support for
parallel thread execution on multiple CPU/core systems. Run times for
complex problems are my biggest difficulty at the moment. Among mixed
effect modelling programs only S-ADAPT supports parallel execution and
as far as I know the other main programs are still stuck with a single
threaded programming model for the forseeable future.

My suggestion would be to work on creating a scripting language similar
to NM-TRAN that allows the user to specify the data, the parameters and
the model in a SINGLE text file script. In principle this text based
script would allow a smart programmer like yourself to write all the
subroutines and create the special data sets just like NM-TRAN does for
NONMEM users.

If S-ADAPT had a coherent and integrated text based script then this
would make it far more usable to people like me who cannot afford to
spend weeks developing the code and data for just the base model. If
necesssary developers could write GUI front ends to hold the hands of
beginners who are not comfortable with writing the full script.

In the long run it should be possible to create a common mixed effect
modelling language that would be independent of the backend estimation
program. MLX-TRAN for Monolix has made some progress in that direction.
The NLME consortium (http://www.nlme.org/) has proposed in some detail
the steps needed to do this and there is strong interest in persuing
this idea.

Best wishes,

Nick

Serge Guzy wrote:
>
> Dear colleagues
>
> POP-PHARM would like to know if there would be interest from the
> Pharmacometric community in the potential development of a
> user-friendly interface that would facilitate the model building in
> SADAPT.
>
> The template interface would be the program I developed with its
> interface (Iconus) (PDX-MC-PEM) and automatic scripting that would
> built a model template which would include for examples automatic code
> for population mixture, interoccasion and covariate analysis (assuming
> log-linear regression for example). Simple questions would be answered
> by the user and he would have the option to either run the analysis
> with my program or be connected to the SADAPT engine that is usually
> more powerful and gives all the outputs that are usually needed (like
> standard errors, post-hoc etc…)
>
> This project can become reality if the Population community is
> interested and would be available free of charge.
>
> This will become reality once I am getting enough interest from the
> community in building this kind of facilitator.
>
> I would appreciate if anybody interested could give me some feedback
> with also desire features they would like to have implemented.
>
> As you know, we have planned a SADAPT workshop on April 14-15 (
> http://www.mosaicnj.org/2009/02/21/s-adapt-intermediate-workshop ) and
> anybody coming to the workshop could ask me at that time any questions
> about this new potential project. If you need more information about
> the upcoming SADAPT workshop, please visit
> http://www.mosaicnj.org/2009/02/21/s-adapt-intermediate-workshop to
> access to both the agenda and registration.
>
> Best Regards;
>
> Serge Guzy; Ph.D
>
> President, CEO; POP-PHARM; Inc;
>
> cel (510 542 76 48)
>
>
> ------------------------------------------------------------------------
> The information contained in this email message may contain
> confidential or legally privileged information and is intended solely
> for the use of the named recipient(s). No confidentiality or privilege
> is waived or lost by any transmission error. If the reader of this
> message is not the intended recipient, please immediately delete the
> e-mail and all copies of it from your system, destroy any hard copies
> of it and notify the sender either by telephone or return e-mail. Any
> direct or indirect use, disclosure, distribution, printing, or copying
> of any part of this message is prohibited. Any views expressed in this
> message are those of the individual sender, except where the message
> states otherwise and the sender is authorized to state them to be the
> views of XOMA.

--
Nick Holford, Dept Pharmacology & Clinical Pharmacology
University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand
n.holford
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Received on Sun Mar 22 2009 - 04:04:12 EDT

The NONMEM Users Network is maintained by ICON plc. Requests to subscribe to the network should be sent to: nmusers-request@iconplc.com.

Once subscribed, you may contribute to the discussion by emailing: nmusers@globomaxnm.com.