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RE: Proposal to built an interface for SADAPT

From: Serge Guzy <GUZY>
Date: Sun, 22 Mar 2009 18:09:52 -0700

Dear Nick
Thanks for your useful comments and proposals. I think that there a few
steps to be done sequentially in order to reach your goal. Obviously I
do not have the skills to create this kind of translator but I wanted
first to minimize the need to write all these SADAPT subroutines but
only a few that match more with what you are doing when using NONMEM.
Since my intention is to provide this kind of facilitator free of
charge, it is not easy for me to find support in going beyond the basic
idea and create what you suggested. If I can get support for that
project, then I can help a lot in making that happening.
About you not succeeding with a basic problem with SADAPT, it is too bad
you did not ask for my help. I am 100% sure I can fix the code and
getting the results you would expect with SADAPT. If you have still this
problem ready to be tried (dataset and model file), then I would be
happy to take a look and sending you the fixed code with the results.
I think that SADAPT offers more than just parallel processing
capability.
SADAPT has the advantage to work interactively while NONMEM itself still
stays more a kind of batch program. You start your problem, you look at
the results and stop whenever you want, make the changes based on what
you saw and then continue. You have the option to learn during your
exploratory analysis and finally getting optimal results.
Another advantage is the use of scripting code that are an integral part
of SADAPT and allow you to run in a batch mode many different problems
one after the other. For example, you can perform a covariate analysis
starting with the full model and then write a simple script that will
emulate the backward covariate deletion method. All the outputs are
stored automatically and you just have to compare all the log-likelihood
to decide who the remaining covariate parameters are.
My understanding about NONMEM 7 is that NONMEM 7 will not have the
interactive capability like SADAPT, neither the scripting advantage
SADAPT has. Many new methods we (Bob Bauer and I) implemented in the
last 8 years will be available but not scripting and interactive
capability. I think also that the SADAPT offers an integrator engine
that is more powerful than the NONMEM one.
What is missing with SADAPT is a way to help the user writing the model
file and that is what I wanted to concentrate on. The back end of SADAPT
is I think very good as all the outputs files are automatically created
from which you could use other programs if necessary to have optimal
diagnostic tools.
Anybody that want help with first time SADAPT problem solving, I will be
happy to assist free of charge and making their first problem working.
In addition, we provide many workshops at a very cheap price where all
the features of SADAPT are taught. Step by step examples from basic to
advanced problems can be grabbed from my site (just ask me) and you can
learn either by your self or through workshops how to use optimally
SADAPT.
Best Regards;
Serge Guzy;
President, POP-PHARM; Inc;


-----Original Message-----
From: owner-nmusers
On Behalf Of Nick Holford
Sent: Sunday, March 22, 2009 1:04 AM
To: nmusers
Subject: Re: [NMusers] Proposal to built an interface for SADAPT

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)
>
>
>
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--
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


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Received on Sun Mar 22 2009 - 21:09:52 EDT

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