NONMEM Users Network Archive

Hosted by Cognigen

Re: Proposal to built an interface for SADAPT

From: Nick Holford <n.holford>
Date: Tue, 24 Mar 2009 20:49:14 +0200

Bob,

Thanks for letting me know that NPEM/NPAG are parallelised. I know you
told me about that a meeting some years ago and I am afraid I had
forgotten it. I guess I just had'nt heard of anybody doing it to remind
me. My ignorance I am afraid.

As for Phoenix -- I look forward to seeing it and using it. But at
present it remains off the horizon...

Nick


Bob Leary wrote:
> Nick,
> S-ADAPT is not the only parallel NLME system currently available or on
> the near term horizon.
> Pharsight currently has a pharmacometric NLME system ("Phoenix") under
> late stage development that is multithreaded (see PAGE abstract 979,
> Leary and Dunlavey, "Parallel Processing for Nonlinear MIxed effects
> Modeling", 2006) The parallelization is over the subjects, so the
> computations required to find the log likelihood contribution of each
> subject during an evaluation of the population log likelihood can be
> performed on separate threads (and hence separate processors). The
> threads communicate via the MPI (message passing interface) library
> (the de facto standard for distributed memory parallelization as for
> example, in a cluster, although it works equally well for shared
> memory systems such as current generation dual and quad processor chips. )
> Under the right cirucumstances (large numbers of subjects Nsub
> >>Nprocessors, with
> reasonably balanced data per subject ), the parallel speedup can be a
> fairly large fraction of Nprocessors. It has both a GUI for model
> building and expression, as well as a text based modeling language
> that is similar in expressiveness and functionality to NMTRAN,
> although quite a bit different in syntax.
> Also, the NPEM and NPAG nonparametric software from Roger Jelliffe's
> LAPK lab has long been
> parallelized vis MPI and successfully run on a huge variety of
> parallel shared and distributed memory systems.
> Bob Leary
> ------------------------------------------------------------------------
> *From:* owner-nmusers
> *Sent:* Sun 3/22/2009 4:04 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)
> >
> >
> > ------------------------------------------------------------------------
> > 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
>

--
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 Tue Mar 24 2009 - 14:49:14 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.