Re: Proposal to built an interface for SADAPT

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:* [email protected] on behalf of Nick Holford > *Sent:* Sun 3/22/2009 4:04 AM > *To:* [email protected] > *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 > > [email protected] tel:+64(9)923-6730 fax:+64(9)373-7090 > 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 [email protected] tel:+64(9)923-6730 fax:+64(9)373-7090 http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford