RE: New versus old NONMEM

________________________________ From: [email protected] [[email protected]] On Behalf Of Rik Schoemaker [[email protected]] Sent: 27 October 2010 09:11 To: [email protected] Subject: RE: [NMusers] New versus old NONMEM Dear Koen, IMHO NONMEM VII is a far superior product to NONMEM VI even if you forget about all the new estimation methods. To mention some highlights: I find convergence properties for FOCE are more stable than in NM6, error recovery is much improved and there are some pretty nifty features like still being able to obtain your covariance step even if your required number of significant digits may not have been reached entirely. There's automatic calculation of conditional weighted residuals and the new ADVAN13 differential equation solver which is truly a huge step forward. I wouldn't dream of going back to NONMEM VI. Good luck, Rik Schoemaker, PhD Exprimo NV Web: http://www.exprimo.com ________________________________ From: [email protected] [mailto:[email protected]] On Behalf Of Nick Holford Sent: 26 October 2010 9:28 PM To: [email protected] Subject: Re: [NMusers] New versus old NONMEM Koen, You cannot 'buy' NONMEM like you can buy a beer :-) You must buy a license for NONMEM. This allows you to use NONMEM 7 and earlier versions of NONMEM. You cannot just license NONMEM VI by itself. If you have not previously licensed NONMEM VI then I think you will only get NONMEM 7 files if you buy a license today. I expect Icon would be willing to send you NONMEM VI files if you asked nicely :-) Nick Sebastien, WFN can be used to tell NONMEM to create the table files required by Xpose. Saik Urien has created a set of 'R for NONMEM' scripts which do many useful things with NONMEM output. They can be used with standard NONMEM output but also work conveniently with the way WFN arranges NONMEM output in a sub-directory (see http://wfn.sourceforge.net/RFN-900-20090920.zip). Best wishes, Nick On 27/10/2010 2:12 a.m., Sebastien Bihorel wrote: 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. On 27/10/2010 12:32 a.m., 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]> [mailto:[email protected]<mailto:[email protected]>] On Behalf Of Jurgen Bulitta Sent: zaterdag 23 oktober 2010 23:30 To: 'Nick Holford'; [email protected]<mailto:[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]> [mailto:[email protected]<mailto:[email protected]>] On Behalf Of Nick Holford Sent: Saturday, October 23, 2010 2:32 AM To: [email protected]<mailto:[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 Information in this email and any attachments is confidential and intended solely for the use of the individual(s) to whom it is addressed or otherwise directed. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the Company. Finally, the recipient should check this email and any attachments for the presence of viruses. The Company accepts no liability for any damage caused by any virus transmitted by this email. All SGS services are rendered in accordance with the applicable SGS conditions of service available on request and accessible at http://www.sgs.com/terms_and_conditions.htm -- Nick Holford, Professor Clinical Pharmacology Dept Pharmacology & Clinical Pharmacology University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53 email: [email protected]<mailto:[email protected]> http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford Information in this email and any attachments is confidential and intended solely for the use of the individual(s) to whom it is addressed or otherwise directed. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the Company. Finally, the recipient should check this email and any attachments for the presence of viruses. The Company accepts no liability for any damage caused by any virus transmitted by this email. All SGS services are rendered in accordance with the applicable SGS conditions of service available on request and accessible at http://www.sgs.com/terms_and_conditions.htm