[NMusers] Career Opportunities at Metrum Research Group, LLC
*Research Scientist / Senior Scientist / Principal Scientist *Tariffville, CT or Wellesley, MA* Metrum Research Group is seeking enthusiastic and motivated Scientists, at any level of experience, to join our team at the Tariffville, CT headquarters, or Boston-area office. At MetrumRG, you will participate in the research, development, and application of quantitative data analysis methods in biomedical sciences through collaborations with both academia and the pharma/biotech industry. MetrumRG provides a full benefits package and salary is competitive. Professional development is supported. Primary responsibilities: - Modeling and simulation to support drug development decision-making - Consultation and technical guidance for clients - Preparation of reports and presentation of results to clients, at conferences, and in peer-reviewed journals - Participation in both internal and external training opportunities You will also be expected to develop your own research interests, present and publish results, and expand your scientific knowledge and skills through professional development opportunities. Qualifications: - Post-graduate degree in pharmacometrics, statistics, bioengineering, mathematics, or other related quantitative sciences, or relevant work experience - Excellent written and verbal communication skills - Strong work ethic and ability to contribute in a team-based environment - Prior experience in applying modeling and simulation tools such as NONMEM, Monolix, ADAPT, and BUGS to quantitative decision making - Experience programming/statistical tools such as SPLUS, R, MatLab, or SAS - Experience with Bayesian data analysis is highly desirable Metrum Research Group, established in 2004, is a global leader in biomedical modeling and simulation. We have provided strategic decision making for more than 100 companies on over 250 projects. At Metrum Research Group we support our clients in advancing drug development programs by supplying them with the highest quality scientific expertise. Please send resume and a brief cover letter in the body of an email. We prefer to hear directly from candidates. No recruiters please. Apply to: employm...@metrumrg.com Metrum Research Group is an equal opportunity employer. -- ** *Bill Knebel, PharmD, PhD* *President* *Strategic Modeling and Simulation* *Metrum Research Group LLC* *2 Tunxis Road, Suite 112* *Tariffville**, CT 06081* *O: 860.735.7043* *C: 860.930.1370* *F: 860.760.6014*
Re: [NMusers] setup of parallel processing and supporting software - help wanted
Pavel, For a complete solution to modeling and simulation you should take a look at our Metworx Performance product. It is a cloud based solution that allows the user to interface with a high performance computing system via a web browser. The system includes NONMEM (7.2 and 7.3), gfortran or Intel fortran, RStudio, R, Stan (MCMC analysis), PiranaJS, PsN, and grid scheduler. Parallel computing via PiranaJS, PsN, or via the metrumrg R package is supported. The system utilizes encrypted disks in Amazon Web Services cloud and all communications to and from the cloud is over encrypted channels. The cluster will autoscale (grow and shrink automatically) to meet the requirements of an analysis. In addition, the user has the ability to develop and deploy Shiny applications via the Metworx Envision product. More information can be found at the address below: http://metrumrg.com/metworx.html Regards, Bill On Tue, Dec 8, 2015 at 4:54 PM, Pavel Belo wrote: > Hello The Team, > > We hear different opinions about effectiveness of parallel processing with > NONMEM from very helpful to less helpful. It can be task dependent. How > useful is it in phase 3 for basic and covariate models, as well as for > bootstrapping? > > We reached a non-exploratory (production) point when popPK is on a > critical path and sophisticated but slow home-made utilities may be > insufficient. Are there efficient/quick companies/institutions, > which setup parallel processing, supporting software and, possibly, some > other utilities (cloud computing, ...)? A group which used to helped us > a while ago disappeared somewhere... > > Thanks, > Pavel > -- ** *Bill Knebel, PharmD, PhD* *Principal Scientist II* Group Leader, Pharmacology M&S *Metrum Research Group LLC* *2 Tunxis Road, Suite 112* *Tariffville**, CT 06081* *O: 860.735.7043* *C: 860.930.1370* *F: 860.760.6014*
Re: [NMusers] how to output the NONMEM TAD
Janet, You could start by viewing some free courses we have posted to YouTube. The link is below. https://www.youtube.com/user/metruminst Regards, Bill On Mon, Jun 23, 2014 at 1:23 PM, Janet Mifsud wrote: > Dear NMUSERs > > we have just starting using NMEM for some clinical data, learning as we go > alone - but we really need some introductory basic handson experience - > does anyone know of any basic NMEM courses being held in Europe this year > or alternatively would anyone be able to host a couple of our students for > a couple of weeks, working alongside someone who is working on NM? > > thanks > > Janet > > > Prof Janet Mifsud > Department of Clinical Pharmacology and Therapeutics > University of Malta Msida MSD2040 Malta > Tel +356 2340 2582/2845 Fax +356 21320271 > -- ** *Bill Knebel, PharmD, PhD* *Principal Scientist II* *Metrum Research Group LLC* *2 Tunxis Road, Suite 112* *Tariffville**, CT 06081* *O: 860.735.7043* *C: 860.930.1370* *F: 860.760.6014*
Re: [NMusers] Different versions of MPICH2 for NONMEM
Jun, We use mpich2 version 3.0.2 with Ubuntu linux and Intel Fortran version 12 with NONMEM 7.2. You will want to make sure that you are pointing to the correct mpiexec in your NONMEM pnm file. Also, make sure that you replace the libmpich.a in the NONMEM mpi/mpi_lini directory with the version from your lib directory in your mpich2 install. Bill Metrum Research Group On Thu, Jun 27, 2013 at 5:51 PM, Jun Shen wrote: > Hello everyone, > > Just want to get some opinion on the issue of different versions of MPICH2 > to work with NONMEM 7.2. Our Linux cluster already has a MPICH2 in the > latest version 3.0.4. But we haven't been able to make it work with NONMEM > 7.2 and getting the "Exit code: 139" error (see below). Dr. Bauer suggests > we go back to the older version (1.2.1p1) that comes with NONMEM CD. Our > engineer is still working on it and it seems it would be much easier for us > if we can make NONMEM work with the new version of MPICH2. Just wonder if > anyone has made any newer version of MPICH2 work with NONMEM. Appreciate > any comment. > > Thanks > > Jun Shen, > Vertex Pharmaceuticals > > > === > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > = EXIT CODE: 139 > > = CLEANING UP REMAINING PROCESSES > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > > === > > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault > (signal 11) > > This typically refers to a problem with your application. > > Please see the FAQ page for debugging suggestions > >
Re: [NMusers] RE: Where to download the Linux installation file of NONMEM7
Fengbo, You might want to give NMqual a try. It is a freely available NONMEM installer that we (Metrum Research Group) distributes. You will need to famaliarize yourself with the options in the config file but we use it to handle NONMEM install on Ubuntu using intel fortran or gfortran. It can be downloaded from the link below: http://code.google.com/p/nmqual/ There is a wiki page at that location as well that demonstrates how to use it. Regards, Bill Bill Knebel, PharmD, PhD Principal Scientist II Metrum Research Group LLC 2 Tunxis Road, Suite 112 Tariffville, CT 06081 O: 860.735.7043 (tel:860.735.7043) C: 860.930.1370 (tel:860.930.1370) F: 860.760.6014 (tel:860.760.6014) On Wednesday, March 20, 2013 at 11:34 AM, Bauer, Robert wrote: > At present we do not have an easy install system for Linux, because of the > inconsistent environment. You will need to install from the CD. > > Robert J. Bauer, Ph.D. > Vice President, Pharmacometrics, R&D > ICON Development Solutions > 7740 Milestone Parkway > Suite 150 > Hanover, MD 21076 > Tel: (215) 616-6428 > Mob: (925) 286-0769 > Email: robert.ba...@iconplc.com (mailto:robert.ba...@iconplc.com) > Web: www.iconplc.com (http://www.iconplc.com/) > > > From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On > Behalf Of Xie, Fengbo [MEDCN] > Sent: Wednesday, March 20, 2013 4:08 AM > To: nmusers@globomaxnm.com (mailto:nmusers@globomaxnm.com) > Subject: [NMusers] Where to download the Linux installation file of NONMEM7 > > Dear NM users, > I’d like to install NONMEM 7 on Ubuntu, where can I download the installation > files? > There seems no such files on the ICON’s FTP site. > Thanks in advance. > > Xie, Fengbo PhD > Modeling and Simulation Specialist, Clinical Pharmacology > Janssen R&D > 6F, Tower 2, China Central Place No.79 Jian Guo Road,Chao Yang District, > Beijing, China 100025 > Tel: +86 (0) 10-5952-3243 > Email: fx...@its.jnj.com (mailto:fx...@its.jnj.com) > > > ICON plc made the following annotations. > -- > This e-mail transmission may contain confidential or legally privileged > information that is intended only for the individual or entity named in the > e-mail address. If you are not the intended recipient, you are hereby > notified that any disclosure, copying, distribution, or reliance upon the > contents of this e-mail is strictly prohibited. If you have received this > e-mail transmission in error, please reply to the sender, so that ICON plc > can arrange for proper delivery, and then please delete the message. Thank > You, ICON plc South County Business Park Leopardstown Dublin 18 Ireland > Registered number: 145835 > >
Re: [NMusers] MPI on linux Exit status=1
Nick, There is also a run#.log file that shows the parallelization as it occurs. You can verify that the running is working as expected by looking at the file and seeing that parts of the data are being sent out to the nodes and back. We also use SGE with linux for parallel runs and have not had any major issues. Bill Bill Knebel, PharmD, PhD Principal Scientist II Metrum Research Group LLC 2 Tunxis Road, Suite 112 Tariffville, CT 06081 O: 860.735.7043 (tel:860.735.7043) C: 860.930.1370 (tel:860.930.1370) F: 860.760.6014 (tel:860.760.6014) On Friday, September 28, 2012 at 7:41 AM, Elassaiss - Schaap, J (Jeroen) wrote: > Hi Nick, > > We have a working nm7 parallel setup using MPI on linux over our SGE cluster. > Based on your e-mail I found a match somewhere in the SGE stdout capture: > > CREATING MUMODEL ROUTINE... > Recompiling certain components > > USING PARALLEL PROFILE mpihydra.pnm > MPI TRANSFER TYPE SELECTED > Exit status = 1 > IN MPI > Starting MPI version of nonmem execution ... > > And thereafter I had a decent parallel run. Does the system create > subdirectories for each worker etc in your situation? > You might also want to look for this kind of statement in nonmem's report: > #PARA: PARAFILE=mpihydra.pnm, PROTOCOL=MPI, NODES= 16 > > Hope this helps, > Jeroen > > J. Elassaiss-Schaap Senior Principal Scientist Phone: + 31 412 66 9320 > MSD | PK, PD and Drug Metabolism | Clinical PK-PD Mail stop KR 4406 | PO Box > 20, 5340 BH Oss, NL > > > > -Original Message- > From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On > Behalf Of Nick Holford > Sent: Friday, September 28, 2012 10:25 > To: nmusers > Subject: [NMusers] MPI on linux Exit status=1 > > Hi, > > I'm trying to help our local grid computing guys to get NONMEM running > with MPI on a Linux based grid. > > We have NONMEM running with a pnm file asking for 8 nodes but the actual > run time is 10% longer than with a regular 'transfer' run. The only clue > I can see to the problem is the "Exit status=1" after the "MPI TRANSFER > TYPE SELECTED" message. The NONMEM runs appears to execute OK except for > no evidence that MPI is operating. Can anybody tell me if this exit > status is normal under Linux? If not what might it mean? > > Nick > > Recompiling certain components > > USING PARALLEL PROFILE wfn_mpi8.pnm > MPI TRANSFER TYPE SELECTED > Exit status = 1 > IN MPI > Starting MPI version of nonmem execution ... > > -- > Nick Holford, Professor Clinical Pharmacology > Dept Pharmacology & Clinical Pharmacology, Bldg 503 Room 302A > 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: n.holf...@auckland.ac.nz (mailto:n.holf...@auckland.ac.nz) > http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford > > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. > >
Re: [NMusers] Error files when using multicore runs and psn ==> Fatal Error: Record SIZES is not valid
Pascal, That error looks like a PSN error rather than NONMEM. I can confirm that for NM7.2 the $SIZES record must be the first record of the control stream. You might try bypassing PSN if possible and I bet you will not get that error. Bill Bill Knebel, PharmD, PhD Principal Scientist II Metrum Research Group LLC 2 Tunxis Road, Suite 112 Tariffville, CT 06081 O: 860.735.7043 C: 860.930.1370 F: 860.760.6014 On Thursday, July 12, 2012 at 11:09 AM, pascal.gir...@merckgroup.com wrote: > Hi Nastia, > > I tried your trick which would have broken the first table law rule "The > first NM-TRAN control record must be a $PROBLEM record" and put $SIZES as > very first record and got following error: > > >_read_problems: First non-comment line in modelfile run.mod is not a $PROB > >record. NONMEM syntax violation. > > So the first table law rule still resists or you may have a different NONMEM > version. :-) > > I also checked the bug list > ftp://nonmem.iconplc.com/Public/nonmem720/nm720_bug_list.pdf , but nothing is > mentioned. > > Anyway, thanks for the suggestion! > > Kind regards > > Pascal > > > > > From:"Kassir Nastya" (mailto:nastya.kas...@umontreal.ca)> > To: (mailto:pascal.gir...@merckgroup.com)>, "Bauer, Robert" > mailto:robert.ba...@iconplc.com)> > Date:12/07/2012 16:13 > Subject:RE: [NMusers] Error files when using multicore runs and psn > ==> Fatal Error: Record SIZES is not valid > > > > Hi Pascal, > > $SIZES goes at the begginning of your control stream, before $PROB. > > I hope it helps. > > Best regards, > > Nastya > > > Nastya Kassir, Pharm.D. > > Senior Scientist > > Pharsight Consulting Services(tm) > A division of Certara(tm) > Email: nkas...@pharsight.com (mailto:nkas...@pharsight.com) > <mailto:nkas...@pharsight.com> > > Phone: 1 (514) 789-2180 # 2157 > Mobile: 1 (438) 862-0935 > > Fax: (514) 789-2192 > > www.pharsight.com <http://www.pharsight.com/> > > > > > From: owner-nmus...@globomaxnm.com (mailto:owner-nmus...@globomaxnm.com) on > behalf of pascal.gir...@merckgroup.com (mailto:pascal.gir...@merckgroup.com) > Sent: Thu 7/12/2012 09:21 > To: Bauer, Robert > Cc: nmusers@globomaxnm.com (mailto:nmusers@globomaxnm.com); > "olaf.lichtenber...@merckgroup.com > (mailto:olaf.lichtenber...@merckgroup.com)"@merck.de; > "orestis.papasoulio...@merckgroup.com > (mailto:orestis.papasoulio...@merckgroup.com)"@merck.de; > owner-nmus...@globomaxnm.com (mailto:owner-nmus...@globomaxnm.com) > Subject: RE: [NMusers] Error files when using multicore runs and psn ==> > Fatal Error: Record SIZES is not valid > > > Hi Robert, > > Thanks for your quick reply. Unfortunately, I could not make it work. > > I have 17,000 records. So just after $PROB. I inserted your suggestion: >$SIZES LIM1 = 2 > and I got the following error : >> Fatal Error: Record SIZES is not valid > > So I tried also the default value for LIM1: >$SIZES LIM1=1 > and also the example given on page 166 of Help guide viii >$SIZES LIM1=3 MAXFCN=200 NO=500 > and always got the "Fatal Error: Record SIZES is not valid" message. > > I looked into Help guide viii (pp 166-167 and 463-464) but did not find any > relevant information how to set $SIZES. What would be your suggestion? > > Thanks again for your help, because it's highly frustrating not being able to > use the multi-cores when you have such long runs. > > Kind regards > > Pascal Girard, PhD > pascal.gir...@merckgroup.com (mailto:pascal.gir...@merckgroup.com) > Head of Modeling & Simulation - Oncology > Global Exploratory Medicine > Merck Serono S.A. · Geneva > Tel: +41.22.414.3549 > Cell: +41.79.508.7898 > > > > > From:"Bauer, Robert" (mailto:robert.ba...@iconplc.com)> > To:"pascal.gir...@merckgroup.com > (mailto:pascal.gir...@merckgroup.com)" (mailto:pascal.gir...@merckgroup.com)>, "nmusers@globomaxnm.com > (mailto:nmusers@globomaxnm.com)" (mailto:nmusers@globomaxnm.com)> > Cc:"orestis.papasoulio...@merckgroup.com > (mailto:orestis.papasoulio...@merckgroup.com)" > (mailto:orestis.papasoulio...@merckgroup.com)&g
Re: [NMusers] CycleCloud BigScience Challenge giving away ~8-hours on 30000 core cluster for research
David, Some limited benchmarking results are listed at the bottom of this email. It is also important to remember that there are ways that cloud-computing helps beyond parallel NONMEM. Cloud-computing allows on demand, user specific, clusters that can grow and shrink depending on user requirements. This allows for rapid completion of large bootstrap processes (500 - 1000 jobs) in the time it takes to run one, non-parallel job. Users can also evaluate model variants simultaneously with cluster size being increased or decreased as needed. Users do not have to worry about competing for resources (compute cores) with other users because cloud-computing clusters are user and/or project specific. The performance gains are evident in parallel NONMEM jobs and single modeling projects, but it is important to look beyond the simple benefits of individual job/project speed-up and more towards the impact of cloud-computing on the entire portfolio of modeling and simulation projects in a given group or company. Bill Model 1 - ADVAN6, 1000 subjects, dual linear and non-linear elimination CoresRuntime (hr) 1 80.7 8 16.8 16 8.9 24 6.2 48 3.8 96 2.5 Model 2 - ADVAN6 - 70 subjects, PKPD model Cores Runtime (hr) 1 4 hr 8 1.1 16 0.66 24 0.4 48 0.31 cores = number of compute cores (value of "NODES=" argument in NONMEM pmn file) On Nov 9, 2011, at 9:28 PM, David Foster wrote: > I agree with Julia, > > Thanks for this Bill, but quantitative benchmarking would be very much > appreciated. > > Regards, > > David > > > On 10/11/11 9:55 AM, "Ivashina, Julia" wrote: > > Bill, > > This is nice to hear about the speed improvements for NONMEM you received. > > Could you please describe gains in performance in a qualitative manner with > model examples you used. > I think everyone will benefit from such NONMEM 7.2 benchmarking. > > I posted a similar question in March but not many responded. > > Thanks, > Julia > > -Original Message----- > From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On > Behalf Of Bill Knebel > Sent: Wednesday, November 09, 2011 5:03 PM > To: nmusers@globomaxnm.com > Cc: Jason Stowe; Nick Holford; William Bachman > Subject: Re: [NMusers] CycleCloud BigScience Challenge giving away ~8-hours > on 3 core cluster for research > > Since there seems to be some questions around cloud-based NONMEM, we wanted > to share our experience of utilizing parallel NONMEM in a cloud-based > environment. We use the enterprise-licensed version of NONMEM(R) 7.2. to > perform modeling and simulation, both serial and parallelized, on an AWS > cloud infrastructure. Briefly, we used a combination of recent MPICH2 > libraries, the Sun Grid Engine integrated ORTE parallel environment, and > StarCluster to deploy parallel NONMEM(R) on linux AWS EC2 instances of up to > 100 cores for estimation (which appears to be the current NONMEM(R) 7.2 limit > for parallel computing), and a virtually unlimited number of cores for > simulation or use of other open-source modeling tools (R, OpenBUGS). The > gains in performance are very real, and probably the best we've experienced > on any multi-user distributed computing infrastructure. > > Bill > > > Bill Knebel, PharmD, PhD > Principal Scientist II > > Metrum Research Group LLC > 2 Tunxis Road, Suite 112 > Tariffville, CT 06081 > > O: 860.735.7043 > C: 860.930.1370 > F: 860.760.6014 > > > On Nov 4, 2011, at 3:06 PM, Bachman, William wrote: > > > Cloud computing on a system like this requires an unlimited enterprise > > license for NONMEM. Pricing is available from idssoftw...@iconplc.com. > > > > > > William J. Bachman, Ph.D. > > Director, Pharmacometrics R&D > > Icon Development Solutions > > 6031 University Blvd., Suite 300 > > Ellicott City, MD 21043 > > Office 215-616-8699 > > william.bach...@iconplc.com > > > > > > > > From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On > > Behalf Of Jason Stowe > > Sent: Friday, November 04, 2011 2:12 PM > > To: Nick Holford > > Cc: nmusers@globomaxnm.com > > Subject: Re: [NMusers] CycleCloud BigScience Challenge giving away ~8-hours > > on 3 core cluster for research > > > > Hi Nick, > > On Thu, Nov 3, 2011 at 8:59 AM, Nick Holford > > wrote: > > Jason, > > > > If I was a winner of your competition how would I go about using NONMEM? > > How do you manage NONMEM li
Re: [NMusers] CycleCloud BigScience Challenge giving away ~8-hours on 30000 core cluster for research
Since there seems to be some questions around cloud-based NONMEM, we wanted to share our experience of utilizing parallel NONMEM in a cloud-based environment. We use the enterprise-licensed version of NONMEM(R) 7.2. to perform modeling and simulation, both serial and parallelized, on an AWS cloud infrastructure. Briefly, we used a combination of recent MPICH2 libraries, the Sun Grid Engine integrated ORTE parallel environment, and StarCluster to deploy parallel NONMEM(R) on linux AWS EC2 instances of up to 100 cores for estimation (which appears to be the current NONMEM(R) 7.2 limit for parallel computing), and a virtually unlimited number of cores for simulation or use of other open-source modeling tools (R, OpenBUGS). The gains in performance are very real, and probably the best we’ve experienced on any multi-user distributed computing infrastructure. Bill Bill Knebel, PharmD, PhD Principal Scientist II Metrum Research Group LLC 2 Tunxis Road, Suite 112 Tariffville, CT 06081 O: 860.735.7043 C: 860.930.1370 F: 860.760.6014 On Nov 4, 2011, at 3:06 PM, Bachman, William wrote: > Cloud computing on a system like this requires an unlimited enterprise > license for NONMEM. Pricing is available from idssoftw...@iconplc.com. > > > William J. Bachman, Ph.D. > Director, Pharmacometrics R&D > Icon Development Solutions > 6031 University Blvd., Suite 300 > Ellicott City, MD 21043 > Office 215-616-8699 > william.bach...@iconplc.com > > > > From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On > Behalf Of Jason Stowe > Sent: Friday, November 04, 2011 2:12 PM > To: Nick Holford > Cc: nmusers@globomaxnm.com > Subject: Re: [NMusers] CycleCloud BigScience Challenge giving away ~8-hours > on 3 core cluster for research > > Hi Nick, > On Thu, Nov 3, 2011 at 8:59 AM, Nick Holford wrote: > Jason, > > If I was a winner of your competition how would I go about using NONMEM? > How do you manage NONMEM licensing on you cloud cluster? > What NONMEM license fee would one have to pay for 3 cores? > > Nick > Hi Nick, > Unfortunately, I can't speak to an individuals user's NONMEM license. We do > have commercial clients running NONMEM on CycleCloud clusters at varying > scales. A winner with appropriate licensing doesn't need to run 8 hours on > 30k cores, you could also run for 24 hours on 1 cores, etc. If your > license relates to compilation vs. execution, or if you have a site-wide > license, we can't say, so you'll need to look at your license to deal with > that. > > Perhaps someone from Icon could talk about this kind of non-profit licensing? > > Thanks, > Jason > > > > On 2/11/2011 2:19 p.m., Jason Stowe wrote: > Hi all, > > Long time reader, first time poster. > > Cycle recently announced that we're giving away the equivalent of 8-hrs on a > 3 core CycleCloud HPC cluster for a grand prize winner in the CycleCloud > BigScience Challenge. Up to five finalists will win 4 hours on 3000 core > clusters as well. The Compute time is to benefit academic and non-profit > researchers that are doing science which could benefit humanity. > > Some current applicants are in life sciences and CycleCloud currently > supports reliable/large-scale clusters running NONMEM for Top 5 Pharma, so I > wanted to welcome more researchers in the NONMEM community to enter. > > We describe the challenge and why we're excited about it here: > http://bit.ly/BigScience > > The application process is simply answering 4 questions (takes less than half > an hour): State who you are, what is your research, why it is important, and > how you currently run computation. The applicatiopn is available here: > http://cyclecomputing.com/big-science-challenge/overview > > So far, response has been great, and Inside HPC covered descriptions of some > of the recent applications we've received: > http://insidehpc.com/2011/10/27/24209/ > http://blog.cyclecomputing.com/ > > Submissions are due by November 7th, so submit early and we hope to help some > of you get some BigScience done quickly. > > Best, > Jason > > -- > > > == > Jason A. Stowe > cell: 607.227.9686 > main: 888.292.5320 > > http://twitter.com/jasonastowe/ > http://twitter.com/cyclecomputing/ > > Cycle Computing, LLC > Leader in Open Compute Solutions for Clouds, Servers, and Desktops > Enterprise Condor Support and Management Tools > > http://www.cyclecomputing.com > http://www.cyclecloud.com > > > -- > Nick Holford, Professor Clinical Pharmacology > Dept Pharmacology& C
[NMusers] Position at Metrum Research Group
Opening for a Data Programmer Metrum Research Group is seeking a full-time data programmer to support our biomedical modeling and simulation services. This is an excellent opportunity to develop as a data programmer while gaining exposure to cutting edge problems in the growing field of pharmacometrics. The individual will work as an integral member of our team, based in Tariffville, CT. We provide a full benefits package and salary is competitive. Professional development is supported. Primary responsibilities: * Data set preparation and data quality control. * Exploratory data analysis. * Optimization and automation of data flow processes. * Code review. * Depending on experience level, responsibilities may also include the development of model fitting and/or simulation code. Qualifications: * Bachelor's degree required, Master's degree preferred. * Experience involving code management and/or data management and/or data analysis is required. * Proficiency with the R (or S+) language is highly desirable. Experience with other high-level languages for scripting and/or data analysis (e.g. Matlab, Python, Perl) is desirable. * Experience with code versioning systems (e.g. Subversion) is highly desirable. * Experience with Amazon Web Services and/or parallel computing is desirable. * Excellent communication skills are required. * Excellent attention to detail is required. Metrum Research Group is a leading provider of biomedical modeling and simulation services in the U.S.A. and internationally. Founded in 2004, Metrum Research Group has worked with over 85 clients on more than 250 projects. Our experience spans R&D efforts for small molecule pharmaceuticals, biologic therapeutics, diagnostics, and medical device/drug-device combinations, across multiple therapeutic areas. Please send resume to employm...@metrumrg.com, including a brief cover letter in the body of the email. We prefer to hear directly from candidates. No recruiters please.
[NMusers] Position at Metrum Research Group
Opening for a Data Programmer Metrum Research Group is seeking a full-time data programmer to support our biomedical modeling and simulation services. This is an excellent opportunity to develop as a data programmer while gaining exposure to cutting edge problems in the growing field of pharmacometrics. The individual will work as an integral member of our team, based in Tariffville, CT. We provide a full benefits package and salary is competitive. Professional development is supported. Primary responsibilities: * Data set preparation and data quality control. * Exploratory data analysis. * Optimization and automation of data flow processes. * Code review. * Depending on experience level, responsibilities may also include the development of model fitting and/or simulation code. Qualifications: * Bachelor's degree required, Master's degree preferred. * Experience involving code management and/or data management and/or data analysis is required. * Proficiency with the R (or S+) language is highly desirable. Experience with other high-level languages for scripting and/or data analysis (e.g. Matlab, Python, Perl) is desirable. * Experience with code versioning systems (e.g. Subversion) is highly desirable. * Experience with Amazon Web Services and/or parallel computing is desirable. * Excellent communication skills are required. * Excellent attention to detail is required. Metrum Research Group is a leading provider of biomedical modeling and simulation services in the U.S.A. and internationally. Founded in 2004, Metrum Research Group has worked with over 85 clients on more than 250 projects. Our experience spans R&D efforts for small molecule pharmaceuticals, biologic therapeutics, diagnostics, and medical device/drug-device combinations, across multiple therapeutic areas. Please send resume to employm...@metrumrg.com, including a brief cover letter in the body of the email. We prefer to hear directly from candidates. No recruiters please.
Re: [NMusers] Question Re Calling nmfe7 from R
Shelley, You may want to consider the R package (MIfuns), developed and released by Metrum Institute. It is available on CRAN (R package repository) and via googlecode (http://code.google.com/p/mifuns/). Using this package along with the free NONMEM installer (NMQual), also available via googlecode (http://code.google.com/p/nmqual/) , will allow you to call nonmem from R and also provides a complete set of R functions for performing analyses, preparing data sets, generating and analyzing bootstraps, and generating post analyses tables and figures. It is more than just running NONMEM from R so you will likely find it helpful in the other aspects of data prep and modeling I just mentioned. Regards, Bill On May 4, 2011, at 11:50 AM, Xiao Hu wrote: > > Dear NONMEM users, > > I recently have NONMEM 7.1.0 upgraded to 7.1.2, which only worked in Intel > Fortran compiler, but not in DOS. > > When I tried to call nmfe7 from R, it apparently called DOS command and > failed to run. Is there a way to link nmfe7 to Intel, instead of DOS? I've > been waiting for an answer for my IT rep for two weeks and am wondering if I > can get some guidance from our discussion group. > > Best regards, > Shelley > > > Xiao Hu (Shelley), Ph.D. > Senior Scientist, > Clinical Pharmacology and Pharmacometrics > Biogen Idec, Inc. > 14 Cambridge Center > Cambridge, MA 02142
