Piraña and PCluster: a modeling environment and cluster infrastructure for NONMEM

Computer Methods and Programs in Biomedicine
Ron J KeizerAlwin D R Huitema

Abstract

Pharmacokinetic-pharmacodynamic modeling using non-linear mixed effects modeling (NONMEM) is a powerful yet challenging technique, as the software is generally accessed from the command line. A graphical user interface, Piraña, was developed that offers a complete modeling environment for NONMEM, enabling both novice and advanced users to increase efficiency of their workflow. Piraña provides features for the management and creation of model files, the overview of modeling results, creation of run reports and handling of datasets and output tables, and the running of custom R scripts on model output. Through the secure shell (SSH) protocol, Piraña can also be used to connect to Linux clusters (SGE, MOSIX) for distribution of workload. Modeling with NONMEM is computationally burdensome, which may be alleviated by distributing runs to computer clusters. A solution to this problem is offered here, called PCluster. This platform is easy to set up, runs in standard network environments, and can be extended with additional nodes if needed. The cluster supports the modeling toolkit Perl speaks NONMEM (PsN), and can include dedicated or non-dedicated PCs. A daemon script, written in Perl, was designed to run in the background on each n...Continue Reading

References

Apr 9, 1999·Computer Methods and Programs in Biomedicine·E N Jonsson, M O Karlsson
Jun 24, 2004·Computer Methods and Programs in Biomedicine·Lars LindbomE Niclas Jonsson
May 19, 2005·Computer Methods and Programs in Biomedicine·Justin J Wilkins
Jul 19, 2005·Computer Methods and Programs in Biomedicine·Lars LindbomNiclas Jonsson
Jan 13, 2006·Journal of Pharmacokinetics and Pharmacodynamics·Chantal Csajka, Davide Verotta

❮ Previous
Next ❯

Citations

Jun 21, 2013·Journal of Pharmacokinetics and Pharmacodynamics·Manuel IbarraHartmut Derendorf
Jul 12, 2013·Journal of Pharmacokinetics and Pharmacodynamics·Dinko RekićUlrika S H Simonsson
Feb 25, 2014·European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences·Paolo DentiNeil H Davies
Nov 16, 2011·Antimicrobial Agents and Chemotherapy·Gudrun WürthweinAndreas H Groll
May 16, 2012·Antimicrobial Agents and Chemotherapy·Thomas P C DorloPeter J de Vries
Jan 22, 2013·Antimicrobial Agents and Chemotherapy·Gudrun WürthweinAndreas H Groll
Jan 11, 2013·Archives of Disease in Childhood. Fetal and Neonatal Edition·Marcel P H van den BroekFloris Groenendaal
Mar 14, 2014·Journal of Pharmacokinetics and Pharmacodynamics·Elin M Svensson, Mats O Karlsson
Jan 21, 2014·The Journal of Infectious Diseases·Thomas P C DorloAlwin D R Huitema
Jul 30, 2014·Journal of Pharmacokinetics and Pharmacodynamics·Manuel IbarraPietro Fagiolino
Mar 7, 2013·Journal of Pharmaceutical Sciences·Muhammad Waqas SadiqMargareta Hammarlund-Udenaes
Sep 17, 2014·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Ahmed Abbas SuleimanUwe Fuhr
Feb 24, 2016·Molecular Pharmaceutics·Annika LindqvistMargareta Hammarlund-Udenaes
Nov 8, 2015·Clinical Gastroenterology and Hepatology : the Official Clinical Practice Journal of the American Gastroenterological Association·Johannan F BrandseGeert R D'Haens
Oct 3, 2012·Computer Methods and Programs in Biomedicine·Timothy T BergsmaMarc R Gastonguay
Nov 30, 2015·Drug Metabolism and Pharmacokinetics·Sebastian FrechenUwe Fuhr
Jul 10, 2013·CPT: Pharmacometrics & Systems Pharmacology·R J KeizerA Hooker
Apr 23, 2013·British Journal of Clinical Pharmacology·J G Coen van HasseltAlwin D R Huitema
Mar 28, 2012·Basic & Clinical Pharmacology & Toxicology·Merja KokkiHannu Kokki
Feb 3, 2012·British Journal of Clinical Pharmacology·Ron J KeizerAlwin D R Huitema
Jun 7, 2013·British Journal of Clinical Pharmacology·Mariam H Abdel JalilJames C McElnay
May 2, 2014·Journal of Clinical Pharmacology·Dorota Tomalik-ScharteUwe Fuhr
Oct 10, 2014·British Journal of Clinical Pharmacology·Richard M HoglundJoel Tarning
Nov 14, 2014·British Journal of Clinical Pharmacology·Huixin YuAlwin D R Huitema
Jun 21, 2014·Clinical Pharmacology and Therapeutics·D GonzalezUNKNOWN Best Pharmaceuticals for Children Act – Pediatric Trials Network Administrative Core Committee

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.