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Published on: June 10, 2021
Piraña and PCluster: a modeling environment and cluster infrastructure for NONMEM
Ron J Keizer1, Michel van Benten, Jos H Beijnen
1Department of Pharmacy & Pharmacology, The Netherlands Cancer Institute/Slotervaart Hospital, Amsterdam, The Netherlands. ronkeizer@gmail.com
Piraña and PCluster software streamline complex pharmacokinetic-pharmacodynamic modeling with NONMEM. These tools enhance workflow efficiency and enable distributed computing for computationally intensive tasks.
Area of Science:
- Pharmacometrics
- Computational Biology
- Data Science
Background:
- Pharmacokinetic-pharmacodynamic (PK/PD) modeling using non-linear mixed effects modeling (NONMEM) is essential but challenging due to its command-line interface.
- Efficient management of datasets, model files, and results is crucial for complex PK/PD analyses.
- Computational demands of NONMEM modeling necessitate efficient workload distribution.
Purpose of the Study:
- To introduce Piraña, a graphical user interface (GUI) that simplifies NONMEM modeling.
- To present PCluster, a platform for distributing NONMEM modeling workloads to computer clusters.
- To enhance the efficiency and accessibility of PK/PD modeling for both novice and advanced users.
Main Methods:
- Development of Piraña GUI providing comprehensive features for NONMEM model management, execution, and reporting.
- Implementation of PCluster, a scalable platform utilizing a Perl-based daemon for job distribution across network nodes.
- Integration of Piraña and PCluster for seamless access to distributed computing resources via SSH protocol.
- Support for the Perl speaks NONMEM (PsN) toolkit within the PCluster environment.
Main Results:
- Piraña offers a user-friendly environment for NONMEM, improving workflow efficiency.
- PCluster facilitates workload distribution to Linux clusters (SGE, MOSIX), alleviating computational burdens.
- The integrated Piraña and PCluster system has been extensively tested on a large academic network.
- Both software solutions are available under an open-source license.
Conclusions:
- Piraña and PCluster significantly enhance the usability and efficiency of NONMEM-based PK/PD modeling.
- These open-source tools democratize access to advanced computational modeling techniques.
- The developed software provides a robust solution for managing and executing complex modeling tasks on distributed systems.
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