# PML School **URL:** https://forum.certara.com/c/phoenix/certara-forums/pml-school/31.md [Latest](https://forum.certara.com/latest.md) · [Categories](https://forum.certara.com/categories.md) · [Tags](https://forum.certara.com/tags.md) --- ## [About the PML School category](https://forum.certara.com/t/about-the-pml-school-category/4128)
**Author:** [@system](https://forum.certara.com/u/system)\ **Replies:** 0\ **Last updated:** [March 24, 2025, 2:28am UTC](https://forum.certara.com/t/about-the-pml-school-category/4128 "2025-03-24T02:28:54Z")
--- ## [Intro to PML School and Lesson 1 on nonlinear clearance](https://forum.certara.com/t/intro-to-pml-school-and-lesson-1-on-nonlinear-clearance/3042)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 31\ **Last updated:** [July 30, 2024, 9:18am UTC](https://forum.certara.com/t/intro-to-pml-school-and-lesson-1-on-nonlinear-clearance/3042 "2024-07-30T09:18:13Z")
Thanks all for joining the first session of our PML School. Topics covered during this session were: Introduction to PML School Lesson 1: nonlinear clearance (3-compartment model) Here are the materials: presentati… --- ## [How to introduce correlations between random effects?](https://forum.certara.com/t/how-to-introduce-correlations-between-random-effects/3744)
**Author:** [@cryptocurrencysmite](https://forum.certara.com/u/cryptocurrencysmite)\ **Replies:** 0\ **Last updated:** [March 19, 2024, 5:50pm UTC](https://forum.certara.com/t/how-to-introduce-correlations-between-random-effects/3744 "2024-03-19T17:50:16Z")
Can we explore the impact of introducing correlations between random effects in PK/PD modeling on the accuracy of predictions and the understanding of complex drug disposition mechanisms? --- ## [How to introduce correlations between random effects?](https://forum.certara.com/t/how-to-introduce-correlations-between-random-effects/3731)
**Author:** [@linda](https://forum.certara.com/u/linda)\ **Replies:** 3\ **Last updated:** [January 25, 2024, 1:24pm UTC](https://forum.certara.com/t/how-to-introduce-correlations-between-random-effects/3731 "2024-01-25T13:24:45Z")
I am working on a population PK model. If I know that there are two parameters (CL and V) have a strong correlation between each other. How can I code in the PML model structure to fit the correlated coefficient? How to … --- ## [Q&A from Lesson 2: Metabolite Kinetics](https://forum.certara.com/t/q-38-a-from-lesson-2-metabolite-kinetics/3057)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 4\ **Last updated:** [January 9, 2024, 2:52pm UTC](https://forum.certara.com/t/q-38-a-from-lesson-2-metabolite-kinetics/3057 "2024-01-09T14:52:12Z")
QUESTION: Where on the structure tab did you select the M-M elimination? ANSWER: Simply check the “Saturating” box on the structure tab to specify M-M elimination. QUESTION: Can you comment on the error model to use… --- ## [PML code to restrict model coefficients](https://forum.certara.com/t/pml-code-to-restrict-model-coefficients/3724)
**Author:** [@wolowich](https://forum.certara.com/u/wolowich)\ **Replies:** 2\ **Last updated:** [December 16, 2023, 3:34pm UTC](https://forum.certara.com/t/pml-code-to-restrict-model-coefficients/3724 "2023-12-16T15:34:58Z")
I am trying to use the general empirical dynamic model given as equation 3:51 on page 226 of Gabrielsson and Weiner 5th edition. there are several restrictions on model coefficients that need to be coded: 0 \<= alpha\*bet… --- ## [Transit compartment codes](https://forum.certara.com/t/transit-compartment-codes/3582)
**Author:** [@davidq8](https://forum.certara.com/u/davidq8)\ **Replies:** 12\ **Last updated:** [November 20, 2023, 5:46pm UTC](https://forum.certara.com/t/transit-compartment-codes/3582 "2023-11-20T17:46:16Z")
Hi, I am building a population Pk model for an oral drug. The plasma concentration-time curve suggests two compartments for the Structural model. Adding a Tlag function to delay absorption has improved the fit; however, … --- ## [Lesson 6: Target-Mediated Drug Disposition](https://forum.certara.com/t/lesson-6-target-mediated-drug-disposition/3091)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 6\ **Last updated:** [July 20, 2023, 8:23am UTC](https://forum.certara.com/t/lesson-6-target-mediated-drug-disposition/3091 "2023-07-20T08:23:09Z")
Here is the material of the webinar on Target-Mediated Drug Disposition that we presented on Dec 15th: Textual Model file: \[attachment=2886:TMDD.txt\] Slide Deck: \[attachment=2887:PK27 and TMDD mini lecture .pdf\] Lin… --- ## [NonLinear Ka](https://forum.certara.com/t/nonlinear-ka/3673)
**Author:** [@vetpharma](https://forum.certara.com/u/vetpharma)\ **Replies:** 4\ **Last updated:** [March 23, 2023, 2:04pm UTC](https://forum.certara.com/t/nonlinear-ka/3673 "2023-03-23T14:04:19Z")
Hi, I modeling a compound using pop PK which follows a non linear absorption. For dose dependent Ka, could you please confirm if the following syntax is correct? test(){ covariate(Dose) deriv(Aa = - Ka \* Aa) deriv(A… --- ## [How to code fraction excreted for sequential metabolism model](https://forum.certara.com/t/how-to-code-fraction-excreted-for-sequential-metabolism-model/3663)
**Author:** [@tienle](https://forum.certara.com/u/tienle)\ **Replies:** 2\ **Last updated:** [February 21, 2023, 3:46pm UTC](https://forum.certara.com/t/how-to-code-fraction-excreted-for-sequential-metabolism-model/3663 "2023-02-21T15:46:26Z")
Good afternoon, I am trying to build a PopPk model for a drug with its metabolite as a sequential model (parent drug → metabolite 1 → metabolite 2). I am trying to model the fraction excreted in urine compartment and f… --- ## [Modeling Dose-Response-Time data](https://forum.certara.com/t/modeling-dose-response-time-data/3656)
**Author:** [@mercuri](https://forum.certara.com/u/mercuri)\ **Replies:** 6\ **Last updated:** [January 10, 2023, 9:49am UTC](https://forum.certara.com/t/modeling-dose-response-time-data/3656 "2023-01-10T09:49:41Z")
Hello and Happy New Year! I am trying to write a model for describing Dose-Response-Time data of oligonucleotides using PML. I am using the data from Tsimikas et al. 2015 Lancet 386, 1472-1483 and the model described in… --- ## [PML School - Learn how to build custom PK and PK/PD models](https://forum.certara.com/t/pml-school-learn-how-to-build-custom-pk-and-pk-pd-models/3036)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 3\ **Last updated:** [December 19, 2022, 8:28am UTC](https://forum.certara.com/t/pml-school-learn-how-to-build-custom-pk-and-pk-pd-models/3036 "2022-12-19T08:28:58Z")
PML School - Learn how to build custom PK and PK/PD models Phoenix WinNonlin utilize the Pharsight Modeling Language (PML) to encode pharmacokinetic (PK) and pharmacodynamic (PD) models. While most models can be built w… --- ## [Running simulation in command line mode](https://forum.certara.com/t/running-simulation-in-command-line-mode/3611)
**Author:** [@vetpharma](https://forum.certara.com/u/vetpharma)\ **Replies:** 4\ **Last updated:** [June 22, 2022, 9:38pm UTC](https://forum.certara.com/t/running-simulation-in-command-line-mode/3611 "2022-06-22T21:38:55Z")
Hi, I am trying to run simulations from the command line. My final model (.MDL) is a simple one compartment (following) model. I would like to run a simulation with a different dose level from the command line. so I cre… --- ## [Lesson 4: Multiple Absorption Routes via Graphical Model Builder](https://forum.certara.com/t/lesson-4-multiple-absorption-routes-via-graphical-model-builder/3078)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 18\ **Last updated:** [June 2, 2022, 3:13pm UTC](https://forum.certara.com/t/lesson-4-multiple-absorption-routes-via-graphical-model-builder/3078 "2022-06-02T15:13:53Z")
On Nov 17th we have presented an exercise on multiple absorption routes where we used the graphical model builder in Phoenix to setup the model. Here are the materials from this session. Slide deck: \[attachment=2845:P… --- ## [PML for absorption model with 2 first order absorption rate](https://forum.certara.com/t/pml-for-absorption-model-with-2-first-order-absorption-rate/3595)
**Author:** [@davidq8](https://forum.certara.com/u/davidq8)\ **Replies:** 2\ **Last updated:** [March 18, 2022, 5:23pm UTC](https://forum.certara.com/t/pml-for-absorption-model-with-2-first-order-absorption-rate/3595 "2022-03-18T17:23:24Z")
Hi, I am working on a population Pk model focusing on the absorption phase of an oral drug. I found this study with an interesting absorption scenario (please see figure): After oral administration, the drug goes to an … --- ## [The gamma Delay statement](https://forum.certara.com/t/the-gamma-delay-statement/3589)
**Author:** [@davidq8](https://forum.certara.com/u/davidq8)\ **Replies:** 3\ **Last updated:** [March 3, 2022, 11:52am UTC](https://forum.certara.com/t/the-gamma-delay-statement/3589 "2022-03-03T11:52:59Z")
Hi, I am trying to build a population model with the gamma Delay statement to delay the absorption of the drug. I wrote a PML statement using the knowledge from certara phoenix assistance that described this concept. Th… --- ## [Fit TMDD model to total ligand data](https://forum.certara.com/t/fit-tmdd-model-to-total-ligand-data/3528)
**Author:** [@bwakbwak10](https://forum.certara.com/u/bwakbwak10)\ **Replies:** 1\ **Last updated:** [September 10, 2021, 12:41pm UTC](https://forum.certara.com/t/fit-tmdd-model-to-total-ligand-data/3528 "2021-09-10T12:41:05Z")
Hello, I am trying to fit TMDD model for a mAb with nonlinear PK and I used the sample TMDD model code provided by the PML school. I only have the total ligand and total receptor data. The sample full TMDD model code f… --- ## [Lesson 2: Parent and Metabolite Kinetics](https://forum.certara.com/t/lesson-2-parent-and-metabolite-kinetics/3054)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 22\ **Last updated:** [February 18, 2021, 4:29pm UTC](https://forum.certara.com/t/lesson-2-parent-and-metabolite-kinetics/3054 "2021-02-18T16:29:28Z")
Metabolite\_Kinetics\_PK19.txt (741 Bytes)Metabolite\_Kinetics\_Webinar.pdf (743 KB) --- ## [Q&A from Lesson 7: Enterohepatic Recirculation](https://forum.certara.com/t/q-38-a-from-lesson-7-enterohepatic-recirculation/3114)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 7\ **Last updated:** [February 5, 2021, 1:39am UTC](https://forum.certara.com/t/q-38-a-from-lesson-7-enterohepatic-recirculation/3114 "2021-02-05T01:39:43Z")
Question: Are you fixing the time for release from gall bladder? Would this not be a parameter to be estimated? Answer: You are right that we have used a constant value (Ri=10 hours) for the time of release from gall bl… --- ## [PML School Schedules 2016/2017](https://forum.certara.com/t/pml-school-schedules-2016-2017/3503)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 1\ **Last updated:** [August 5, 2020, 1:01pm UTC](https://forum.certara.com/t/pml-school-schedules-2016-2017/3503 "2020-08-05T13:01:16Z")
Nonlinear Clearance October 6, 2016 | 10am EST Presenter: Dan Weiner https://support.certara.com/forums/topic/916-intro-to-pml-school-and-lesson-1-on-nonlinear-clearance/?p=3921 Metabolite Kinetics Simultaneously mo… --- ## [PML School Schedules 2018 onwards](https://forum.certara.com/t/pml-school-schedules-2018-onwards/3355)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 2\ **Last updated:** [August 5, 2020, 8:31am UTC](https://forum.certara.com/t/pml-school-schedules-2018-onwards/3355 "2020-08-05T08:31:14Z")
Introduction to NONMEM-NLME Comparisons - PK 1-compartment IV Bolus Model - FOCE Feb 8, 2018 | 10am EST Presenter: Bernd Wendt https://support.certara.com/forums/topic/1165-nonmem-nlme-comparisons-1-intro-1-compartmen… --- ## [PML codes for a precursor model](https://forum.certara.com/t/pml-codes-for-a-precursor-model/3493)
**Author:** [@mike.liu](https://forum.certara.com/u/mike.liu)\ **Replies:** 3\ **Last updated:** [June 18, 2020, 5:04pm UTC](https://forum.certara.com/t/pml-codes-for-a-precursor-model/3493 "2020-06-18T17:04:13Z")
Hi, I’m working on using Phoenix WinNonlin 8.2 on a PKPD model project. The model scheme is in the attached figure. I used IDR in Phoenix model to work out the part in the red box. To move forward, it seems I need to us… --- ## [Enterohepatic Recycling - clearance problem](https://forum.certara.com/t/enterohepatic-recycling-clearance-problem/3461)
**Author:** [@xiuqinggao](https://forum.certara.com/u/xiuqinggao)\ **Replies:** 2\ **Last updated:** [December 25, 2019, 11:07pm UTC](https://forum.certara.com/t/enterohepatic-recycling-clearance-problem/3461 "2019-12-25T23:07:34Z")
Hi Everyone I am working on a small molecule with enterohepatic recycling on pharmacokientic study after extravascular administration. However, the model fitting and CV% seems good for pharmacokinetic parameters except … --- ## [Which PML syntax does the Procedure block in Phoenix Model's Graphical model mode not support?](https://forum.certara.com/t/which-pml-syntax-does-the-procedure-block-in-phoenix-model-39-s-graphical-model-mode-not-support/3462)
**Author:** [@0521](https://forum.certara.com/u/0521)\ **Replies:** 1\ **Last updated:** [December 20, 2019, 10:22am UTC](https://forum.certara.com/t/which-pml-syntax-does-the-procedure-block-in-phoenix-model-39-s-graphical-model-mode-not-support/3462 "2019-12-20T10:22:52Z")
Hi Support, Which PML syntax does the Procedure block in Phoenix Model’s Graphical model mode not support? I found that the “Sequence” statement and the “delay” function cannot be used in the “Procedure block”. Is it … --- ## [user definition for user defined Tabove in NCA?](https://forum.certara.com/t/user-definition-for-user-defined-tabove-in-nca/3450)
**Author:** [@dan.hines](https://forum.certara.com/u/dan.hines)\ **Replies:** 3\ **Last updated:** [November 13, 2019, 5:52pm UTC](https://forum.certara.com/t/user-definition-for-user-defined-tabove-in-nca/3450 "2019-11-13T17:52:01Z")
If I wanted to cfalculated the time spent above a given concentration as a user defined parameter that is to be included in my NCA analysis, what would I input under the definition? --- ## [Third peak on PK profiles](https://forum.certara.com/t/third-peak-on-pk-profiles/3449)
**Author:** [@xiuqinggao](https://forum.certara.com/u/xiuqinggao)\ **Replies:** 4\ **Last updated:** [November 4, 2019, 10:18am UTC](https://forum.certara.com/t/third-peak-on-pk-profiles/3449 "2019-11-04T10:18:58Z")
Question1: My drug is going through the enterohepatic recycling, but it had second peak at 3hr and third peak at 24hr, how can i build the texual mode with this situation? Can I manually add the another switch variable? … --- ## [Error message](https://forum.certara.com/t/error-message/3447)
**Author:** [@etellez](https://forum.certara.com/u/etellez)\ **Replies:** 1\ **Last updated:** [October 28, 2019, 4:42pm UTC](https://forum.certara.com/t/error-message/3447 "2019-10-28T16:42:21Z")
I am in trying to use PML in a learning exercise, I keep getting this error message: Error line 8: Expected: ‘)’ C = A1/V ^ Error line 25: Error: Assignment only allowed at top level fixef(tvCl = c(, 12, )) ^ Any … --- ## [PML School teams up with Certara University](https://forum.certara.com/t/pml-school-teams-up-with-certara-university/3446)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 0\ **Last updated:** [October 28, 2019, 8:25am UTC](https://forum.certara.com/t/pml-school-teams-up-with-certara-university/3446 "2019-10-28T08:25:11Z")
I would like to announce that PML School is joining forces with Certara University. Future PML School sessions will be part of their Phoenix Express Webinar series. This allows us to focus on preparing new topics on the … --- ## [Turnover model with zero baseline and response is by subtraction](https://forum.certara.com/t/turnover-model-with-zero-baseline-and-response-is-by-subtraction/3398)
**Author:** [@pradeepsharma](https://forum.certara.com/u/pradeepsharma)\ **Replies:** 3\ **Last updated:** [April 8, 2019, 10:23am UTC](https://forum.certara.com/t/turnover-model-with-zero-baseline-and-response-is-by-subtraction/3398 "2019-04-08T10:23:15Z")
Anyone tried modelling turnover model using the response data which is difference of drug treated and vehicle treated animals. Baseline in this case is zero. There is case study PD28 in Johan Gabrielsson/Dan Weiner book … --- ## [Materials from session about NONMEM-NLME: PD Count Analysis](https://forum.certara.com/t/materials-from-session-about-nonmem-nlme-pd-count-analysis/3395)
**Author:** [@bwendt](https://forum.certara.com/u/bwendt)\ **Replies:** 0\ **Last updated:** [April 1, 2019, 9:25am UTC](https://forum.certara.com/t/materials-from-session-about-nonmem-nlme-pd-count-analysis/3395 "2019-04-01T09:25:57Z")
You can download the materials (slide deck and Phoenix project file) here: https://lnkd.in/dQCvxqW The recorded session can be watched on our YouTube channel: https://lnkd.in/dMDHEzE [Next page](https://forum.certara.com/c/phoenix/certara-forums/pml-school/31.md?page=1)