Tutorial Notebooks

Detailed step-by-step instructions of various quantitative pharmacology workflows

Can't find the workflow you need, just ask us at support@pumas.ai

Table of contents

Introduction

  1. Introduction to Pumas
  2. Generating and Simulating Populations
  3. Fitting models with Pumas
  4. Introduction to Noncompartmental Analysis (NCA)
Workshop Materials

  1. Workshop Exercises
Models

  1. Absorption models
  2. Discrete response models
  3. Bayesian models
Data Wrangling in Julia

  1. Getting Started with Julia
  2. Julia Basics
  3. Functions
  4. Reading and Writing Data
  5. Manipulating Tables with DataFramesMeta.jl
  6. Strings
  7. Reshaping DataFrames
  8. Handling Factors and Categorical Data with CategoricalArrays.jl
  9. Handling NAs and Missing Values
  10. Handling Dates and Times
Plotting in Julia

  1. Introduction to AlgebraOfGraphics.jl
  2. Plotting Different Geometries with AlgebraOfGraphics.jl
  3. Plotting Statistical Visualizations with AlgebraOfGraphics.jl
  4. Customization of AlgebraOfGraphics.jl Plots
  5. Grammar of Graphics with AlgebraOfGraphics.jl
  6. Wide Data with AlgebraOfGraphics.jl
  7. Advanced Layouts with AlgebraOfGraphics.jl
PKPD Data Analysis Book

Pharmacokinetics

  1. PK1 - One-compartment intravenous bolus dosing

  2. PK2 - One-compartment oral dosing

  3. PK3 - One-compartment 1st; and 0-order input

  4. PK4 - One-compartment oral dosing (part 1 & 2)

  5. PK4 - One-compartment oral dosing (part 3 & 4)

  6. PK8 - Two-compartment distribution models

  7. PK9 - Modeling of fraction absorbed and nonlinear bioavailability across the liver: Simultaneously fitting intravenous and oral data

  8. PK10 - Simultaneous fitting of IV/PO data

  9. PK12 - Intravenous and oral dosing

  10. PK13 - Bolus plus constant rate infusion

  11. PK14 - Multi-compartment model oral dosing

  12. PK17 - Nonlinear kinetics - Capacity I

  13. PK18 - Capacity II - Ethanol kinetics

  14. PK19 - Capacity III - Metabolite kinetics

  15. PK20 - Capacity IV - Nonlinear kinetics

  16. PK21 - Nonlinear kinetics - Heteroinduction

  17. PK22 - Nonlinear kinetics - Autoinduction

  18. PK24 - Nonlinear kinetics - Flow II

  19. PK26 - Modeling of antibody kinetics after i.v. doses to man

  20. PK27 - Target mediated drug disposition

  21. PK28 - Allometry - Elementary Dedrick plot

  22. PK30 - Turnover I - Sc dosing of hormone

  23. PK31 - Turnover II - Intra-venous dosing of hormone

  24. PK32 - Turnover III - Nonlinear disposition

  25. PK33 - Transdermal input and kinetics

  26. PK34 - Reversible metabolism

  27. PK37 - In vitro/in vivo extrapolation I

  28. PK38 - In vitro/in vivo extrapolation II

  29. PK39 - Two-compartment data - Experimental design issues

  30. PK41 - Multiple intravenous infusions - NCA versus regression

  31. PK42 - Saturable absorption via transporters

  32. PK43 - Multiple absorption routes

  33. PK44 - Estimation of inhibitory constant Ki (part 1)

  34. PK44 - Estimation of inhibitory constant Ki (part 2)

  35. PK45 - Reversible metabolism of drug A and its metabolite drug B

  36. PK46 - Long infusion and short half-life

  37. PK47 - Plasma protein binding modeling

  38. PK48 - One-compartment Michaelis-Menten kinetics - Drug and metabolite in urine

  39. PK49 - Turnover IV - Factor II data in healthy volunteers

  40. PK50 - Analysis of multiple subjects concentration and response-time profiles

  41. PK51 - Multi-compartment drug/metabolite

  42. PK52 - Simulated impact of disease on r-hSOD kinetics

  43. PK53 - Linear antibody kinetics

Pharmacodynamics

    Coming soon
Global Sensitivity Analysis

  1. HCV PKPD model
  2. Voriconazole PBPK model