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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

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

Workshop Materials

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 1. Workshop Exercises
    

Models

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 1. Absorption models
 2. Discrete response models
 3. Bayesian models

Data Wrangling in Julia

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 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

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 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

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Pharmacokinetics

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 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

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Coming soon

Global Sensitivity Analysis

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 1. HCV PKPD model
 2. Voriconazole PBPK model


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