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Tutorial Catalog

Introduction

  • Introduction to Pumas
  • Fitting models with Pumas
  • Covariate models
  • Introduction to Noncompartmental Analysis
  • Introduction to Optimal Design
  • Non-Gaussian Random Effect

Advanced Topics

  • Absorption Models

From NONMEM to Pumas

  • Comparing NONMEM and Pumas models
  • NONMEM style BQL models (M1-M4) in Pumas
  • Translation from NONMEM to Pumas of ACCP Case Study I
  • Translation from NONMEM to Pumas of ACCP Case Study II
  • Translation from NONMEM to Pumas of ACCP Case Study III

ACCP Introduction Tutorials to PKPD modeling in Pumas

  • Case Study I - Building a Covariate Model
  • Case Study II - Building a PopPK model with multiple doses
  • Case Study III - Development of a population PKPD model using Pumas

Simulations

  • Generating and Simulating Populations
  • Reproducibility when doing Simulations
  • Multivariate Covariate Simulations in Pumas with Copulas.jl

Discrete Response Models

  • Logistic Regression
  • Ordinal Regression
  • Poisson Regression
  • Negative Binomial Regression
  • Time to Event Models

Covariate Selection Methods

  • Introduction to Covariate Selection Methods
  • Forward Selection
  • Backward Elimination
  • Mixed Covariate Selection Methods
  • Running in a Distributed Batch Job

Bayesian Models

  • Introduction to Bayesian Models in Pumas
  • Random Effects in Bayesian Models
  • Posterior Postprocessing - Plots and Queries
  • Markov Chain Monte Carlo Convergence
  • Model Comparison with Crossvalidation
  • Fitting Non-Identifiable Models

Data Wrangling in Julia

  • Getting Started with Julia
  • Julia Syntax
  • Functions
  • Reading and Writing Data
  • Manipulating Tables with DataFramesMeta.jl
  • Strings
  • Reshaping DataFrames
  • Handling Factors and Categorical Data with CategoricalArrays.jl
  • Handling NAs and Missing Values
  • Handling Dates and Times
  • How to Handle XPT Files

Plotting in Julia

  • Introduction to AlgebraOfGraphics.jl
  • Plotting Different Geometries with AlgebraOfGraphics.jl
  • Plotting Statistical Visualizations with AlgebraOfGraphics.jl
  • Customization of AlgebraOfGraphics.jl Plots
  • Grammar of Graphics with AlgebraOfGraphics.jl
  • Wide Data with AlgebraOfGraphics.jl
  • Advanced Layouts with AlgebraOfGraphics.jl
  • Inserting Custom Vertical/Horizontal Lines with AlgebraOfGraphics.jl

Plot Customization

  • Plot customization for Noncompartmental analysis - Single dose
  • Plot customization for Noncompartmental analysis - Multiple dose

Reporting

  • Creating tables with SummaryTables.jl
  • Generated quarto documents with QuartoTools

Introduction to PK Modeling

  • PK1: One-compartment intravenous bolus dosing
  • PK2: One-compartment oral dosing
  • PK3: One-compartment 1st and 0-order input
  • PK5: One-compartment intravenous plasma/urine I
  • PK6: One-compartment intravenous plasma/urine II
  • PK7: Two-compartment intravenous bolus dosing
  • PK8: Two compartment distribution models
  • PK16: Two-compartment intravenous plasma/urine
  • PK37: Invitro/Invivo Extrapolation I
  • PK38: Invitro/Invivo Extrapolation II

Oral Absorption & Bioavailability

  • PK04 (Part 1): One-compartment oral dosing
  • PK04 (Part 2): One-compartment oral dosing
  • PK9: Modeling of fraction absorbed and nonlinear bioavailability across the liver
  • PK10: Simultaneous fitting of IV/PO data
  • PK42: Saturable absorption via transporters

Multi-Compartment & Complex Dosing

  • PK12: Intravenous and oral dosing
  • PK13: Bolus plus constant rate infusion
  • PK14: Multi-compartment model oral dosing
  • PK41: Multiple intravenous infusions – NCA versus regression
  • PK43: Multiple absorption routes
  • PK46: Long infusion and short half-life

Nonlinear & Special Kinetics

  • PK17: Nonlinear Kinetics (Capacity I-IV, Flow, Hetero/Autoinduction)
  • PK18: Capacity II - Ethanol kinetics
  • PK19: Two compartment with limited capacity metabolite model
  • PK20: One-compartment model with capacity limited elimination for IV bolus
  • PK21: Heteroinduction model
  • PK22: Non-linear Kinetics - Autoinduction
  • PK24: Non-linear Kinetics - Flow II
  • PK44 (Part 1): Estimation of inhibitory constant Ki
  • PK44 (Part 2): Estimation of inhibitory constant Ki
  • PK48: One-compartment Michaelis-Menten kinetics - Drug and metabolite in urine

Physiological & Drug-Specific Models

  • PK26: Target mediated drug disposition
  • PK27: Allometry - Elementary & Complex Dedrick plot
  • PK30: Turnover I - SC Dosing of Hormone
  • PK31: Turnover II - Intravenous Dosing of Hormone
  • PK32 - Turnover III - Non-linear Disposition
  • PK33: Transdermal input and kinetics
  • PK34: Reversible metabolism
  • PK40: Enterohepatic recirculation
  • PK45: Reversible metabolism of drug A and its metabolite B
  • PK47: Plasma protein binding modeling
  • PK49: Turnover IV - Factor II data in healthy volunteers
  • PK52: Simulated impact of disease on r-hSOD kinetics

Population & Clinical PK

  • PK50: Analysis of multiple subjects concentration and response-time profiles
  • PK51: Multi-compartment drug/metabolite
  • PK53: Linear antibody kinetics

DeepPumas

  • Getting started with DeepNLME
  • Discovery of complex feedback in a neural-embedded Friberg model using real world data