• Pumas 2.5

Introduction

• Introduction to Pumas
• Fitting models with Pumas
• Covariate models
• Introduction to Noncompartmental Analysis
• Introduction to Superposition in Pumas
• Introduction to Optimal Design
• Understanding Interoccasion Variability (IOV) Modeling in Pumas
• Non-Gaussian Random Effect
• Understanding Normal vs LogNormal for Modeling PK Parameters

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 "Case Study I: Building a Covariate Model"
• Translation from NONMEM to Pumas of "Case Study II: Building a PopPK model with multiple doses"
• Translation from NONMEM to Pumas of "Case Study III: Development of a population PKPD model"

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

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

Forests Plots

• A Forest Plot Workflow in Pumas

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
• Adjusting legend `linewidth`, `markersize`, and `alpha` 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 DeepPumas
• Discovery of complex feedback in a neural-embedded Friberg model using real world data
• DeepPumas Epidemiology: force-of-infection across heterogeneous countries