Learning Paths
Path 1: Julia Fundamentals for Pumas
Module 1: Introduction to Julia
Module 2: Data Wrangling and Visualization in Julia
Path 2: Pumas Fundamentals of Data and Model Structure
Module 3: Introduction to Pumas
Module 4: Population PK and PK/PD Modeling with Pumas
- Data Representation
- Model Representation
- Model Representation Using Latexify
- Compartmental PK Models
- Parameter Estimation and Estimating Parameter Uncertainty
- Interpretation of Pumas Model Output
- Model Diagnostics and Evaluation
- Bootstrap and Sampling Importance Resampling
- Sequential and Simultaneous PKPD Models
- Comparison to NONMEM for NONMEM Users (see from NONMEM to Pumas)
Path 3: Pumas Fundamentals of Model Development
Module 5: Structural Model Definitions
Module 6: Absorption Models
Module 7: Random Effect Models
Module 8: Error Models
Module 9: Covariate Model Definitions
Path 4: Pumas Fundamentals of Model Simulation
Module 10: Simulations in Pumas
Module 11: Visual Predictive Checks
Path 5: Pumas Workflows
Module 12: Covariate Modeling
Module 13: Censored Data Modeling
Path 6: Reporting in Pumas
Module 14: Reporting
Tutorials Catalog
Julia
Fundamentals
Data Wrangling
Plotting
- Introduction to AlgebraOfGraphics.jl
- Grammar of Graphics with AlgebraOfGraphics.jl
- Geometries
- Statistical Visualizations
- Plot Customization
- Using Wide Data Formats
- Advanced Layouts
- Inserting Custom Vertical/Horizontal Lines
- Add Text Labels
- Adjusting Legend Markers
- Empirical Cumulative Density Function Plots
Pumas
Introduction
Advanced Topics
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
Simulations
Discrete Response Models
Covariate Selection Methods
Forests Plots
Bayesian Models
Plot Customization
Reporting
PK Modeling
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
- PK8: Two compartment distribution models
- PK16: Two-compartment intravenous plasma/urine
- PK37: Invitro/Invivo Extrapolation I
- PK38: Invitro/Invivo Extrapolation II
Oral Absorption & Bioavailability
Multi-Compartment & Complex Dosing
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