emodpy-malaria Tutorials

These tutorials walk through the core emodpy-malaria workflow step by step, from running a single simulation to calibrating transmission and evaluating intervention impact against a population with a realistic history of infections and immunity. Each tutorial builds directly on the previous one — the Python script for each tutorial is a clean diff of the last, so the diff itself is the lesson.

Prerequisites

Before starting, complete the setup page to install dependencies and confirm your environment is working.

If you are new to EMOD, read EMOD input files for a brief overview of the configuration, demographics, campaign, and report concepts used throughout the tutorials.

The tutorials run on the Container platform by default (Docker, works locally or in Codespaces). Each script also shows commented-out COMPS and SLURM platform blocks if you are going to run on a cluster.

Tutorials

#	Title	What you'll learn
1	Run your first simulation	EMODTask, demographics, config callbacks, running an experiment
2	Reports	MalariaSummaryReport, downloading results, plotting InsetChart
3	Interventions	Campaign files, treatment seeking, ITNs, comparing scenarios
4	Seasonality	LINEAR_SPLINE habitat, multi-year runs, seasonal transmission patterns
5	Sweep parameters	SimulationBuilder, cross-product sweeps, parametrized campaigns
6	Calibration	CalibManager, OptimTool, scoring simulations against reference data
7	Serialization	Burnin to build immunity, serialized population files, pickup with interventions

Tutorial scripts

All Python scripts live in the tutorials/ directory alongside this documentation:

tutorials/
    manifest.py               shared paths and platform settings
    tutorial_1_intro.py
    tutorial_2_reports.py
    tutorial_3_interventions.py
    tutorial_4_seasonality.py
    tutorial_5_sweep.py
    tutorial_6_calibration.py
    tutorial_6_reference_pfpr.csv
    tutorial_7_burnin.py
    tutorial_7_pickup.py

Tutorials 1–6 can be run independently — each script is self-contained. Tutorial 7 has two values that must be carried forward from earlier tutorials: CALIBRATED_LOG10_X_LARVAL_HABITAT from Tutorial 6 (a default is provided so you can run without it) and BURNIN_EXP_ID in the pickup script, which requires the burnin to have been run first.