Overview of MultiMalModPy

MultiMalModPy provides a unified Python framework for running and comparing simulations across multiple malaria models.
It includes both model-agnostic (global) scripts and model-specific modules:

  • Global scripts handle parameter definition and simulation management.
  • Model-specific scripts manage tasks like input generation, output processing, and simulation logic.

All user-defined parameters are stored in a Python serializable object, ensuring consistency during both pre-processing and post-processing steps across models.

MultiMalModPy framework

How It Works

The simulation process begins with user-defined inputs in setup_sim.py.
Once configured, simulations are launched via launch_sim.py. During this step:

  • All relevant parameters are bundled into a serialized Python object (exp.obj).
  • Platform-specific job submission scripts (e.g., .sh on HPC) are automatically generated to streamline execution.

Shell scripts ensure reproducibility and automation across high-performance environments.

Output and Visualization

Each model produces standardized CSV outputs, which are used to generate a predefined set of visualizations. These include:

  • Relationships between disease transmission and outcomes
  • Time-series trends
  • Age-specific patterns

The plotting system is modular and easily extendable. MultiMalModPy includes three standard plotting scripts:

Repository Layout and Directory Structure

MultiMalModPy is organized for clarity and modularity. It includes:

  • An experiments folder, where simulations are configured and executed.
  • A simulation output folder, which stores results in standardized formats.

folder structure

Repository Breakdown

🔹 Back-End (Model-Specific Logic)

Each model has its own directory with input handling, simulation execution, and output processing logic:

  • EMOD/ — EMOD-specific scripts
  • malariasimulation/ — malariasimulation-specific scripts
  • OpenMalaria/ — OpenMalaria-specific scripts
  • utility/ — generic helper functions

🔹 Front-End (User Scripts)

Located in the project root, these user-facing components control setup and execution:

  • manifest.py — manages system paths, environment config, and dependencies
  • setup_sim.py — defines experiment inputs and simulation options
  • launch_sim.py — runs the experiment
  • interventions/ — optional: parameter scripts for intervention scenarios

🔹 Support and Infrastructure

  • dependencies/ — virtual environment setup, requirements.txt, and install scripts
  • target_calibration/ — model-specific simulation outputs used for transmission calibration
  • tests/ — unit and integration tests for validating MultiMalModPy and model installations
  • docs/ — Markdown files and assets used to build the documentation site (via MkDocs)

Experiments folder

Contains all input files, logs, and generated job scripts for running simulations. This includes:

  • Input configurations
  • Log files (.err, .out)
  • Shell scripts for HPC job scheduling and reproducibility

Simulation output folder

Standardized results are saved here to ensure comparability across models. Includes:

  • Output CSVs for:
  • EMOD
  • malariasimulation
  • OpenMalaria
  • Auto-generated plots for rapid evaluation

Next Up

→ How to use MultiMalModPy
→ Input parameters and predefined options
→ Glossary
→ Installation and requirements
→ First time configurations (manifest.py)