MONID - MODELING NETWORK FOR SEVERE INFECTIOUS DISEASES

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Published August 1, 2025 | Version v2.1.0
Software Open

MEmilio v2.1.0 - A high performance Modular EpideMIcs simuLatIOn software

Authors/Creators

  • 1. ROR icon Deutsches Zentrum für Luft- und Raumfahrt e. V. (DLR)
  • 2. Helmholtz Centre for Infection Research (HZI)
  • 3. ROR icon University of Bonn
  • 4. ROR icon Forschungszentrum Jülich

Contributors

  • 1. ROR icon Deutsches Zentrum für Luft- und Raumfahrt e. V. (DLR)
  • 2. ROR icon University of Bonn
  • 3. Helmholtz Centre for Infection Research (HZI)

Description

MEmilio implements various models for infectious disease dynamics, ranging from simple compartmental models to complex Integro-Differential and agent-based models. Its modular design enables the combination of different models with distinct mobility patterns. Through efficient implementation and parallelization in C++ and an easy-to-use python interface, MEmilio delivers cutting-edge and compute-intensive epidemiological models to broad range of applications and users, providing precise and high-resolution spatiotemporal infectious disease dynamics. MEmilio is continuously extended and is available open-source for community use.

We here publish version 2.1.0, our most recent major release.

v2.1.0 Changes

Added features / functionality:

  • Added a temporal hybrid ODE-ABM-based model
  • Added spatially resolved feedback simulation
  • Extended integrator classes and reimplemented SDE models
  • Adjusted memilio-generation for flow models and automatic differentiation
  • Added setup for performance monitoring with LIKWID
  • Introduction of a timing framework
  • Export TimeSeries objects into csv files
  • Added quarantine effectiveness parameter to ABM
  • C++ Code creation based on standardized formats for ODEs
  • Added GitHub bot to inform on new discussions

General changes:

  • Reworked ABM state transitions
  • Updated minimum and latest Ubuntu and Windows versions which are tested in CI
  • Fully reworked and extended documentation
  • Deactivated old GitHubPages
  • Enhanced testing logic in ABM
  • Improved trip addition in ABM
  • Changes in model initializations due to changes in provision of intensive care and SARS-CoV-2 vaccination data
  • Streamline code for reading in data in model specific IO files
  • Updated simple surrogate models
  • Renamed compartmentalmodel.h to compartmental_model.h

Corrections:

  • Corrected the different output on Mac
  • Fix population download handling
  • Property of MobilityParametersEdge was not accessible in python bindings

Minor changes

  • Updated citations
  • Updated coding guidelines and pull request template
  • Cancel concurrent and redundant CI runs

For more details, see https://github.com/SciCompMod/memilio and our novel documentation: https://memilio.readthedocs.io/en/latest/ 

Files

memilio-2.1.0.zip

Files (2.6 MB)

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Additional details

Is part of
Publication: 10.1371/journal.pcbi.1012630 (DOI)
Publication: 10.1016/j.amc.2025.129636 (DOI)
Publication: 10.1016/j.compbiomed.2025.110269 (DOI)
Publication: 10.1016/j.idm.2024.12.015 (DOI)
Publication: 10.48550/arXiv.2411.06500 (DOI)
Publication: 10.48550/arXiv.2412.09140 (DOI)
Publication: 10.1016/j.chaos.2025.116782 (DOI)

Funding

Federal Ministry of Transport and Digital Infrastructure
PANDEMOS: Pandemic Mobility Scenarios FKZ19F2211A
Helmholtz Association of German Research Centres
LOKI: Integrated Early Warning System for Local Recognition, Prevention, and Control for Epidemic Outbreak KA1-Co-08
Federal Ministry of Education and Research
INSIDe: Integrative modelling of the spread of serious infectious diseases 031L0297B
Helmholtz Association of German Research Centres
Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) 0
Deutsche Forschungsgemeinschaft
MESID 528702961
Federal Ministry of Education and Research
AIMS 031L0319A & 031L0319B

Dates

Available
2023-12-20
Initial release
Available
2024-03-08
v1.1.0
Available
2024-06-07
v1.2.0
Available
2024-08-19
v.1.2.1
Available
2024-11-28
v1.3.0
Available
2025-04-07
v2.0.0
Available
2025-08-01
v2.1.0

Software

Repository URL
https://github.com/SciCompMod/memilio
Programming language
C++ , Python
Development Status
Active

References