MIRA
MIRA is a framework for representing systems using ontology-grounded meta-model templates, and generating various model implementations and exchange formats from these templates. It also implements algorithms for assembling and querying domain knowledge graphs in support of modeling.
Resources
Template JSON schema: schema.json
Epidemiology Domain Knowledge Graph (DKG) service: DKG service
MIRA Metaregistry service: Metaregistry service
Example notebooks
Defining multiple model variants using MIRA Templates: Notebook 1
Generating an executable model from MIRA Templates and running simulation: Notebook 2
Stratifying and visualizing MIRA models, and exporting as Petri nets: Notebook 3
Processing an SBML model from BioModels, visualizing and exporting into Petri nets: Notebook 4
Using the MIRA Domain Knowledge Graph REST API: Notebook 5
Using the Model REST API to perform various model operations: Notebook 6
Using the web client in python that connects to the REST API: Notebook 7
Demonstrating MIRA TemplateModel capabilities Notebook 8
Rapid construction of DKGs in ASKEM: Notebook 9
Implement a masking intervention in a compartmental model to simulate epidemic trajectories under different scenarios: Notebook 10
Benchmarking the efficacy of DKG groundings on a set of COVID EPI Models: Notebook 11
Installation
The most recent code and data can be installed directly from GitHub with:
python -m pip install git+https://github.com/indralab/mira.git
To install in development mode, use the following:
git clone git+https://github.com/indralab/mira.git
cd mira
python -m pip install -e .
If you wanted to install extra dependencies that aren’t listed under install_requires
such as the packages required for running ode simulations, use the following:
python -m pip install -e .[ode]
To install multiple dependency blocks listed in setup.cfg
, run the following:
python -m pip install -e .[ode,docs]
Extra dependency blocks/packages required for modules
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Documentation
Full documentation can be found here.
Funding
The development of MIRA is funded by the DARPA ASKEM program, grant number HR00112220036.