DigiMic is a gateway to independently maintained modelling packages and the resources around them. Package documentation is versioned and validated in the repository that owns each implementation.

Packages and documentation

Python 3.11+

DigiMicPy

The Python implementation, with validated MiCRM parameters, reproducible parameter generators, consumer-resource simulation, examples, and a package-owned Jupyter Book.

Read the documentation Browse the source
Julia 1.8+

DigiMic.jl

The Julia implementation, distributed from source and imported as MiCRM for compatibility with existing users.

Setup and source
Incoming package · GEM → CRM

TPCP: GEM-based CRM parameterisation

TPCP is a separate, general-purpose parameterisation package under development. It will translate genome-scale metabolic models (GEMs) and supporting biological or environmental information into parameters for consumer-resource models (CRMs) used by DigiMicPy or DigiMic.jl.

Temperature-aware growth and metabolic responses are a key application, not the package's only focus. Its wider scope includes resource uptake, secretion and leakage, biomass production, maintenance, and medium constraints. The package manual will live with its own source when the repository is brought under DigiMicOrg.

The documentation ownership policy defines the boundary between this platform and package-owned implementation documentation.

Workflows

The platform owns the scientific definitions, assumptions, interpretation, and reporting guidance for workflows that may span more than one implementation. Package documentation explains how to carry them out with a supported API.

Training and support

The packages are early-stage research software. Check each repository’s README and release history before depending on an API for a long-lived workflow.