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Diatom

Originally forked from https://github.com/mathomics/ecosystem.

Installation

This project uses uv for Python dependency management, Gurobi as an external LP solver, and Jupyter notebooks for analysis.

Requirements

  • Python >= 3.10.
  • Gurobi Optimizer installed and a valid license.
  • If uv is not already installed, check the official installation guide for instructions.

Setup

Clone the repository. From the project's root, run:

uv sync

This will create a local virtual environment in .venv/ and install all Python dependencies defined in pyproject.toml.

Workflow

WIP

About

A framework for analyzing constraint-based metabolism models.

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