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mgrowthctrl: Microbiome Growth Control
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`mGrowthCtrl` is a software package for modeling, visualizing, and controlling microbiome growth dynamics. It provides tools to simulate microbial community behavior, fit predictive models to experimental data, and adjust community composition using control and optimization methods.

The package can be connected via an API to `mGrowthDB`_, a curated database that provides microbiome growth data for model calibration, validation, and exploratory analysis.

.. _mGrowthDB: https://mgrowthdb.gbiomed.kuleuven.be/


Example Usage
=============

.. code-block:: python

   from mgrowthctrl.models import CRModel, CRModelParams
   from mgrowthctrl.models.base import ModelNames
   from mgrowthctrl.utils.data import Dataloader

   # Load experimental data, detecting names of consumer and resource columns:
   data = Dataloader()
   data.load_local_data(
       "examples/datasets/BT_WC_export.csv",
       x_selector="BT counts"
   )
   print(data.names)

   # Initialize model parameters
   params = CRModelParams.from_shapes(n=len(data.X_names), m=len(data.S_names))

   # Create and fit the model
   model = CRModel(names=data.names, params=params)
   model.fit(df=data.df, time_col=data.time_col)

   # Simulate trajectories and print the resulting data:
   sim = model.simulate(data.y0, data.t)
   print(sim)


.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Get Started

   intro/installation
   intro/get_started

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Tutorials

   tutorials/simple_crm
   tutorials/advanced_open_loop_control_fitting
   tutorials/advanced_closed_loop_control_fitting

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Models

   models/consumer_resource_model
   models/diauxic_shift_model
   models/base_model

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Parameter Fitting

   fitting/lsq
   fitting/mcmc

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Control & Optimization

   control/introduction
   control/open_loop
   control/closed_loop
   control/base

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Utilities

   utilities/data_loader
   utilities/visualization
   utilities/saving