Install

First create a fresh Python virtual environment and then activate it:

python -m venv .venv --prompt=maud
source .venv/bin/activate

To install Maud and its python dependencies to your new virtual environment, run this command:

pip install maud-metabolic-models

Cmdstanpy depends on cmdstan, which in turn requires a c++ toolchain. Fortunately, cmdstanpy comes with commands that can install these for you. On windows the necessary dependencies can be installed with the following powershell commands:

python -m cmdstanpy.install_cxx_toolchain
python -m cmdstanpy.install_cmdstan --compiler

On macos or Linux, you must install the c++ requirements manually (see [here](https://cmdstanpy.readthedocs.io/en/v0.9.67/installation.html#install-cmdstan)) for instuctions. Cmdstan can then be installed using this shell command:

install_cmdstan

Usage

To run the simple linear model, use the following command:

maud sample

This will compile the Stan program at src/maud/inference_model.stan, then run the resulting binary file using the data at src/maud/data/example_inputs/linear, storing the results in a folder whose name starts with model_output_linear.

The sample command can be configured in a few ways - to check out all the options try running

maud sample --help

Copyright

• Copyright (c) 2019, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark.

• Free software distributed under the GNU General Public License 3.0