maud-metabolic-models 0.6.0.1

Bayesian statistical models of metabolic networks

Maud is an application that fits Bayesian statistical models of metabolic networks using Python and Stan.

Maud aims to take into account allosteric effects, ensure that the laws of thermodynamics are obeyed and to synthesise information from both steady state experiments and the existing literature.

Installation

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. On some computers you will have to install these in order to use Maud. You will hit an error at the next step if this applies to your computer. Luckily cmdstanpy comes with commands that can do the necessary installing for you. On windows the c++ toolchain can be installed with the following powershell commands:

Usage

Maud is used from the command line. To see all the available commands try running

maud --help

Copyright

• Copyright (c) 2023, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark.

• Free software distributed under the GNU General Public License 3.0