1. Getting started

1.1. Requirements

In order to install ENKIE you need:

  • Windows, Linux or OSX operating system.

  • Python 3.8 or newer.

  • R installation (tested with R >= 4.2.0).

  • ~3GB of free disk space.

1.2. Installation

First, install the R brms package (tested with version 2.17.6). In a R console, run:

install.packages("brms")

Once your system satisfies all the requirements, you can install ENKIE through the Python Package Index:

pip install enkie

Note: at the first run, ENKIE will download the models and identifier mappings, this may take a while.

1.3. Usage

1.3.1. Command Line Interface

Once installed, ENKIE can be used from the command line with the enkie command. This approach is most suitable to estimate parameters for SBML models. Running

enkie --help

will show the available options. A complete example illustrating the usage on the e_coli_core model can be found in the git repository .

1.3.2. API

For more advanced applications and for finer control over the estimation process, ENKIE can be accessed through a Python API. An simple example can be found in the git repository . See the complete API reference for additional information.