Project Overview

This repository contains Jupyter notebooks that showcase COMBINE standards and their libraries around one common theme; the repressilator model.

The following standards are demonstrated

• Systems Biology Graphical Notation (SBGN): Used to describe visually biological knowledge.

• Systems Biology Markup Language (SBML): Used for representing models of biological processes.

• Simulation Experiment Description Markup Language (SED-ML): Used for encoding experiments. SED-ML allows defining the models to use, the experimental tasks to run, and which results to produce. It is a computer-readable format for representing the models of biological processes.

• CellML: Used to store and exchange computer-based mathematical models.

• Synthetic Biology Open Language (SBOL): Used for description and the exchange of synthetic biological parts, devices, and systems.

• NeuroML: Used for XML based description language that provides a common data format for defining and exchanging descriptions of neuronal cell and network models.

Setup/Installation

To work with the notebooks create a virtual environment and install the dependencies:

mkvirtualenv combine_notebooks --python=python3.10
(combine_notebooks) pip install -e .[development] --upgrade

After changes ensure code formatting via:

./fcode.sh

Tests can be run via pytest and tox. To run all tests use:

tox -p

To run individual tests use the following targets flake8, mypy, py38, py39, py310:

tox -e flake8

Notebooks

To run the notebooks install a notebook environment:

pip install jupyterlab

Register the created virtual environment combine_notebooks as jupyter kernel:

ipython kernel install --user --name=combine_notebooks

Or alternatively install the package in an existing virtual environment to get all the dependencies. I.e.:

pip install combine-notebooks

Start the notebooks:

cd ./notebooks
jupyter lab

© 2022 Matthias König & Aditya Singhal