combine_notebooks - COMBINE jupyter notebooks in python.
Project description
combine-notebooks - COMBINE jupyter notebooks in python
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
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