Notebooks for qualitative analysis of Circadian Clock - Cell Cycle coupled SBGN-PD maps

The notebooks can be visualized and downloaded at https://nbviewer.jupyter.org/github/pauleve/ClockCycle-notebooks/tree/main.

They can be executed interactively:

• online, using myBinder service at https://mybinder.org/v2/gh/pauleve/ClockCycle-notebooks/main
• or on your computer, provided you have Docker and Python 3 installed:
  1. download the notebooks and maps from https://github.com/pauleve/ClockCycle-notebooks/archive/main.zip and extract the zip file
  2. execute the following commands, where ClockCycle-notebooks is the folder in which you extracted the notebooks

  sudo pip install -U colomoto-docker # you may have to use pip3 instead of pip
  colomoto-docker --image pauleve/clockcycle -V v1 --bind ClockCycle-notebooks
  

The Docker image pauleve/clockcycle:v1 is based on the CoLoMoTo Docker version 2021-02-01, with additional tools:

• csbgnpy, a Python library for manipulating the conceptual model underlying an SBGN PD map
• sbgn2an, a Python library for computing initial states and stories of a Process Description map
• pintsim, a simulator of Pint models (automata networks) in Python