Welcome!!

SimuCRNs is a simulator for Chemical Reaction Networks (mass action and stochastic). It can build an interactive UI for visualizing CRNs "live".

Getting Started

• Run nix-shell to prepare the running environment. You might encounters issues on MacOS related to the send2trash dependency.
• Copy SimuCRNs_demo.ipynb in the git ignored bin/ folder.
• Add as a first cell:

import os                         
os.chdir("../")

• Have fun :)

Structure

• bin/: git ignored folder for user stuff (notebooks, tests, etc...).
• CRNs/: folder with example CRNs specifications.
• default.nix: nix script to setup the environment.
• Interaction 101.ipynb: ipywidget short tutorial, how to build an UI in notebooks.
• simuCRNs: python package for CRN simulation.
• SimuCRNs_demo.ipynb: main demo (c.f. Getting Started).

TODO

• Adding time in UI
• Stochastic CRNs