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An interactive notebook embedded tool to simulate CRNs.
19 commits 1 branch 0 tags 248 KiB
  • Jupyter Notebook 85.6%
  • Python 13%
  • Nix 1.4%
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Cosmo Stérin fdf1cfb019
 Update README.md
2018-12-05 21:55:13 +00:00
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CRNs CRNs 2018-12-02 20:17:09 +00:00
simuCRNs pfiou 2018-12-04 21:06:09 +00:00
.gitignore more config 2018-12-04 16:49:51 +00:00
default.nix Mini overview of interact logic 2018-11-30 19:41:53 +00:00
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README.md Update README.md 2018-12-05 21:55:13 +00:00
SimuCRNs_demo.ipynb pfiou 2018-12-04 21:06:09 +00:00

README.md

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