Authors

Alex Blokhuis and Philippe Nghe,
ESCPI UMR CNRS ESPCI 8231 Chimie Biologie Innovation

This software is distributed under the Apache license 2.0 (see LICENSE.txt)

Content of the zip file:

Python code to simulate formose reaction in osmotically coupled droplets, and associated data, related to the article
"
Emergent fitness and ecological dynamics of compartmentalised autocatalytic chemical reactions
by
Heng Lu, Alex Blokhuis, Rebecca Turk-MacLeod, Jayaprakash Karuppusamy, Andrea Franconi, Gabrielle Woronoff, Cyrille Jeancolas, Afshin Abrishamkar, Estelle Loire, Fabien Ferrage, Philippe Pelupessy, Ludovic Jullien, Eörs Szathmary, Philippe Nghe and Andrew. D. Griffiths

Software Versions
Python 3.8.5
Jupyter (IPython) 7.19.0
Tested on a Microsoft Windows 10 Professional 10.0.19044

Main programs to run in order 
(and their dependencies)

MAIN1_FittingToyFormose.ipynb
(odeint from scipy.integrate, minimize from scipy.optimize, curve_fit from scipy.optimize)

MAIN2_ExchangeC2andWater.ipynb
(matplotlib, numpy, odeint from scipy.integrate, minimize from scipy.optimize, curve_fit from scipy.optimize, copy)

MAIN3_ExchangeC1_Cn_Formose.ipynb
(odeint from scipy.integrate, matplotlib.patches, openpyxl from pandas) 

MAIN4_SerialTransfer.ipynb
(odeint from scipy.integrate)

MAIN5_DropletDivision.ipynb 
(math, numpy, matplotlib)

Data used by the code is located in:
-folder NMRN
-file ED_FR_CTRL.xlsx

As reference, html versions of the pre-run code are provided in the folder
reference HTMLs

Running time
Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, 2112 MHz, 4 cœur(s), 8 processeur(s) logique(s)