PyCellChemistry, www.artificial-chemistries.org
===============================================

Artificial Chemistry simulations in Python

by Lidia Yamamoto, Belgium, July 2013
version 1.0: July 2015
version 2.0: September 2015
version 2.1: October 2015: committed to GitHub

Basic system (src/artchem folder):
============

- Multiset.py: a bag of chemicals represented as a multiset of objects

- KeyMultiset.py: a multiset indexed by a given key; the key can be a
  substring representing part of the molecule (akin to a binding site)
  or any value that tags a particular molecule or groups of related
  molecules, such that it can be moreq uickly located.

- Reaction.py: explicit chemical reactions composed of an educt
  multiset and a product multiset.

- ReactionParser.py: parser for explicit reactions represented as
  strings in the format "A + B --> C , k=2"

- ReactionVessel.py: ODE integration and Gillespie SSA implementations
  for explicit, non-constructive artificial chemistries

- BinaryStrings.py: routines to manipulate binary strings as
  arbitrarily long integers

- Cell.py: an implementation of hierarchical comopartments akin to P
  Systems; cells may contain multisets of chemicals and other cells
  inside.

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Example applications (src folder):
====================

- Dimer.py: simple reversible dimerization example (chapter 2)

- Chameleons.py: colored chameleon chemistry (chapter 2)

- NumberChem.py: prime number chemistry (chapter 2)

- MatrixChem.py: Matrix Chemistry (chapter 3)

- Logistic.py: logistic equation (chapter 7), with comparison between
  ODE and SSA

- Lotka.py: Lotka-Volterra example (chapter 7), ODE or SSA

- Repressilator.py: stochastic simulation of the repressilator GRN
  (chapter 19)

- Evolution.py: implentation of basic evolution elements, used by
  Quasispecies.py and Tournament.py

- Quasispecies.py: stochastic implementation of a quasispecies
  evolutionary dynamics (chapter 7)

- Tournament.py: genetic algorithm with tournament selection
  implemented as an artificial chemistry

- NKlandscape.py: a simple implementation of Kauffman's NK model of
  rugged fitness landscapes (chapter 18)

- Fraglets.py: interpreter for the Fraglets language (chapter 16)

- NetFraglets.py: networked Fraglets, with CDP example (chapter 16)

- Disperser.py: an artificial chemistry for load balancing in
  distributed systems (chapter 17)

- HighOrderChem.py: a simplified high-order chemistry in which the
  reaction rules are also molecules in a multiset, and are written as
  strings containing a python method call.

- NumberChemHO.py: a reimplementation of NumberChem using HighOrderChem

- MolecularTSP.py: a reimplementation of the Molecular TSP algorithm
  (chapter 17) using HighOrderChem

Running:
-------

python [example.py] > output1.txt 2> output2.txt

depending on the example chosen, the output file(s) will contain
execution traces or data to be plotted (in tab-separated format).

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Reaction-diffusion implementation and demos (src/RD folder):
==================

Reaction-diffusion demos:

- GrayScott.py: a demo of pattern formation in the Gray-Scott system

- ActivatorInhibitor.py: the Gierer & Meinhardt's activator-inhibitor system

- ActivatorSubstrate.py: activator-depleted substrate model by Meinhardt

- DichotomousBranching.py: Dichotomous leaf branching pattern by Meinhardt

Underlying implementation:

- ReactionDiffusion.py: implementation of numerical PDE integration

- WritePNG.py: library of functions to generate PNG files (3rd party code)

Running the reaction-diffusion demos:
-------

* with VPython (vpython.org):

- simply invoke

  python [demo.py]

- more concretely:

  python GrayScott.py

  python ActivatorInhibitor.py

  python ActivatorSubstrate.py

  python DichotomousBranching.py

* without VPython:

- comment out the rsys.animate(...) line in the corresponding demo

- use rsys.writepng(...) instead, to generate PNG files periodically