STAARC: STochastic Atom-based ARtificial Chemistry

This repository contains the files necessary to simulate Hutton Artificial Chemistry (HuAC) using Simulation Stochastic Algorithm (SSA) also known as Gillespie Algorithm

The code

This program is in C# and has been build using Xamarin. Dependencies:

• QuickGraph
• Newton Json both NuGet packages.

Quick start

To start simply add 'greactor` as a reference and the using command

using greactor; 

To create a reactor simply create a new instance:

var rec =  new reactor();

Now you can add your reactions using 'add_rule` method. This method takes a rule object that needs to be created. It is a base class you never instantiate. You need to use the derived class

• b_rule : for bimolecular reactions
• d_rule : for degradation reactions
• o_rule : for production reactions
• m_rule : for unimolecular modifications

Bimolecular reactions: for the moment, the main API is a pain :) but here are examples:

for (t1,s1) + (t2,s2) -> (t1, s3).(t2,s4) at rate r

var r = new b_rule(false,t1,s1,t2,s2,true, t1,s3,t2,s4,idx, r);

for (t1,s1).(t2,s2) -> (t1, s3)+(t2,s4) at rate r

var r = new b_rule(true,t1,s1,t2,s2,false, t1,s3,t2,s4,idx, r);

Then you can add particles using 'add_particles` and the struct particle. To add a particle (t1,s1)

rec.add_particle(new particle (t1, s1));

Then you can run the Gillespie algorithm

int seed = 1;
Random rd = new Random (seed);
int step = 0;
int idx;
double tau, total_time = 0.0;

while (rec.gillespie_step (rd, out tau, out idx)) {
      total_time +=tau;
      step++;
}

The method gillespie_step takes a random generator and exit the time to the next reaction and the index of the method that has been applied. It returns true if there is a reaction actually taking place. If the propensities are all zero gillespie_step returns false.

notes:

1- The idx returned here is internal you can get the method using

rule r = rec.rec.get_rule(idx) 

2- The total_time and step computation are optional it is only to keep track of time and reactions

Versions:

2016/02/26: version is 1.0.0 and should be working

TODOS:

• insert graph command into reactor's methods
• more test functions
• finish trimolecular (enzyme) reaction