About this package
========================

Gillespie is a software package for simulating stochastic chemical 
reactions. The following functionality is included:

1. Reactions via the Gillespie algorithm.
2. Delayed reactions: products appear a specified time after the
reaction took place.
3. The reaction volume V can grow and divide after a user set time 
to simulate the growing and division of cells.


Authors
========================
Pieter Rein ten Wolde @ FOM Institute AMOLF [Founder]
David Zwicker @ FOM Institute AMOLF
Mark Bosman @ FOM Institute AMOLF
Joris Paijmans @ FOM Institute AMOLF

License
========================

This package is distributed under the terms of GNU General Public License
version 2.  See COPYING.


Files in this package
========================

1. README         : This file.
2. COPYING        : GNU license.
3. parse.pl       : Perle script for parsing a model file to input files for the 
                    Gillespie software.
4. kai_analyses.pl: Generate data specific for the kai model. (Specified in kaiABC.mdl)
                    Use by typing: ./kai_analyses.pl <model_name>
                    inside the models directory.
5. Makefile       : makefile to compile the program.
6. Makefile.*     : makefiles which specify the paths to the required libraries.
7. .c,.h          : C source files for the Gillespie program.

Model files

1. kaiABC.mdl     : Example model file for the kai circadian oscillator.
2. kaiKondo.mdl   : 2 state kaiC model used in Nishiwaki et al., JBC - 2012, with 
                    dephosphorylation only via ATP regeneration.        
3. kaiRust        : 4 state kaiC model by Rust.
4. kaiRustl       : 4 state kaiC model by Rust with labeled phosphate groups.

Prerequisites
========================

1. C compiler (gcc)
2. C standard libraries
3. GNU make
3. Perl

Repository
========================
For updates visit the main repository for this project:

https://github.com/TheJoris/Gillespie.git


Installing and Building
========================
Create a directory where you want the files to go

./mkdir <directory_name>

Extract the archive to the directory

./tar -zxvf Gillespie.tar.gz -C <directory_name>

To make the program, first edit the top line of Makefile (./Makefile) 
such that it includes the correct makefile for your system. This file
specifies the paths to the required libaries. Then type

1. ./make clean
2. ./make all

This should compile all the source files and return an executable called
'Gillespie'.


Create and parse a model
========================

First you need a model file. A describtion on how to define components and reactions for a 
chemical model is given by typing:

./parse --help

An example model file (for the kai circadian oscillator) is 
given in 'kaiABC.mdl'.

The model file needs to be parsed such that it can be read by the program. 
To parse the model file, type:

./parse.pl <model_file> > Gillespie.inp

This creates <input_file>.components, <input_file>.reactions
and Gillespie.inp, which are all used by the Gillespie program. Because 
the Gillespie program will generate a lot of output files, it is a good 
idea to put these files in a seperate directory, and run the software from
here.


Running
========================
When <input_file>.components, <input_file>.reactions and Gillespie.inp 
files are present (see 'Create and parse a model'), you can propegate 
your model by typing:

./Gillespie <input_file>

(chmod 744 Gillespie to make file executable)

When the simulator is finished, it will create a file for each component 
in the system containing a timetrace of the number of particles.