Purpose

This is a platform for agent-based modelling developed in Julia for a ten-week bioinformatics project by Ryan Carey, Lewis Kindeleit and Antoine Messager. Here are the installation instructions. For usage instructions and more information, refer to the manual (manual.pdf) Using a graphical user interface or REPL, it allows simulations to be performed, which can be viewed graphically or outputted to pickle for analysis in Python or Julia.

Installation

The CBMP has been developed in Julia 0.4. in RedHat Enterprise Linux Workstation release 6.2, and has also been tested on Ubuntu 14.04 in Julia 0.3. The platform should run on any operating system that has Julia installed, however there may be slight differences between them.

To run the CBMP, first Julia must be installed. If this has already been done, please skip to the Dependencies section.

Detailed Instruction

To install Julia, follow the instructions on the website, http://julialang.org/downloads/. Similarly, install Python at www.python.org/downloads if you do not have it already. The Julia packages Winston, Tk and PyCall are most easily installed using the interactive Julia prompt. The Julia prompt is opened by entering into the command line:

> julia

To install the required packages, enter the following into Julia's interactive prompt:

> Pkg.add("Winston") 

> Pkg.add("Tk") 

> Pkg.add("PyCall")

To return to the command line, enter:

> exit()

You can install the python package Pickle by typing into the command line:

> pip install pickle

If all of the dependencies are already installed, then all you need to do is download the repository and run CBMP.jl.

Dependencies

The installation depends on:

• Julia 0.3 - 0.4 with:
  • Winston
  • Tk
  • PyCall
• Python (tested on 2.8 and 3.4 but it should work for other versions) with:
  • Pickle

Once you have installed the dependencies, all you need to do is download the repository and run CBMP.jl. If you have git installed, you do this by entering into your command line:

> git clone https://github.com/RyanCarey/abm-platform.git 

> julia CBMP.jl

The software comes with 2 different methods of inputting parameters and starting simulations: an easy to use GUI and a command line version. The GUI has been created with experiment design in mind; it gives the user fine-grained control of all parameters that describe the behaviour of cells and the way in which environmental stimuli diffuse through the environment, whilst providing immediate feedback.

The command line version, whilst being more complicated to operate, is much faster at performing simulations due to the lack of simulation display and increased parameter input speed. Parameters are input directly into the code and as such requires slightly more expertise to use. This option is intended to be used when experimental setup is already decided and multiple simulations are required to be run to collect data.

For explanation of how to use these versions, refer to the manual (manual.pdf)