Getting Started

Contents

Download

Installation

To install MI-Sim, copy the downloaded zip file to an appropriate directory (e.g., a MATLAB working directory) and unzip it. Next, you will need to add MI-Sim to the MATLAB path:

It is recommended you add the directory to the permanent MATLAB path using the instructions found at: MATLAB search path.

Alternatively, you can add the MI-Sim directory and sub-directories to the \matlab path. You will need to execute the following lines of code every time you initiate a new MATLAB session.

    
%Replace next line with an appropriate path to your Mi-Sim directory
misim_user_path = 'mysoftware/misim';
g=genpath(misim_user_path);
addpath(g);

Quick Start

To start the GUI with default motif (‘Syntrophy’) and growth function (‘Monod’) use:

    
MI_SIM

from the MATLAB command-line.

Alternatively, specifying the motif and growth function names as input arguments will set-up the GUI environment accordingly.

Ecological interaction Motif name shortname
Commensalism Food chain ‘comm’
Competition Substrate competition ‘comp’
Predation FC with product inhibition ‘pred’
No interaction No common metabolites ‘no_i’
Cooperation Syntrophy ‘coop’
Amensalism Waste product inhibition ‘amen’
Competition/Syntrophy Three species food-web ‘thre’

  Growth function   shortname   Availability  
  Monod   ‘mon’   $\checkmark$  
  Contois   ‘con’   $\checkmark$  
  Tessier   ‘tes’   $\checkmark$  
  Moser   ‘mos’   $\checkmark$  
  Haldane   ‘hal’   $\checkmark$  
  Andrews   ‘and’   $\checkmark$  
  Thermodynamic (inhibition)   ‘the’   $\checkmark$  
  Thermodynamic (Hoh)   ‘hoh’   -  

For example, to start the GUI with a syntrophic motif and the Monod growth function:

    
MI_SIM('coop','mon')

User-Guide

You can download the user-guide via the link below [COMING SOON]. This document contains complete examples to start using the MI-Sim GUI.