MMDEpiCluster

Description

• This repository contains files required to run and replicate the MMDiff association pattern clustering experiment.
• Instructions are provided further down this document.

Instructions

Prerequisites

• Check out this repository.
• Preferred operating system: Linux / OSX.
• Functioning anaconda https://www.anaconda.com package manager.

Environment Setup

• Import the conda environment by running conda env create -f Conda-env/environment.yml from this project folder.
• Activate the conda environment by running source activate experiment_env.

Install MMDiff

• Check out the MMDiff3 package from github [NEEDS LINK].
• Start R.
• From R, load the package devtools by running library("devtools").
• Install MMDiff by running install("/Path/To/MMDiff/").

Run Setup & Generate Configuration Files

• Navigate to MMDEpiCluster directory
• Change permission of setup.sh to an executable file, i.e. chmod 700 ./setup.sh
• Run ./setup.sh. This creates the working directory Experiment_WD, and generates configuration files for the experiment. These will be located in Experiment_WD/Exp_conf
• In order to generate testing configuration files navigate to Experiment_WD/Exp_conf_test. From within this directory run python3 ../../Simulation_Script/generate_config_test1.py & python3 ../../Simulation_Script/generate_config_test2.py

Data Generation.

• Switch directories to Experiment_WD.
• From within Experiment_WD, start up Jupyter by running jupyter notebook.
• In Jupyter, open the notebook Validation Experiment and execute all paragraphs.

Data Analysis

• In Jupyter, open the Data Analysis notebook
• In paragraph 3, set sim_wd variable to point to the simulation directory
• In paragraph 3, set exp_wd variable to point to the experiment directory to be analysed
• Execute all paragraphs