20.440 Problem Set 4 Tutorial

This respository was created as an educational exercise for the MIT class 20.440 Analysis of Biological Networks (Spring 2023).

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Overview & Data

The figure generated comes from data reported by Alfano (2015) in the supplementary section (relevant Excel file linked in ./raw_data). The figure shows a pie chart of various families of microbes found in the gastrointestinal tract of two koalas in captivity.

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Folder Structure

This root directory of this repository contains three main folders:

• src: Contains all needed code to process and visualize and save data and/or figures.
• raw_data: Contains the original, raw data that will be run by code in src.
• fig: Output figure visualizations.

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Installation

To see if everything works, navigate to the projects root directory and type in the command:

source ./run.sh

You can expect for all the figures to populate the fig folder.

Note: Running this shell script will check that you have at least Python 3.8 and create a virtual environment via venv to download dependencies.

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