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🏁 0. Start by cloning this repo

In this notebook we will demonstrate how to set up the contents of this repo on your virtual machine, enabling us to predict interactions between microbial community members in the following markdown files.

💲 Running the code

In the following .md files, the dollar sign symbol within code chunks denotes lines of code that you should run in your terminal window, e.g.

$ echo "down here you can see the expected output of your commands"
Click to see expected output 
down here you can see the expected output of your commands

🌀 Clone this repo

First open the terminal on your virtual machine. Click on the icon at the bottom left of the dekstop to show applications, then search for the terminal. Next, use the cd command to change directory into your local desktop. Do not include the $ when you copy code into your terminal, this symbol is used to indicate commands you should run on your own terminal.

$ cd ~/Desktop

Use the git command to download repo contents to your virtual machine.

$ git clone https://github.com/franciscozorrilla/EMBOMicroCom.git

Copy the code above after the $ into your terminal window.

Click to see expected output 
Cloning into 'EMBOMicroCom'...
remote: Enumerating objects: 38, done.
remote: Counting objects: 100% (38/38), done.
remote: Compressing objects: 100% (33/33), done.
remote: Total 38 (delta 11), reused 17 (delta 4), pack-reused 0
Receiving objects: 100% (38/38), 219.94 KiB | 670.00 KiB/s, done.
Resolving deltas: 100% (11/11), done.

🛑 Note: if you use the built-in code-copy button make sure you delete the $ before entering the commands in your terminal, otherwise you will get an error message such as

$: command not found

⚙️ Configure $ROOT variable

It will be useful to write our working directory to a variable, so we can make sure to be reading and writing files in the correct location. First, move into repo folder using cd.

$ cd EMBOMicroCom

Set the variable ROOT as the root of your EMBOMicroCom repo

$ ROOT=$(pwd)

To navigate to the root folder from your terminal from any directory

$ cd $ROOT

List contents of cloned repo using ls

$ ls $ROOT
Click to see expected output 
LICENSE			README.md		bigg_classes.tsv	exercises		media.tsv		models			plot_interactions.R

Verify the path in your $ROOT variable using echo

$ echo $ROOT
Click to see example output 
/home/training50/Desktop/EMBOMicroCom

🥛 Yeast - Lactic Acid Bacteria interactions

Familiarize yourself with the following case study involving S. cerevisiae and L. lactis:

Fig.1 - Graphical abstract from Ponomarova et al. 2017

In the following exercises, we will use a simple two-species system described in the above publication to model metabolic interactions. In particular, we will focus on the interactions between L. lactis and S. cerevisiae

💎 Discussion questions

  • Do you expect cross-feeding of metabolites between S. cerevisiae and L. lactis? If so, what metabolites?
  • How do environmental media conditions influence metabolic interactions? Do you expect more or less interactions in rich vs minimal media?

Move on to exercise 1