Command Line Start Guide

If you are new to command line / bash, you can start here!

Overview

Reasons you might use command line experiment start:

1. Doing a custom experiment

2. Unable to install GUI or getting errors you aren't able to fix easily (post on the forum first)

Protocol

Set your computer to never fall asleep to prevent experiments from being halted.

1. In a command line window, enter the dpu virtual environment.

   1. Navigate to the DPU directory

      • Use this command: cd <path_to_dpu>

   2. Enter the command:

      • On Mac OS:

        • source dpu-env/bin/activate

      • On Windows PowerShell:

        • dpu-env\Scripts\Activate.ps1

2. Navigate to your experiment folder

   1. This should be in dpu/experiment

3. Copy the template folder and rename it for each experiment

   1. Navigate into your new experiment folder

4. Alter settings in custom_script.py

   1. EVOLVER_PORT = set correct IP of the eVOLVER

   2. Set initial temp and stir settings

   3. custom_script.py has basic settings for running chemostat and turbidostat experiments, but you can also customize. To learn more click here.

5. Start the experiment using the command:

   1. python3 eVOLVER.py -i <your_evolver's_IP_address>

   2. python3 eVOLVER.py -i 192.168.1.9

6. Calibrate to blank

   1. Temperature should be fully equilibrated before this

   2. DO NOT add cells before blanking, whatever OD value the cells + media have will be subtracted from future measurements

7. Stop the experiment using the keyboard shortcut control+C

   1. One control+C pauses the experiment from recording data

   2. Two control+C stops the experiment

8. To change parameters mid-experiment or restart from blank data files:

   1. Stop the experiment fully

   2. Change parameters in custom_script.py

   3. Restart the experiment

      1. Continue to keep your data

         1. Overwrite to make new blank data files and throw away your old experiment. NOTE: you will lose your OD blank and will need to make a new one (a hassle if you have already inoculated with cells)

9. You can run experiments on more than one eVOLVER at a time

   1. Create a new experiment folder (different custom_script.py) and change IP

   2. Follow this procedure in an additional command line window

You can graph your experiment using the graphing tool here.

Ending an Experiment

1. Clean up the experiment

2. Data is in the data files