# Command Line Start Guide

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If you are new to command line / bash, you can start [here](https://khalil-lab.gitbook.io/evolver/guides/command-line-usage)!
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## 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

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Set your computer to never fall asleep to prevent experiments from being halted.
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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](https://khalil-lab.gitbook.io/evolver/software/dpu/custom_script.py).
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](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/od-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

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You can graph your experiment using the graphing tool [here](https://github.com/FYNCH-BIO/dpu/tree/master/graphing).
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## Ending an Experiment

1. [Clean up](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/cleaning-up-after-experiment) the experiment
2. Data is in the [data files](https://khalil-lab.gitbook.io/evolver/software/dpu/experiment-data-files)