Starting an Experiment

You should have completed both setup and calibrations before proceeding to an experiment.

Highly recommended:

1. Read the main Experiment pages for helpful information not listed here and an example experimental workflow.

2. Run an experiment with water before doing so with cells, especially if you change the code

Questions?

Ask about experiments in the relevant category on the forum.

Setup

1. Prepare vials

2. Start the server

3. Sterilize the fluidic lines

   1. Instead of the GUI, use send_command.py

   2. The slow pumps (pink) will need to be run for >200 seconds to fully flush the lines

You will have one command line window for each server and each experiment running. It can also be helpful to have a separate window for send_commands.py

For example for two min-eVOLVER experiments:

• 2 server windows (server environment)

• 2 experiment windows (dpu environment)

• 1send_commands.py window (dpu environment)

An example fluidics layout for basic chemostat or turbidostat. If necessary, inducer can be programmed to be controlled via the low flow-rate pumps (not shown).

1. Load the vials

   1. Use send_command.py to fill the vials to appropriate volumes

Do not inoculate cells until after starting the experiment if you want accurate readings. There is innate variability in the OD of the vials (among other things) and we will blank to your vials during experiment start.

Vials set up for a basic chemostat or turbidostat.

1. Use send_command.py to set to correct temperature

   1. A calibrated temperature command is in your calibration file temperature_calibration.xlsx

   2. Temperature affects OD readings and we need a good initial OD to act as a "blank"

2. Allow min-eVOLVER to come to temperature

Running the Experiment

Make sure that your eVOLVER computer is set to never sleep. If your computer falls asleep while you're running an experiment, you will not be collecting data during that time. See more info here.

In a separate window from your server command line, follow the command line start guide.

1. If running more than one min-eVOLVER at a time: you need a separate experiment folder and command line window for each min-eVOLVER (and different port number)

2. Start the experiment using the command:

   1. python3 eVOLVER.py -i localhost:<your_min-eV_port>

   2. python3 eVOLVER.py -i localhost:5555

Ending an Experiment

1. Clean up the experiment

2. Data is in the data files