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PlasmoTron

Semi-automated culture of malaria parasites

Home - Installation - Deck setup and calibration - PlasmoTron tutorial

Deck set up and calibration

#Deck set-up

The deck layout is defined in equipment.py in the PlasmoTron folder.

Let’s have a look at one of those lines:

equipment['TubMedia']=containers.load('epmotion30', "D1","TubMedia")

The bit on the left-hand-side defines that this is a new piece of equipment called "TubMedia". That name is hardcoded into other parts of the programme so you don’t want to change it. There are two parts you can safely change. One is the second argument of the load function, currently "D1" which specifies where on the deck the container is to be found. Feel free to change these values as you wish.

The other part we could change is "epmotion30". This defines the type of container that is being used which determines its geometry.

OpenTrons has a whole lot of built-in containers. You can see them all here. You can also add your own containers, which we did in this case at the top with:

containers.create("24corning", grid=(4,6), spacing=(19.304,19.304), diameter=16.26,depth=18) #24-well plate

It is important that the deck layout section defines these key components:

This file can be left as it is or edited to suit your preferences.

#Small culture hoods [To add section on transposed tip rack here]

#Calibration Now we are ready to calibrate.

Close the PlasmoTron server and in a new terminal run:

source PlasmoTronPyEnv/bin/activate
cd PlasmoTron
python calibrate.py

If you have already practiced calibrating with the GUI app you will know what to do. Place the pipette in the bottom left well/tip of each container, and calibrate the plunger positions for the pipette.

Next up you can get to grips with PlasmoTron itself in the tutorial.