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PlasmoTron

Semi-automated culture of malaria parasites

Home - Installation - Deck setup and calibration - PlasmoTron tutorial

Prerequisites

Hardware

Liquid handling robot

PlasmoTron is designed for use with OpenTrons OT One-S Hood, installed in a tissue culture hood.

We would suggest that you get familar with calibrating and operating the OpenTrons robot using conventional protocols before you try to establish PlasmoTron, because familiarity with how the robot works will be helpful.

While PlasmoTron could readily be adapted to other robotic systems (see FAQ) this will require a little work.

Computer to control robot and host server

PlasmoTron is intended to run on a dedicated computer, which will both control the robot and also host the web app and database that stores culture information. This computer needs to be near enough the robot to connect by USB. It should also be networked to the internet or an intranet so that users can access their culture information remotely. It is helpful if the computer can be directly controlled (mouse, keyboard, screen) from the tissue culture hood, especially in the event of a network outage. The computer does not need to be powerful.

The approach we ourselves use is to use a $40 Raspberry Pi computer, with an integrated touch screen, which is mounted to outside of the tissue culture hood. The USB and power cables to the robot are run directly into the hood through the gasket seal. Many similar alternatives would be possible, including an i86-based tablet PC.

Software

Operating system

Linux and OSX should both be fine.

OpenTrons app

To calibrate the positions of labware on your robot you will need to install the OpenTrons app This is trivial for many systems. For a Raspberry Pi it is rather more complex as you will need to install from source - describing that process is beyond the scope of these instructions.

In addition if you have a small-screen for the Raspberry Pi, you may want to establish a system for remote connection over VNC to simplify use of the OT App during calibration.

Dependencies

Python

Your environment should be set to use Python 3.6+, which is required for OpenTrons.

OpenTrons API

You need to install the OpenTrons API which provides a package to allow the use of the OpenTrons robot in arbitrary Python scripts.

pip install --upgrade opentrons 
Flask

Flask is the lightweight web server on which PlasmoTron runs. It is a prerequisite for PlasmoTron. We have been using Flask 0.13-dev.

Installation of PlasmoTron

First clone the latest stable version from GitHub.

git clone https://github.com/theosanderson/plasmotron.git

Now navigate to the PlasmoTron directory:

cd plasmotron

First we need to initialise the database:

export FLASK_APP=app.py
flask initdb

First test run

Now let’s try running the app:


flask run

With a bit of luck you will see:

pi@raspberrypi:~/flask $ flask run
 * Running on http://127.0.0.1:5000/ (Press CTRL+C to quit)

Which means the web server is now running.

Fire up your browser on the machine and go to http://127.0.0.1:5000/ Hopefully you will see something like this:

If so, you should be all set in terms of installation.