Octopus provides ability to create control programmes for laboratory automation using Python 3.9 and Twisted, and real-time remote monitoring over http/websockets for running protocols.

It can provide a command-line interface for interacting with machines using virtual instrument interfaces, or for creating scripted protocols to be run.

It is primarily designed for flow chemistry equipment; it is designed to work by defining parameters to set for each virtual instrument interface, rather than by defining methods to be called.

Blocktopus is a web-based user interface for definind octopus experiments based on the Google Blockly block-based programming environment.

Blocktopus Installation

Download Repository

Download by cloning the repository:

git clone https://github.com/richardingham/octopus.git
cd octopus
mkdir data

(Optional) - add plugins:

• Either, rename octopus-plugins.txt.example to octopus-plugins.txt and add any plugins you want to use.
• Or, create a plugins directory and pull any plugins into that directory.

Option 1 - Run in Docker

Build and run docker container:

docker build -t "octopus:latest" .
docker run -it -p 8001:8001 -p 9000:9000 -v /app/data:/app/data octopus:latest

Access the interface:

http://127.0.0.1:8001

Option 2 - Run without Docker

Install requirements and build

pyenv local 3.9.5
pip install -r requirements.txt
pip install -r octopus-plugins.txt
yarn install
yarn run build

Start the application

python octopus/blocktopus/server/server.py --plugins-dir=plugins

Use --help for all options.

Access the interface:

http://127.0.0.1:8001

Octopus only installation

pyenv local 3.9.5
pip install git+https://github.com/richardingham/octopus.git

Octopus - command line

$ python -m octopus.console

>>> reactor = vapourtec.R2R4(serial("/dev/ttyUSB0", baudrate = 19200))
>>> reactor.power.value
off

>>> reactor.pump1.target.set(1000)
>>> reactor.power.set("on")
>>> reactor.power.value
on

>>> reactor.pump1.pressure.value
1866

• [Read the full documentation](doc/Octopus Documentation.md)

I recommend the use of GNU screen when running long experiments on a remote computer, to avoid having a network disconnection terminate the experiment. For a good introduction to screen, visit aperiodic.net.

Plugins

Instrument interfaces are provided via plugins.

A plugin is any python package that provides instruments. These should be installed using pip. For instruments to be auto-discovered by Blocktopus there should be an entry point to blocktopus_blocks defined for each block in the setup.py.

See octopus_wpi for an example.

Available Machine Interfaces

• Gilson - 506C Control Module, 233XL Sample Injector, 402 Syringe Pump, 151 UV/Vis.
• Heidolph - Hei-End Hotplate.
• Kern - PCB Balance
• Knauer - K-120, S-100 HPLC pump.
• [Mettler Toledo](doc/Manufacturer%20-%20Mettler Toledo.md) - Balance, iC IR connector.
• ThalesNano - H-Cube.
• Vapourtec - R2+/R4. (Contact author for access.)
• VICI - Multi-Position Valve.
• World Precision Instruments - Aladdin Syringe Pump.

Using Phidgets

Drivers for some Phidgets devices are available. Before use, the DLL and API must be installed.

• [Phidgets](doc/Manufacturer - Phidgets.md).