Jun 07, 2024

Setting and Customizing OT-2 for LAP Entries

DOI
https://dx.doi.org/10.17504/protocols.io.3byl49jxjgo5/v1
Setting and Customizing OT-2 for LAP Entries
  • 1Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
Biocomputation Lab
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DOI: https://dx.doi.org/10.17504/protocols.io.3byl49jxjgo5/v1
Protocol Citation: Ana Mariya Anhel, Lorea Alejaldre, Ángel oñi-Moreno 2024. Setting and Customizing OT-2 for LAP Entries. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl49jxjgo5/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: May 16, 2024
Last Modified: June 07, 2024
Protocol Integer ID: 99941
Keywords: experiments with the lap entry script, lap entries automation script, lap entry script, custom labware to the ot app, lap repository, experimental validation protocol, lap entry run, lap repository entry, files between the robot, uploading custom labware, ot app, running experiment, more information on each script, robot, essential for execution, robot system, documentation, experimental process, execution
Funders Acknowledgements:
Comunidad de Madrid
Grant ID: Y2020/TCS-6555,2019-T1/BIO-14053
MCIN/AEI
Grant ID: CEX2020-000999-S,PID2020-117205GA-I00
ERC
Grant ID: 101044360
Abstract
Automation scripts such as those included in the LAP repository (https://www.laprepo.cbgp.upm.es/repository/) require set up steps that not directly part of the experimental process but are essential for execution.

This protocol is divided into 5 sections: connecting to an OT-2, transferring files between the robot and the user system, creating and uploading custom labware to the OT app and robot system and preparing the robot system.
These steps establish the necessary environment for running experiments with the LAP entry scripts and user-specific variables.

Not all sections are required for every LAP entry run. For more information on each script in the LAP repository, visit www.laprepo.com and refer to the documentation attached to each entry. LAP repository entries can contain links to protocols.io entry to provide a step by step experimental validation protocol.
Before start
This protocol consists of various sections with interlinked steps to transfer files to an OT-2 robot such as variables files, script or customized labware. It is not always necessary to complete all of them to run a LAP entry protocol (i.e your protocol does not use customized labware)
Connect to the OT-2
Creation ssh-key connection

An OT-key should be generated to connect to the robot, and it is done with the ssh-keygen command and transferring the public key to the OT.
For more information about how to generate and set the connection between your computer and the Opentrons robot, visit https://support.opentrons.com/s/article/Setting-up-SSH-access-to-your-OT-2
Connect to the robot

To connect to the robot's system to perform different actions such as installing packages, check files that are in the system, etc.

Find the IP of the robot

In the OT app go to Devices -> Robot you want to connect -> Superior 3 dots -> Robot Settings -> Networking





Note
Take into account that the IP of the robot could chang from time to time or if you change the network where the robot is connected so it is a good practise to check the IP regularly

Note
In case you are phyisically connected to the robot via USB the IP will appear in the same window but under the section Wired USB

Connect to the robot

Either in a bash (unix systems) or powershell (windows systems) use the command ssh
Command
Connect to Linux based OT via ssh
ssh -i [path ot_key] root@[Robot_IP]

Expected result

Window in a Powershell that shows an OT logo which is a sign of being inside of the robot system


Transferring files between user system and robot system
Connect to the robot

You can either connect on the same inalambric network as the robot or by USB
Find the IP of the robot


Transfer the files

In different systems you can/must transfer the files in different ways always taking in account that the system of the OT-2 robot is a Linux Raspberry
MacOS/Linux

We can use the bash or command line to transfer the file(s) with the following command
Command
Passing Files to OT
scp -i [ot_key] [file_to_send] root@[IP_OT]:[final_path]
The ot_key is referring to the private key created in step 1,

You can face difficulties transferring files in MacOS Ventura (13) and Sonoma (14). These problems can be solved by adding the argument -O (uppercase o) to the command
Command
Transferring files to OT (MacOS 13 and 14)
scp -O -i [ot_keypath] [file path to send] root@[IP_robot]:[final_path]

Windows

There are several ways to send files from a Windows to a Linux system (for example, with a virtual machine or Windows Powershell in the latest versions of Windows). With the latter you can use the same steps as in 5.1

Another way is using FileZilla (https://filezilla-project.org/download.php?type=client).

You can set the connection between your computer and the OT-2 robot system as follows.
Open Filezilla -> File (in the toolbar) -> Site Manager -> New Site (Press button) -> Rename Site
Now that the site is created you can see on the right the settings of that particular site. In the General tab Change Protocol to SFTP. Then, introduce in Host the OT IP, change the Logon Type to key file, change User to root and give the directory where the OT key is. It should look something like the following image

Example of setting the FileZilla to transfer files from Windows (our computer) to Linux (OT)

Then press Connect, and we will have a connection between our computer and the robot.

After this connection, we should be able to move the files that we want to the final path of the robot that we desire to send them.
This method can be used as well in some Linux and MacOS systems
Exit the robot

To return to your system you only need to type exit in the command line
Preparing Robot OS
Check needed packages and versions of LAP entry

In the Requirements Section of each LAP Entry you can find that the protocol/entry needs more packages than the ones are installed in the OT-2 system
Check python packages of robot

To know which packages are needed to be installed in the opentrons robot you can connect to the robot ()and get a list of all the packages and their versions installed in that scpecific python

Take in account that there are some packages like math or random which versions are specified or linked to the python version
Connect to robot

Use pip command

You can use the pip command to get the entire packages that are installed in your robot's version of python. Take in account that the packages that are by default in python such as math will not appear in that list
Command
List installed pip packages (Unix)
pip list
To store the packages of the robot in a file for the future you can use the pipe >
Command
List installed pip packages and save (Unix)
pip list > [name_file_store_packages]
If you want to store this information in your computer you can transfer that created file

You can check for a specific package with the following command
Command
List installed pip specific package (Unix)
pip show [name_package]
With this last command you can have 2 type of results:

  1. A small piece of text giving you the name, version and summary of the package, within other information. This will mean that the package is installed on the python
  2. Warning message telling you that the package does not exist. This means that either the package has not been installed in that version of python or that it is not installed with pip (it is by default in python or it is installed with other vias like conda)

Install needed packages

To install 1 or more packages you can use any of the following 2 commands
Command
Install package Python
python -m pip install [name_package_1] [name_package_2] [name_package_3]

Command
Install packages with pip
pip install [name_package_1] [name_package_2] [name_package_3]
Make sure that the robot has access to the internet so it can download the packages

Note
For more information about installing packages in the opentrons robots, check the following Opentrons page: https://support.opentrons.com/s/article/Using-Python-packages-in-Python-API-protocols

Exit the robot

To return to your system you only need to type exit in the command line
Uploading custom labware
Creation of .json custom labware file

The description file can be obtained by describing the labware dimensions at https://labware.opentrons.com/create/

Expected result
You will receive from this page a zip with a .py script in which you can test the labware and a .json file that is the actual definition of the labware

Uploading file to the OT App
In the OT app, we need to perform the following route: Labware -> Import -> Choose File -> Select file we have created in step 9


Expected result
After uploading the labware you should be able to see the new labware in the Labware tab of the OT App, all custom labware can be found more easily in the category Custom Labware


In some LAP entries or in versions of them there is a need to upload in 2 places the created files so you need to complete as well the following steps.
Uploading definition to OT robot system

Note
We do not need to execute this part every time the protocol is used, only when that labware is not included in the OT official labware and the labware file is not in the robot

Create a directory with the defintion

We need to create a directory with the API name of the labware, the name that we are going to use to load it in the opentrons
Rename .json file

We need to rename the .json file that the opentrons labware creation to 1.json and place it inside of the directory created in Step 13.1
Transfer the directory to a specific location

To upload the directory with the .json file that represents the custom labware that has been created in step 11 to the robot systems we are going to use the steps from 3 to 6 transferring the file to the final path /data/labware/v2/custom_definitions/custom_beta with some changes with the argument -r as shown in the following command
Command
Transferring the used custom labware to OT (Linux)
scp -i [ot_key] -r [custom labware directory path] root@[IP_OT]:/data/labware/v2/custom_definitions/custom_beta
You can face difficulties transferring files in MacOS Ventura (13) and Sonoma (14). These problems can be solved by adding the argument -O (uppercase o) to the command
Command
Transferring the used custom labware to OT (Linux)
scp -O -i [ot_key] -r [custom labware directory path] root@[IP_OT]:/data/labware/v2/custom_definitions/custom_beta