Creating and editing config files

Experiment config files

This file contains the experimental parameters of your experiment and is referenced at various points during the execution of the workflow.

• Format: Each config file is a JSON, which has particularly formatting requirements. You can learn more and validate your JSON drafts here.
• Creation: You can manually create your own config files, but we advise using the notebook titled "Create_Expt_Config" and simply fill in the prompts to ensure that everything is correctly formatted. A JSON is a set of key-value pairs and the keys need to be exactly right or the workflow execution notebooks won't work because they won't be able to pull the information stored with those keys.
• Storage: Experiment config files should all be stored in one directory, and the path to that directory should be correct in the top part of every workflow execution notebook, that way you'll be able to select the correct experiment whenever you run the notebook.

Hardware-Labware config files

Jubilee is equipped with a set of limit switches that are activated at the start of each work session to define the dimensions of the work envelope. But the positions of tools and labware relative to each other within that envelope must be defined in absolute numbers of jubilee motor units. Basically the Jubilee doesn't "know" where anything is and you have to tell it precisely, and update these numbers if you use new labware or new tools/bedplates.

Use the Duet Web Controller to manually adjust the positions of the toolhead (x,y) and the bedplate (z) to get things where you want them and then you can read the numbers off the screen and save them into the relevant config files.

Some additional notes for specific harware/labware items:

• 'media_reservoir' is whatever vessel you want to use to hold media for dispensing into 24-well plates. Currently the system assumes you will use vessels of the same dimension for all media. The vessel should also fit inside the rectangle of position 0 on the bedplate. We recommend a deepwell petri dish or a reagent reservoir. The media_reservoir object in the config file just carries the x,y coordinates of the center of the reservoir, which is where the syringe tool will aim.

*'z_dict' covers the z-positions associated with dispensing. The "aspirate" height must be adjusted to a position that will put the end of the syringe just above the floor of the media reservoir. The "disepense" height should be just above each well in the target 24-well plates.

*Tool positions Each Jubilee has an index defining the different tools available to it (see "Tool configuration" for more details). The names of the tools in each position are defined in the hardware-labware config file so that tools can be called by name in the notebooks. When you set up your system your tools may be at different positions within Jubilee's internal index so make sure that these numbers are updated.

*#Volume calculations

dispenses_per_syringe_fill = 20 dispense_mL = 1.5 #In mL vol_conversion = 3.9 #One mL is 3.9 units. dispense_offset = dispense_mL * vol_conversion

• "inoculation_loop_z_dict" : {"collect": -34.7, # what height fully immerses the inoculation loop in the reservoir? "move" : -7, # what height clears all labware to move between reservoir/well plates? "transfer" : -32 # what height fully immerses the innoculation loop in the well plate? }