Sometimes a protocol has variable inputs each time it is run --- different volumes to pipette for each well, different wells to pick in the plate, etc. -- and the best way to input those values is with a comma separated values, or CSV, file (also known as a spreadsheet). Some examples of these protocols are:
- Normalizing concentrations in a plate, where each well and requires a different amount of volume.
- Hit picking, where the wells that should be transferred into a destination plate are defined by an upstream assay (plate reader, etc).
- Combinatorial mixes, where each well has a different volume and combination of compounds to be added
For each of these protocols a CSV input is a convenient way to streamline automating these protocols. The below is a guide for how to request a protocol from us that uses a CSV input.
Using a CSV in your Protocol
In order to develop a protocol that uses a CSV input for you, we will need to know a few things.
Expected values: we'll need to understand what values you're expecting to be in each cell of the spreadsheet. Are there multiple values (volume and compound name, for example)? Are they integers, names, or true/false indicators?
Value Meanings: now that we know what values to expect, we need to know what those values mean. Are they volumes to dispense into the well, or aspirate out? Does "true" mean to pick that well, or skip it?
Value Format Example: now that we know what values to expect and what they mean, we need to see an example of the format those values will be in when you input them into the protocol. The best way to do this is to include an example of a spreadsheet you'll be using with the protocol request you make. Just attach that file to the protocol request!
Using your CSV Input
Once you submit all of the above information to us, we will develop your protocol. When it is done, we will put it on our Protocol Library (protocols.opentrons.com) and send you a link to it.
On the Library, you'll be presented with an "Upload File" field. This is where you will input your CSV.
Simply click "choose file" and browse to your CSV file on your computer. Once you have selected it, our software will compile your protocol using that CSV input, and you'll be able to download your protocol to run on your OT-2!