Hah! You raise a good point. This is on my to-do list but evidently not high enough to get seen-to in a reasonable amount of time. Some things to get you started:

If you look at the SI for the PLoS Biology paper there is a superior modelling SI section which includes some additional diagramatic description of the software:
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000794

After reading that I would look at how the “customprogram” sections are structured in the python code, as these are easily adaptable for many experimental protocols one might want to implement.

If you want more customisation (i.e. new features in the GUI) it is also not too difficult, there are essentially four primary things you need to add, and each of these can be copied from any of the features already in there. They are:

1. You need to add new buttons/fields to the html file with new “id” attributes related to what you want them to do.
2. You need to add new scripts at the bottom of the html file which define how the data from the above buttons/fields is sent to the python back-end.
3. You need to add new lines to the .js file that update any labels/fields in the html that need to dynamically respond to changes in the python back-end.
4. Finally, you need to adjust the python back-end to do the hardware implementation of whatever function you are trying to do.

I realise just looking at those instructions is a bit confusing – to figure it out in practice just pick one of the features (say, the stirring interface) and trace through its corresponding html / javascript / python code.