The standing source plate: what is in each well, how concentrated it is, and how much is left.
This is a physical object on a shelf, not a description of one run. Nobody re-racks eight plasmids before every build — you keep a normalized working plate and draw from it, so the app keeps its own record of what is in yours.
Concentration enters the data model here. A GenBank file records a sequence, not how much of it is in your freezer, and the fmol maths needs both. A well may override the library’s measured value, because the same plasmid diluted into two wells is two numbers.
Volume is tracked across runs. A sweep draws from a connector well ninety-six times. Running dry at column 9 is not something worth discovering at the plate reader, so a run is checked against what is left before it starts.
Wells naming a plasmid the library no longer has are flagged on load. A plate is edited over weeks and the index is rebuilt under it.