Circuit netlist
The signal flow of a genetic circuit, drawn as the graph it is — which sensor feeds which repressor gate, and where two wires converge on one.
What it does
A logic function is not a list of gates, it is a shape. A AND B becomes three NOR/NOT gates
arranged so that two inverted inputs meet at a third gate, and the arrangement is the thing that
makes it compute — the same three gates wired differently compute something else. A gate list in
declaration order does not show convergence at all, which is the one feature of the circuit a
reader needs to check.
This is that graph. Signal flows left to right: input sensors on the left, the output reporter on the right, and each repressor gate placed one column to the right of the deepest input it reads, so a gate is always drawn after everything that feeds it. An edge is a wire — the promoter one gate drives and the next one reads.
What this computes
| Readout | What it is |
|---|---|
| Signal-flow layout | The position of each node by longest path from the sensors. A gate sits one level right of the deepest wire it reads, so convergence is visible as two edges arriving at one node. |
| Gate type | NOR or NOT, per node. A NOR is ON only when both its inputs are OFF; a NOT inverts its one input. These are the only two gate types a repressor library realises directly. |
| Repressor group | The family of the transcription factor assigned to that node — the protein that does the inverting. |
| Physical gate | The specific characterized variant of that repressor chosen for this design. The netlist is the same for every assignment; the variant names are what this particular one picked, and they are what the predicted dynamic range depends on. |
How to read it
Two edges arriving at one node is a NOR, and it is where the circuit actually computes. A single chain with no convergence is an inverter cascade, which changes the signal's level and its polarity but not what it means.
The group name and the variant name are different facts. A group is a repressor — PhlF, AmtR, SrpR — and a library usually carries several characterized variants of each, differing in the ribosome binding site in front of them and therefore in where their transition sits. The design chose one, and the transfer function drawn for that node belongs to the one it chose.
Electropherogram
Every dye channel of a fragment run on one axis in bases, with the size standard's own fragments drawn on it — the picture the peak table is read from.
Circuit transfer functions
Each repressor gate's measured dose-response, with the points this circuit actually operates at drawn on it.