design_genetic_circuit
Read-only
Design a genetic circuit that computes: give it a logic function and it synthesizes a NOR/NOT netlist, assigns real characterized repressor gates from a Cello UCF library, predicts the dynamic range between ON and OFF, and emits the construct's DNA. The gate parameters are MEASURED, from the published libraries, with the host and growth conditions they were measured under reported alongside — never estimated here.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| logic | No | the function the circuit computes: a named gate (NOT, AND, OR, NAND, NOR, XOR, XNOR, AND3, OR3, MAJORITY-3), or a truth table as one bit per input combination with the first input most significant (AND is `0001`). | AND |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| groups | No | comma-separated repressor groups the search may draw on. Narrowing this is how a large search is made tractable — and how a gate you cannot obtain is kept out of the design. Advanced. | |
| library | No | the characterized gate library to build from. Each was measured in one host under one growth condition, and the prediction inherits both. | Eco1C1G1T1 |
| sensors | No | comma-separated input sensors the search may use. Leave unset to consider every sensor the library carries. Advanced. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| reporters | No | comma-separated output reporters the search may use. Leave unset to consider all of them. Advanced. | |
| max_assignments | No | refuse rather than search past this many assignments. A ceiling, not a target: the search is EXHAUSTIVE, so it is never sampled — a best-of-some reported as a best-of-all is a wrong answer rather than a slow one. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| dna | Yes | the construct broken into devices and parts, each with its own sequence, plus the solved device order and every placement constraint the library declares | |
| score | Yes | the predicted dynamic range: the dimmest ON output divided by the brightest OFF, across every input combination | |
| curves | Yes | each assigned gate's transfer function sampled around its own midpoint, with this design's operating points on it — one curve per physical gate that won a row, so a group won by two gates gives two curves | |
| netlist | Yes | the NOR/NOT netlist synthesized from the logic function, and the table it was checked to compute | |
| sequence | Yes | the construct's DNA, the devices concatenated in the order the library's placement rules put them | |
| toxicity | Yes | what the circuit costs the host: relative growth per truth-table row, the worst row, and per-gate detail — plus how many of the assigned gates actually carried a measured growth table, because a growth of 1.00 means something different when nothing was measured | |
| libraries | Yes | every shipped library with its host, growth conditions and gate count, so a caller can choose one | |
| placement | Yes | how the device order was solved: the arrangement including the library's landing pads, how many of its placement constraints bound this construct, and any rule whose operator is not implemented | |
| assignment | Yes | which sensors, gate groups and reporters the winning design uses | |
| truthTable | Yes | every input combination with its logic values and its analog levels in RPU, per node | |
| explanation | Yes | the derivation chain: conclusion, interpretation, earned cautions and machinery, generated from this run |