design_combinatorial_library
Design a combinatorial library in one step: SLOTS, each offering a bin of interchangeable parts, plus the CONSTANTS every member carries.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| bins | Yes | the variable slots: each {slot, parts} names a slot and the interchangeable parts (record names/ids, or wired `record` outputs) that may fill it. The member set is the Cartesian product across bins. | |
| rules | No | j5/Eugene design rules that prune combinations: {kind:'notWith',a,b} (never together), {kind:'with',a,b} (if a then b), {kind:'notMoreThan',part,count} (at most count copies, constants included). Advanced. | |
| _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. | |
| _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. | |
| topology | No | Gibson only: which products to enumerate per member. Values: circular (Circular), linear (Linear), both (Both). Advanced. | circular |
| chemistry | No | `gibson` is terminal-homology assembly (Gibson/NEBuilder/In-Fusion/homology, one engine); `concat` is a deterministic head-to-tail join with no homology or digest. Values: gibson (End homology (Gibson)), concat (Concatenation). | gibson |
| constants | No | parts every member carries, assembled before the slot choices — the backbone and any fixed linker. | |
| max_members | No | cap on Cartesian members enumerated, before pruning. Advanced. | |
| min_homology_bp | No | Gibson only: shortest terminal homology that counts as a join. In bp. Advanced. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| built | Yes | members that closed at least one construct | |
| pruned | Yes | every combination removed before assembly, each with the rule that removed it — never dropped silently | |
| record | Yes | the first member's construct, as a record | |
| members | Yes | every built member: its slot→part lineage, the parts assembled, the construct(s) and any flaws | |
| reading | Yes | what was enumerated, built and pruned, read off the run | |
| cartesian | Yes | Cartesian product size, before pruning (the product of the bin sizes) |