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Jean — Molecular Biology & Genomics

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

NameRequiredDescriptionDefault
binsYesthe 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.
rulesNoj5/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.
_filesNoThe 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.
_subjectNoThe 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.
topologyNoGibson only: which products to enumerate per member. Values: circular (Circular), linear (Linear), both (Both). Advanced.circular
chemistryNo`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
constantsNoparts every member carries, assembled before the slot choices — the backbone and any fixed linker.
max_membersNocap on Cartesian members enumerated, before pruning. Advanced.
min_homology_bpNoGibson only: shortest terminal homology that counts as a join. In bp. Advanced.

Output Schema

NameRequiredDescriptionDefault
builtYesmembers that closed at least one construct
prunedYesevery combination removed before assembly, each with the rule that removed it — never dropped silently
recordYesthe first member's construct, as a record
membersYesevery built member: its slot→part lineage, the parts assembled, the construct(s) and any flaws
readingYeswhat was enumerated, built and pruned, read off the run
cartesianYesCartesian product size, before pruning (the product of the bin sizes)

Schema Changelog

Changes observed during successful MCP inspections.

  1. Added

TDQS

B3.2/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The description's claim of designing/creating is consistent with readOnlyHint=false, destructiveHint=false and openWorldHint=false, so no contradiction. Beyond the annotations it only supplies the slots/constants mental model; it says nothing about the member cap, rule-based pruning, homology requirements, or what the call produces, all of which matter for a generative tool.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

A single front-loaded sentence with no filler, using capitalization to anchor the two key concepts. It is efficient, though the terseness means the sentence is doing little work beyond framing.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists and the input schema is fully described, so return values and parameter details are covered elsewhere. Still, for a 9-parameter generative tool with nested objects and enum-driven chemistry/topology modes, the one-sentence description leaves the agent entirely dependent on the schema to understand scale, pruning and assembly semantics.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100% and the schema already documents bins, rules, constants, chemistry, topology and the advanced knobs in detail. The description's slots/constants framing adds a modest conceptual clarification of how bins and constants relate, but no syntax, defaults, or constraints beyond what the schema states.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description names a specific verb and resource ("Design a combinatorial library") and adds a conceptual model, SLOTS with bins of interchangeable parts plus CONSTANTS every member carries. It does not name any sibling it displaces (e.g. crispr_design_library, write_structure_library, assemble_multiple_inserts), so the domain is only inferred from the schema rather than stated.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

There is no explicit when-to-use, when-not-to-use, or alternative naming. "in one step" hints at a contrast with multi-step assembly tools, but that contrast is never made explicit, so the agent must guess whether to call this or a lower-level assembly sibling.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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