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jean — Molecular Biology & Genomics

run_gel_lane

Read-only

Resolve a gel lane (ladder / plasmid / digest / pcr) into [bp, form] bands for the open plasmid.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
_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.
detailNofor a ladder: its name; for a digest: comma-separated enzymes. Unused for plasmid/pcr lanes. Only applies when source is ladder or digest.
sourceYeswhat this lane holds. Values: ladder (DNA ladder), plasmid (Uncut plasmid), digest (Restriction digest), pcr (PCR product).
_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.
product_bpNofor a pcr lane: the product length, e.g. the length of the record `pcr_amplify` emits. Required for a pcr lane. In bp. Only applies when source is pcr.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
bandsYes[bp, form] gel bands

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, openWorldHint=false, and destructiveHint=false, so the safety profile is covered. The description adds domain scope ('for the open plasmid' and the lane types), but it does not disclose side effects, authentication needs, rate limits, or any further behavioral trait beyond what the annotations provide.

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

Conciseness5/5

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

The description is a single front-loaded sentence that states the action, the input domain, and the output form without any filler. Every word contributes to identifying the operation.

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

Completeness4/5

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

Given that an output schema exists and schema coverage is 100%, the description need not explain return values or parameter details. Annotations cover safety. The remaining gap is sibling differentiation, but the combination of description, schema, and annotations is sufficient for an agent to invoke the tool correctly.

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%, so the schema already documents source, detail, product_bp, _subject, and _files, including the conditional rules for detail and product_bp. The description only restates the source values that are already present in the enum description and adds no extra parameter syntax or conditional meaning. Baseline 3 is appropriate when the schema does the heavy lifting.

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 uses a specific verb, 'Resolve', and names the resource, 'gel lane', plus the output shape, '[bp, form] bands'. It enumerates the lane types (ladder / plasmid / digest / pcr) so the agent can tell what inputs are accepted, but does not explicitly differentiate this tool from sibling tools such as run_gel_plate or draw_gel.

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 guidance, no when-not-to-use guidance, and no named alternatives. The phrase 'for the open plasmid' implies a context, but it does not tell the agent how to choose this lane-level tool over run_gel_plate or draw_gel.

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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