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Jean — Molecular Biology & Genomics

list_experiments

Read-only

Your lab-notebook entries, newest first — id, title, tags, collection, when they changed, and the @plasmid / !action / &gel cross-references each one names.

Input Schema

NameRequiredDescriptionDefault
tagNoonly entries carrying this tag.
limitNohow many entries to return, newest first.
_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.
searchNomatch on title or body text, case-insensitively. Left unset, every entry is listed.
_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.
collectionNoonly entries filed in this collection.

Output Schema

NameRequiredDescriptionDefault
countYeshow many matched — branch on this rather than counting the array
totalYeshow many entries the notebook holds in all, so a filter that matched nothing can say whether the notebook is empty or the filter was wrong
entriesYesthe matching entries: id, title, tags, collection, created_at, updated_at, the three cross-reference lists and the body length. The BODY itself is not here — a notebook is long and a listing is for finding, so read one with the id this gives you
collectionsYesevery collection you have, with how many entries it holds

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.5/5.0
Behavior4/5

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

The annotations already establish read-only, non-destructive, closed-world behavior. The description adds the ordering ('newest first'), returned fields, and the presence of cross-references, which is useful beyond the annotations; it does not discuss permissions, pagination beyond schema, or filter-combination behavior.

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?

It is a single front-loaded sentence that names the resource, ordering, and output fields without preamble. The field list is dense but relevant, and no sentence is wasted.

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?

Annotations and output schema remove the need to explain safety and return structure in detail, and the description covers the core listing scope and output identity. However, it omits routing guidance and does not explain the roles of the less obvious _files/_subject parameters, leaving some context to the schema.

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 coverage is 100%, including descriptions for tag, limit, search, collection, _files, and _subject, so the baseline is 3. The description mentions tags, collection, and cross-references as output concepts but does not add filter syntax, default behavior, or semantics for the generic _files/_subject parameters beyond the schema.

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 identifies the resource as 'Your lab-notebook entries' and specifies newest-first ordering plus the returned fields, so an agent can tell it is a listing tool. It does not explicitly contrast with record_experiment or notebook_cross_refs, so sibling differentiation is implied 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?

No sentence states when to choose this tool over record_experiment, list_samples, or notebook_cross_refs, nor does it mention exclusions. The listing purpose implies basic usage, but an agent receives no routing guidance.

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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