jean — Molecular Biology & Genomics

record_experiment

Write what just happened into your lab notebook: a new entry, or more text appended to one you name. The body is markdown and its @plasmid / !action / &gel references are extracted as you write, so an entry made by a run is cross-linked exactly like one you typed — and carries the automated tag, so you can always tell which is which. Use it to end a pipeline with a record of itself instead of a reminder to write one.

Input Schema

TableJSON Schema

Name	Required	Description
`tags`	No	tags to file it under, beyond the `automated` tag every entry written here carries.
`title`	No	the entry title. A new entry needs one. On an append, giving a title RENAMES the experiment, so leave it out to keep the name it has.
`_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.
`body_md`	Yes	the entry body, markdown. `@plasmid-name`, `!action-id` and `&gel-id` references in it are extracted into the entry's cross-reference lists, which is what makes a notebook searchable by construct.
`_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.
`entry_id`	No	append to this entry instead of creating one — the id `list_experiments` returns. A pipeline that runs twice should append to its own entry rather than leaving two.
`collection`	No	file it in this collection, creating the collection if it does not exist — the notebook's own grouping, the same one the panel lists.

Output Schema

TableJSON Schema

Name	Required	Description
`tags`	Yes	the tags as stored, including `automated` — the engine caps and cleans these, so read them back rather than assuming
`title`	Yes	the title it now carries
`created`	Yes	true for a new entry, false when text was appended to an existing one
`entry_id`	Yes	the entry written — pass it back to append to this same experiment next time
`bodyChars`	Yes	the stored body length. The engine caps a body at 1,000,000 bytes, so a long append can be shorter here than what was sent — read it rather than assuming the write was whole
`crossRefs`	Yes	the @plasmid / !action / &gel references the engine extracted from the body — empty lists are a real answer and mean the body named no construct, which is worth noticing in an entry about one
`collection`	Yes	the collection it is filed in, or an empty string when it is filed in none

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.7/5.0

Behavior4/5

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

Annotations already declare the write/not-destructive/not-open-world profile, so the bar is lower, and the description still adds non-obvious behavior: every entry carries the `automated` tag, `@plasmid`/`!action`/`&gel` references are extracted into cross-reference lists as you write, and appends cross-link exactly like hand-typed entries. It omits the append-renews-title hazard (left to the schema) and says nothing about error or auth behavior.

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?

The core action is front-loaded in the first sentence and each clause carries information rather than filler. It is slightly padded with persuasive framing ('so you can always tell which is which', 'instead of a reminder to write one') that could be trimmed without loss.

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?

An output schema exists, so return values need no explanation, and annotations carry the safety profile. The description covers the write semantics, the automated tag, and cross-linking well; the remaining gap is that it never surfaces the rename-on-append behavior, which lives only in the title field description.

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 all seven parameters and the baseline is 3. The description restates the markdown reference-extraction semantics of body_md but adds no syntax or format detail beyond what the field description already provides for entry_id, collection, tags, or title.

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 states a specific verb and resource — write/append a lab notebook entry — and clearly splits the two operating modes ('a new entry, or more text appended to one you name'). It does not explicitly contrast itself with siblings like list_experiments or notebook_cross_refs, so an agent must infer the boundary rather than being told it.

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

Usage Guidelines3/5

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

One genuine when-to-use is given: 'Use it to end a pipeline with a record of itself instead of a reminder to write one.' That is real guidance about intent, but there is no explicit when-not, no named alternative tool, and no stated prerequisite (e.g. that entry_id must come from list_experiments). Usage is implied more than specified.

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

All jean — Molecular Biology & Genomics tools Inspect

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