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.

Input 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

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
`unresolved`	Yes	`{ references, citations }`: every `@` / `!` / `&` reference in the stored body that names nothing in this workspace, as written, and every citation key that is not a DOI, PMID or PMCID. Empty lists mean every reference resolves; fix and append when they are not. Null when the write ran without the check (a blocking workflow run)

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedOct 23, 2026

addedOutput schema / properties / unresolved

Added value: +{
+  "description": "`{ references, citations }`: every `@` / `!` / `&` reference in the stored body that names nothing in this workspace, as written, and every citation key that is not a DOI, PMID or PMCID. Empty lists mean every reference resolves; fix and append when they are not. Null when the write ran without the check (a blocking workflow run)"
+}

changedOutput schema / required

Previous value: -[
-  "entry_id",
-  "created",
-  "title",
-  "tags",
-  "crossRefs",
-  "collection",
-  "bodyChars"
-]New value: +[
+  "entry_id",
+  "created",
+  "title",
+  "tags",
+  "crossRefs",
+  "collection",
+  "unresolved",
+  "bodyChars"
+]

First observedOct 20, 2026

TDQS

A3.6/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=false, destructiveHint=false and openWorldHint=false, so the safety profile is covered and the description adds the persistence/visibility framing of a lab notebook. It does not disclose the notable behaviors beyond annotations, such as the automatic cross-reference extraction from body text or that supplying a title on append renames the experiment — those caveats sit only in the schema.

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?

A single front-loaded sentence that states the action, the destination, and the two modes with zero filler. Nothing is redundant or buried.

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?

With an output schema present, full schema coverage, and annotations covering the mutation/scope profile, the short description is nearly sufficient for a write-an-entry tool. It falls just short of complete because the create-vs-append trade-off and rename pitfall are only discoverable by reading the parameter docs.

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 parameter docs are unusually rich (entry_id append behavior, title renaming, @plasmid/!action/&gel reference extraction). The prose description adds no parameter meaning beyond that, so the baseline of 3 applies.

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 gives a concrete verb and resource ("Write ... into your lab notebook") and explicitly frames the two modes: creating a new entry versus appending text to a named one. It is clearly distinguishable from read-side siblings like list_experiments, though it never names a contrasting sibling such as add_notebook_figure in the description itself.

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?

The phrase "a new entry, or more text appended to one you name" implies the create-vs-append decision, but the actual selection rule and the guidance to prefer appending on repeat runs live only in the entry_id schema description. No alternatives or exclusions are stated at the description level.

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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