jean — Molecular Biology & Genomics

build_addgene_deposit

Read-only

Fill Addgene's own deposit spreadsheet from a record: one row per plasmid with its name and sequence, plus your answers for every plasmid (purpose, plasmid type, cloning method, resistance, growth strain and the other drop-downs). The sheet is fetched from Addgene each run, so its columns and choices are current; a value it would refuse is left out and named, and columns lists every column with its choices. It WRITES A FILE and sends nothing.

Input Schema

TableJSON Schema

Name	Required	Description
`_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.
`answers`	No	the sheet's columns to fill for every plasmid, header → value, e.g. {"Purpose": "Expresses EGFP in E. coli", "Bacterial Resistance": "Ampicillin"}. A drop-down column takes one of its own choices; run once without answers to read them from `columns`.
`genbank`	Yes	the plasmids to deposit, as GenBank text: one row per nucleotide record.
`_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.

Output Schema

TableJSON Schema

Name	Required	Description
`file`	Yes	the filled workbook: `name`, and its bytes as `base64`
`columns`	Yes	every column of Addgene's sheet: its header, Addgene's help text, and its choices where it has a drop-down
`reading`	Yes	what was written and what is left for the depositor, generated from the run
`written`	Yes	plasmids written into the sheet
`problems`	Yes	every value left out because the sheet would refuse it, with the plasmid, the column and the reason

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.5/5.0

Behavior1/5

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

The annotations declare readOnlyHint=true and openWorldHint=false, but the description explicitly says 'It WRITES A FILE' (a write side effect) and 'The sheet is fetched from Addgene each run' (external network interaction). Both statements contradict the annotations, making this a serious consistency failure.

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 description is front-loaded with the core action and is reasonably tight, though listing example drop-down values adds slight verbosity. Every sentence still carries useful information about behavior or validation.

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 not be explained. The description covers key behaviors (fetching current sheet, rejecting and naming refused values, writing a file, not sending anything), but omits practical details such as the output file's location or format, which would be helpful for a file-writing tool.

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 four parameters thoroughly. The description adds minor examples of answer columns (purpose, plasmid type, etc.) but does not meaningfully extend the parameter semantics beyond what the schema provides, matching the baseline of 3.

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

Purpose5/5

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

The description states a specific verb and resource: 'Fill Addgene's own deposit spreadsheet from a record', and details the row content (one row per plasmid with name and sequence plus answers). This clearly distinguishes it from sibling submission builders like build_genbank_submission and build_ena_submission.

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

Usage Guidelines4/5

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

It gives clear context for use (depositing to Addgene from a record) and a useful workflow hint: 'run once without answers to read them from `columns`.' However, it does not explicitly state when to choose this tool over alternatives such as build_genbank_submission or build_ena_submission.

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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