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jean — Molecular Biology & Genomics

resume_research_run

Read-only

Continue a research run from its file after an interruption or a failed test: the seal is checked, every pinned input the corpus still holds must have the content it had (a changed file is refused by name), and only the hypotheses with no evidence whose last attempt failed or was deferred are run, each with the settings it was registered with. Answered, settled and cancelled hypotheses are never run again, so a resumed run reaches the verdicts an uninterrupted one would. With budget_seconds, a long run continues in slices: call again with the returned file until nothing is pending. Returns the updated run file with the same outputs as run_discovery_programme.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
runYesthe run file to continue.
_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.
_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.
sequencesNothe corpus the run was registered over: library document or file names, or wired records.
budget_secondsNoseconds this call may spend running tests: whole tests run until the budget is spent and the rest are deferred, so a long programme returns before a client's timeout and resume_research_run continues it. A test is never cut short and at least one runs per call. Unset: every test runs in this call. In s. Advanced.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
runYesthe whole programme as a sealed jane.research-run file: the ledger, every corpus input pinned by SHA-256, the last attempt at each hypothesis. Pass it back to continue
reportYesthe resume as text lines: what ran, what was refused, the verdicts
resumedYesthe hypotheses this call ran
decisionsYesevery hypothesis: verdict, merged e-value, tests and merge rule

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.4/5.0
Behavior5/5

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

Annotations cover the safety profile (read-only, closed-world, non-destructive), and the description adds substantial behavior far beyond them: the seal check, pinned-input content validation with changed files refused by name, the exact selection rule for which hypotheses run, the guarantee that answered/settled/cancelled hypotheses never re-run, and the budget-slicing loop. This is unusually rich disclosure for a resumption tool.

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?

Three sentences, front-loaded with the core action and condition before descending into validation and scheduling detail. It is dense and clause-heavy, but essentially every clause carries a distinct behavioral fact, so little could be cut without losing information.

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

Completeness5/5

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

For a high-complexity, nested-object tool with five parameters, the description covers trigger, validation constraints, execution selection rules, continuation protocol and output equivalence. An output schema exists, so the brief return-value note is a bonus cross-reference rather than a necessity.

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 run, sequences, _files, _subject and budget_seconds in detail. The description adds only the slicing-loop semantics for budget_seconds ('call again with the returned file until nothing is pending'), which is useful but marginal against a fully documented schema — the baseline 3 applies.

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 first clause gives a specific verb and resource — 'Continue a research run from its file' — plus the triggering condition (interruption or failed test). It is clearly distinguishable from siblings like cancel_research_run, research_run_status and run_discovery_programme, the last of which it explicitly anchors itself to by output equivalence.

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 states when to use it: after an interruption or a failed test, and repeatedly with the returned file when budget_seconds is set. The resume-only framing implicitly excludes starting a fresh run, but it never names run_discovery_programme as the alternative for that case, so the routing guidance is clear but not exhaustive.

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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