Skip to main content
Glama

jean — Molecular Biology & Genomics

list_samples

Read-only

Browse the bundled sample library: the real bio files a new project can start from (GenBank and SnapGene plasmids, FASTA sets, alignments, Sanger traces, structures, variant calls and more), each with its id, format and size, and its archive provenance where the corpus records one. This is the headless form of starting a project from a sample: pass an id as a _subject or _files entry's sample and the file is read exactly as the lobby opens it.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
kindNorestrict to one importer kind (sequence, msa, trace, structure, variants, alignment, tabular, …). Each entry reports its own, so the vocabulary is whatever the library holds.
limitNomost entries to return; `total` says how many matched.
queryNowords that must all appear in the sample’s id, name, category or format label (case-insensitive), e.g. "pUC", "genbank plasmid", "ab1". Empty lists everything.
_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.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
idsYesjust the ids, in the same order — the list to scatter a per-sample step over
totalYeshow many entries matched before `limit` was applied
samplesYesthe matching entries: id, name, category, format, label, kind, size and provenance when recorded

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.9/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is fully covered by structured data. The description adds useful behavioral context (entries carry id/format/size plus archive provenance 'where the corpus records one', and ids are replayable downstream), but nothing about ordering, pagination behavior, or corpus size.

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?

Two sentences, front-loaded with what the library contains, then the downstream usage. The parenthetical enumeration is long but informative; only minor trimming ('and more') would be possible.

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, full annotation coverage, and 100% parameter coverage, the description only needs to frame the tool's role — which it does by tying it to the lobby/headless workflow. Complete enough; loading/inference caveats are not needed for a pure read-listing 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% and the _subject.sample param already documents that it takes 'an id from list_samples', so the description largely restates the schema link rather than adding new syntax or format detail. Baseline 3 is appropriate when the schema does the heavy lifting.

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?

States a precise verb (browse) and resource (bundled sample library), enumerates concrete contents (GenBank/SnapGene plasmids, FASTA, alignments, traces, structures, variant calls), and implicitly separates itself from list_library/list_traces by scoping to the bundled sample corpus. An agent can immediately tell what this returns.

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?

Explains the intended flow clearly: it is the 'headless form of starting a project from a sample', and a returned id is meant to be passed as a `_subject`/`_files` `sample`. It gives strong context but no explicit when-not-to-use or named alternative (e.g., list_library, list_traces).

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

Try in Browser

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources