benchos-standard

name	benchos-standard
description	Standard BenchOS workflow for workspace updates, memory operations, and LabBook API tasks via benchos-cli. Use for routine BenchOS execution requests (files, memory, APIs, onboarding rules).
license	Proprietary
compatibility	Requires BenchOS agent runtime with `labbook_cli` available and `benchos-cli` in PATH.
metadata	{"author":"benchos","version":"2"}
allowed-tools	labbook_cli

BenchOS Standard Skill

Use this skill whenever the user asks for standard BenchOS tasks:

• Read or write files in /workspace
• Maintain long-term memory and daily notes
• Call LabBook API routes from inside the agent runtime

Required Tool

Use the labbook_cli tool with args values that call benchos-cli subcommands.

Command Patterns

Inspect runtime context

{"args": ["whoami"]}

Workspace operations

{"args": ["workspace", "ls", "."]}
{"args": ["workspace", "read", "LAB.md"]}
{"args": ["workspace", "write", "LAB.md", "--content", "..."]}
{"args": ["workspace", "write", "USER.md", "--content", "..."]}

Memory operations

{"args": ["memory", "ensure"]}
{"args": ["memory", "remember", "--fact", "User prefers 24h time", "--section", "User preferences"]}
{"args": ["memory", "note", "--note", "Initialized onboarding context"]}

API operations

{"args": ["api", "--method", "GET", "--path", "/api/agent/status"]}
{"args": ["api", "--method", "GET", "--path", "/api/uniprot/Q9UNN5/domains"]}
{"args": ["api", "--method", "GET", "--path", "/api/calendar/experiments"]}
{"args": ["api", "--method", "POST", "--path", "/api/calendar/experiments", "--body", "{\"experiment\":{\"title\":\"CryoEM screen\",\"project\":\"Example Lab\",\"startDate\":\"2026-03-03\",\"endDate\":\"2026-03-03\"}}"]}
{"args": ["api", "--method", "GET", "--path", "/api/equipment-calendar"]}
{"args": ["api", "--method", "POST", "--path", "/api/equipment-calendar/bookings", "--body", "{\"bookings\":[{\"title\":\"Talos slot\",\"date\":\"2026-03-03\",\"start\":\"09:00\",\"end\":\"10:00\",\"equipmentIds\":[\"<equipment-id>\"],\"notes\":\"Auto-booked\"}]}"}}
{"args": ["api", "--method", "POST", "--path", "/api/registry/157/attachments", "--file", ".chat-context/TIM-TIPIN.dna"]}
{"args": ["api", "--method", "GET", "--path", "/api/registry/157/attachments"]}
{"args": ["skills", "list"]}
{"args": ["skills", "create", "--name", "benchos-protocol-notes", "--description", "Lab-specific protocol conventions."]}
{"args": ["skills", "request-share", "--name", "benchos-protocol-notes", "--note", "Validated by user; request shared rollout."]}

Search operations

{"args": ["search", "entries", "--query", "akt"]}
{"args": ["search", "registry", "--query", "TIM", "--kind", "Plasmid"]}

Safe execution and web access

{"args": ["capabilities", "list"]}
{"args": ["capabilities", "install", "--name", "node-basic"]}
{"args": ["capabilities", "install", "--name", "python-basic"]}
{"args": ["exec", "--capability", "node-basic", "--cwd", ".", "--", "scripts/example.mjs"]}
{"args": ["exec", "--capability", "python-basic", "--cwd", ".", "--", "-c", "print('hello from python')"]}
{"args": ["web", "allowlist"]}
{"args": ["web", "fetch", "--url", "https://www.uniprot.org/uniprotkb/P05067/entry"]}

Registry/SeqViz attachment rule

• A file uploaded into /workspace or .chat-context is not a Registry attachment yet.
• To make SeqViz render, upload the file to /api/registry/:id/attachments and then confirm it appears in GET /api/registry/:id/attachments.
• Only report success after the attachment endpoint returns 200 and the new attachment is listed.

Search and API output rule

• Prefer search for discovery because search entries returns titles only by default.
• api list responses may also be compacted by default; use api --raw when the full payload is required.

Safe execution rule

• Script execution must go through curated capability packs plus benchos-cli exec.
• Do not run arbitrary interpreters directly in the chat container when a sandboxed exec job is intended.
• Exec jobs run with no direct network access; use benchos-cli web fetch for allowlisted sites.
• Skills should rely on curated capability packs for extra runtimes or packages; do not install pip, npm, or OS packages inside the persistent sandbox at runtime.

User vs Shared skills

• New skills authored by a user must be created as user-local via benchos-cli skills create.
• User-local skills are private to that user's agent.
• Shared rollout requires an explicit request via benchos-cli skills request-share and admin approval.

Universe / UniProt lookups

• For UniProt domain annotations, call /api/uniprot/:id/domains.
• Universe compatibility aliases also exist: /api/universe/uniprot/:id/domains and /api/universe/:id/domains.
• Prefer the canonical route (/api/uniprot/:id/domains) in new prompts.

Calendar and Equipment rules

• To create calendar events, use /api/calendar/experiments (or /api/lab-calendar/experiments alias).
• To create equipment bookings, use /api/equipment-calendar/bookings (or /api/bookings and /api/equipment/bookings aliases).
• Legacy aliases available if encountered in old prompts/tools: /api/calendar-events, /api/schedule, /api/resource-bookings, /api/equipment-calendar/events.
• Do not treat /api/entries metadata as the source of truth for Lab Calendar or Equipment Calendar views.
• Never prefer /api/entries when the user asks for true calendar booking/event creation.

Onboarding and Long-term Memory Rules

• Start onboarding with: Hello <user>, can you answer several questions to help me be of assistance to you?
• Do not ask onboarding detail questions until the user explicitly agrees.
• If onboarding placeholders exist in USER.md or LAB.md, ask one focused question at a time.
• After each user answer, write updates immediately to workspace files.
• Keep onboarding profile/context facts in USER.md, LAB.md, STOCKS.md, and TOOLS.md.
• Do not store onboarding profile facts in memory files.
• Capture session events with memory note.