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Benchling Integration

Lets an agent work with Benchling lab data (registry, inventory, ELN, workflows) via the Python SDK or v2 API.

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
6 files

What it does

Once installed, the agent knows how Benchling, a cloud platform many labs use to manage sequences, samples, inventory and electronic lab notebook entries, expects to be queried and updated. It writes code using the benchling-sdk 1.25.0 library and v2 API, follows safer steps (read a small page first, check payloads, read results back, keep IDs so retries don't create duplicates), and offers examples such as importing FASTA sequences, auditing inventory, and exporting sequences to CSV. It does not replace checking your tenant's schemas or the scientific correctness of the data.

Great for

  • Bioinformatics or lab software developers automating Benchling tasks
  • Lab data teams exporting or auditing sequences and inventory from a Benchling tenant
  • Engineers migrating or maintaining existing benchling-sdk v2 integrations

Skip it if

  • Users without a Benchling tenant and API credentials, since the examples cannot run without them
  • Production writes done without a test tenant or review, because the examples create and update real records and the skill notes they were not run against a live tenant
  • Non-Benchling lab systems, which this skill does not cover

Try asking

  • “Write a Python script that exports all DNA sequences in a given schema to a CSV file”
  • “Import sequences from a FASTA file into my Benchling registry folder, keeping a mapping of external IDs to Benchling IDs”
  • “List every container under a specific freezer box in Benchling and print barcodes”
  • “Check that my Benchling API credentials can read sequences before I build a larger integration”
Step-by-step guide: how to use Benchling IntegrationInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 6 original files, the MIT licence and an attribution note.

    benchling-integration.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip benchling-integration.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip benchling-integration.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Use a sandbox or staging tenant and a least-privilege OAuth app before running any write operation
  • Confirm the schema, folder and registry IDs in your tenant first; valid Python models do not guarantee tenant-required fields are satisfied
  • Check async task status after polling, since a completed poll can still report FAILED

What's inside

  • references/api_endpoints.md
  • references/authentication.md
  • references/core_capabilities.md
  • references/eventbridge.md
  • references/sdk_reference.md
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.