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Benchling Integration

Automate Benchling registry entities, inventory, ELN entries, workflows, Apps, and Data Warehouse queries with the Python SDK or v2 REST API.

Web & APIIntermediate★ 41,485⑂ 3,824AI score 8/10Last updated: Aug 31, 2026

What it does

Teaches Claude how to script against Benchling, the life-sciences R&D cloud platform.

  • Auth setup: API key and OAuth app flows using named env vars (BENCHLING_TENANT_URL, BENCHLING_API_KEY, prod/staging variants)
  • Registry & entities: DNA/AA sequences, custom entities, schemas, registration
  • Inventory: containers, boxes, plates, locations, transfers
  • Notebook & workflows: ELN entries, structured tables, tasks, assay runs
  • Events & analytics: AWS EventBridge subscriptions, Data Warehouse SQL
  • Best practices: RetryStrategy tuning, generator-based pagination, fields() helper, credential hygiene

Deep dives live in references/authentication.md, sdk_reference.md, api_endpoints.md, and eventbridge.md.

Who it's for

  • Biotech/pharma R&D teams already standardized on Benchling
  • Bioinformatics engineers building lab data pipelines
  • Backend developers syncing Benchling with internal systems

Example uses

  1. Bulk FASTA import: parse sequences.fasta with Biopython and create DNA sequences in a target folder
  2. Inventory audit: page through every container under a box and print names plus barcodes
  3. Workflow automation: auto-validate pending workflow tasks, mark them complete, then export matching sequences to CSV

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/benchling-integration/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on AI Skill Mart.
Copy the skills/benchling-integration folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/benchling-integration/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/benchling-integration ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills directory: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r scientific-agent-skills/skills/benchling-integration ~/.claude/skills/
  4. Install the SDK: uv pip install benchling-sdk
  5. Export your credentials: export BENCHLING_TENANT_URL=https://your-tenant.benchling.com and export BENCHLING_API_KEY=your_key
  6. Restart Claude Code and try a prompt like "Write a script that lists all DNA sequences in Benchling folder fld_abc123".
  7. Never commit keys — keep them in .env or your shell profile, and prefer OAuth apps for multi-user production setups.
View source on GitHub ↗License: MIT