Skills benchling-integration

🔬

benchling-integration

Name: benchling-integration
Author: K-Dense-AI

Safe ⚡ Contains scripts🌐 Network access🔑 Env variables⚙️ External commands📁 Filesystem access

Integrate with Benchling R&D Platform

Also available from: davila7

Automate laboratory workflows and manage biological data by integrating with the Benchling R&D platform. Access DNA sequences, protein data, inventory, and electronic lab notebooks through the Python SDK or REST API.

Supports: Claude Codex Code(CC)

📊 71 Adequate

Download the skill ZIP

Upload in Claude

Go to Settings → Capabilities → Skills → Upload skill

Toggle on and start using

Test it

Using "benchling-integration". How do I set up authentication with Benchling using environment variables?

Expected outcome:

Use os.environ to retrieve credentials from environment variables for secure authentication.
Recommended approach: Store your API key in BENCHLING_API_KEY and tenant URL in BENCHLING_TENANT_URL.
Example: api_key = os.environ.get('BENCHLING_API_KEY')
This keeps credentials out of your source code and supports secure deployment practices.

Using "benchling-integration". Show me how to create a DNA sequence and register it in the Benchling registry

Expected outcome:

Use DnaSequenceCreate with entity_registry_id parameter to register upon creation.
Example: Set naming_strategy='NEW_IDS' for automatic registry ID generation.
Link to notebook entries using benchling.entry_links.create() with entry_id and entity_id.
The SDK handles pagination automatically with generator-based iteration.

Security Audit

Safe

v4 • 1/17/2026

This is a documentation-only skill containing reference materials for the Benchling R&D platform API. Static analysis flagged 476 patterns in markdown files, but ALL findings are FALSE POSITIVES. The scanner detected markdown code formatting (backticks), example URLs, and placeholder credentials in documentation examples - not actual executable code with security implications.

Files scanned

5,064

Lines analyzed

findings

Total audits

Risk Factors

⚡ Contains scripts (3)

evaluation_output.json:51 evaluation_output.json:54 references/sdk_reference.md:536-541

🌐 Network access (43)

🔑 Env variables (46)

⚙️ External commands (336)

📁 Filesystem access (1)

SKILL.md:466

Audited by: claude View Audit History →

Quality Score

Architecture

100

Maintainability

Content

Community

100

Security

Spec Compliance

What You Can Build

Automate Sequence Registration

Bulk import DNA and protein sequences from FASTA files directly into the Benchling registry with proper naming and custom fields.

Inventory Tracking

Monitor sample locations, track container transfers, and audit inventory changes across freezer locations and storage units.

Research Analytics

Export experimental data from the Data Warehouse for compliance reporting and integration with external BI tools.

Try These Prompts

Basic Connection

Show me how to authenticate with Benchling using an API key and create a connection to my tenant.

Sequence Operations

How do I create a new DNA sequence, register it in the registry, and link it to a notebook entry?

Inventory Management

Create a workflow to transfer containers between locations and track the movement history.

Automation Script

Write a script to find all sequences with a specific schema and export their names, bases, and creation dates to CSV.

Best Practices

Store API credentials in environment variables or secret managers, never hardcode them in scripts
Use HTTPS for all API connections - Benchling requires secure communication
Implement proper error handling with retry logic for rate limits and transient failures

Avoid

Do not commit API keys or credentials to version control systems
Avoid making requests without checking rate limits or implementing backoff strategies
Do not hardcode tenant URLs - use configuration files or environment variables instead

Frequently Asked Questions

How do I get my Benchling API credentials?

Log into Benchling, go to Profile Settings, and generate an API key. Store it securely as it is shown only once.

What Python version is required?

The Benchling SDK requires Python 3.7 or higher. Check your version with python --version.

Can I use this skill offline?

No, this skill requires an active internet connection to communicate with the Benchling API.

How do I handle rate limits?

The SDK automatically retries on 429 errors with exponential backoff. Configure max_retries in RetryStrategy if needed.

What authentication methods are supported?

API Key authentication for scripts and OAuth 2.0 Client Credentials for multi-user applications.

Does this skill include the SDK?

No, you must install the benchling-sdk package separately using pip or poetry.

Developer Details

Author

K-Dense-AI

License

MIT

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/benchling-integration

Ref

main

File structure

📁 references/

📄 api_endpoints.md

📄 authentication.md

📄 sdk_reference.md

📄 evaluation_output.json

📄 SKILL.md