Benchling Integration — R&D Platform SDK

Benchling Integration — R&D Platform SDK

Overview

Benchling is a cloud platform for life sciences R&D. The Python SDK provides programmatic access to registry entities (DNA, proteins), inventory, electronic lab notebooks, and workflows. All operations require a Benchling tenant URL and API key or OAuth credentials.

When to Use

• Creating, updating, or querying biological sequences (DNA, RNA, proteins) in Benchling registry
• Automating inventory operations (containers, boxes, locations, sample transfers)
• Creating or querying electronic lab notebook (ELN) entries programmatically
• Building workflow automations (task creation, status updates, bulk operations)
• Bulk importing entities from FASTA files or spreadsheets into Benchling
• Exporting Benchling data to CSV or external databases for analysis
• Syncing Benchling with external systems via event-driven integrations
• For local sequence analysis (BLAST, alignment), use biopython instead
• For chemical compound databases, use pubchem-compound-search instead

Prerequisites

pip install benchling-sdk

Authentication setup: Obtain an API key from Benchling Profile Settings. Store securely in environment variables — never commit to version control.

import os
from benchling_sdk.benchling import Benchling
from benchling_sdk.auth.api_key_auth import ApiKeyAuth

benchling = Benchling(
    url="https://your-tenant.benchling.com",
    auth_method=ApiKeyAuth(os.environ["BENCHLING_API_KEY"])
)

OAuth (for multi-user apps):

from benchling_sdk.auth.client_credentials_oauth2 import ClientCredentialsOAuth2