How does it handle large datasets or lists of sequences?

It utilizes generator-based pagination through the Benchling Python SDK to ensure memory-efficient processing of large entity lists.

Is it possible to automate lab notebook entries?

Yes, the skill provides methods to programmatically create, update, and link entities or results to electronic lab notebook (ELN) entries.

Does this skill support real-time data synchronization?

Yes, it includes patterns for event-driven integrations using AWS EventBridge to trigger actions based on Benchling platform events.

Does this skill require a Benchling account?

Yes, you need an active Benchling tenant and either an API key or OAuth credentials to interact with the platform's programmatic interfaces.

Can I manage physical lab inventory with this skill?

Absolutely. The skill supports creating and transferring containers, boxes, and locations within the Benchling inventory system.

Benchling R&D Integration

Name: Benchling R&D Integration
Author: pur3v4d3r

bypur3v4d3r

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Data Science & ML

Automates laboratory data management and R&D workflows by integrating Benchling's registry, inventory, and ELN systems via Python SDK and REST API.

About

The Benchling Integration skill empowers researchers and developers to programmatically interact with the Benchling cloud platform for life sciences R&D. It facilitates the management of biological sequences, sample inventory, and electronic lab notebook (ELN) entries, while supporting complex workflow automations and data warehouse synchronization. This skill is ideal for automating repetitive lab tasks, building custom Benchling Apps, and ensuring data consistency across external systems and internal research databases.

Key Features

1 GitHub stars
Real-time event-driven integration support via AWS EventBridge
Electronic Lab Notebook (ELN) entry creation and documentation automation
Comprehensive registry management for DNA, RNA, and protein sequences
Automated inventory operations for samples, containers, and location transfers
Workflow task orchestration with status updates and asynchronous monitoring

Use Cases

Syncing experimental results and metadata between Benchling and external analytics platforms
Bulk importing biological sequences from FASTA files into the Benchling registry
Automating inventory audits and tracking sample transfers across lab locations

About

Key Features

1 GitHub stars
Real-time event-driven integration support via AWS EventBridge
Electronic Lab Notebook (ELN) entry creation and documentation automation
Comprehensive registry management for DNA, RNA, and protein sequences
Automated inventory operations for samples, containers, and location transfers
Workflow task orchestration with status updates and asynchronous monitoring

Use Cases

Syncing experimental results and metadata between Benchling and external analytics platforms
Bulk importing biological sequences from FASTA files into the Benchling registry
Automating inventory audits and tracking sample transfers across lab locations