How does the skill handle large-scale data retrieval?

The skill utilizes Benchling's generator-based pagination patterns, allowing for memory-efficient iteration through thousands of registry entities or inventory items.

Can I manage physical laboratory inventory with this skill?

Yes, it provides comprehensive tools for creating and managing containers, boxes, and locations, as well as executing physical item transfers within Benchling.

Can I use this skill to automate Benchling Workflows?

Yes, it includes patterns for creating workflow tasks, updating statuses, and handling asynchronous operations to streamline laboratory processes.

Does it support biological sequence management?

Absolutely. You can create, update, and register DNA, RNA, and protein sequences, including support for custom schema fields and registry naming strategies.

What authentication methods are supported by this Benchling skill?

The skill supports both API Key authentication for standalone scripts and OAuth 2.0 Client Credentials for secure, multi-user application integrations.

Benchling R&D Integration

Name: Benchling R&D Integration
Author: Microck

byMicrock

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Data Science & ML

Automates laboratory data management and life sciences R&D workflows by integrating with the Benchling platform via Python SDK and REST API.

About

This skill provides a comprehensive toolkit for developers and bioinformaticians to programmatically interact with Benchling, the leading cloud platform for life sciences R&D. It streamlines the management of biological sequences, registry entities, physical inventory, and electronic lab notebooks (ELN). By offering standardized implementation patterns for authentication, workflow automation, and data warehouse querying, it enables users to build robust integrations, automate repetitive lab tasks, and maintain a single source of truth for experimental data across their organization.

Key Features

Event-driven integration support via AWS EventBridge and Benchling workflows
Full support for Benchling Python SDK and REST API authentication patterns
Physical inventory automation for samples, containers, and plate locations
Electronic lab notebook (ELN) entry creation and template management
Programmatic management of DNA, RNA, and protein registry entities
81 GitHub stars

Use Cases

Synchronizing physical sample transfers and inventory audits between lab hardware and the Benchling cloud
Automating the bulk import of biological sequences from FASTA files into the Benchling Registry
Building automated data pipelines that trigger external analysis when Benchling workflow tasks are completed

About

Key Features

Event-driven integration support via AWS EventBridge and Benchling workflows
Full support for Benchling Python SDK and REST API authentication patterns
Physical inventory automation for samples, containers, and plate locations
Electronic lab notebook (ELN) entry creation and template management
Programmatic management of DNA, RNA, and protein registry entities
81 GitHub stars

Use Cases

Synchronizing physical sample transfers and inventory audits between lab hardware and the Benchling cloud
Automating the bulk import of biological sequences from FASTA files into the Benchling Registry
Building automated data pipelines that trigger external analysis when Benchling workflow tasks are completed