eln-openbis

Manage and track life-science samples and experiments in openBIS LIMS/ELN.

6|2|Updated Jun 11, 2026

Search Tags:#ELN #experiment management #openBIS #sample tracking #instrument integration

Ready to run

npx skills add https://github.com/pradyumnasagar/open-research-skills --skill eln-openbis

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: eln-openbis
Source: https://github.com/pradyumnasagar/open-research-skills/tree/main/skills/lab-automation/eln-openbis
Command: npx skills add https://github.com/pradyumnasagar/open-research-skills --skill eln-openbis

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pyopenBIS, pandas, requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill streamlines the management and tracking of life-science samples and experiments within the openBIS LIMS/ELN, simplifying workflows for core facilities and multi-user labs.

Core Features & Use Cases

Sample Tracking: Track samples across collections, spaces, datasets, and vocabularies.
Instrument Integration: Connect with instruments and high-throughput pipelines.
Access Control: Enforce lab/team-level access control for shared resources.
Use Case: Ideal for core facilities handling genomics, proteomics, or screening campaigns, or for replacing paid LIMS with an open-source solution.

Quick Start

Use the eln-openbis skill to create a new sample and dataset for a sequencing run.

Frequently Asked Questions about eln-openbis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I track life-science samples and experiments in openBIS?▼

You can track life-science samples and experiments in openBIS by running Python scripts that interact with the openBIS LIMS/ELN instance. This Skill manages sample collections, spaces, and datasets through the pyopenBIS API.

Can I use Python to manage sample tracking across openBIS collections and spaces?▼

Yes, you can use Python to manage sample tracking across openBIS collections and spaces. The Skill uses the pyopenBIS API to automate interactions and manage samples across datasets and vocabularies.

Does openBIS support instrument integration for high-throughput screening pipelines?▼

Yes, openBIS supports instrument integration for high-throughput screening pipelines. This Skill connects your openBIS LIMS/ELN instance with instruments and pipelines, which is ideal for core facilities handling genomics or proteomics campaigns.

What is needed to set up access control for shared lab resources in openBIS?▼

To set up access control for shared lab resources in openBIS, you need an active openBIS instance and the pyopenBIS Python API. This Skill enforces lab and team-level access control for shared core facility resources.

Is openBIS a good open-source alternative to paid LIMS for core facilities?▼

Yes, openBIS is a good open-source alternative to paid LIMS for core facilities. This Skill streamlines experiment management and sample tracking, replacing paid solutions while supporting multi-user lab workflows.

Why do I need pandas and requests to manage experiments in openBIS?▼

You need pandas and requests because this Skill relies on these Python dependencies to handle data manipulation and HTTP communication with the openBIS LIMS/ELN instance during experiment and sample management.