Can I use bfabricpy to upload experimental results?

Yes, the library provides an upload_resource function that allows you to attach files to specific workunits using base64 encoding.

How do I handle authentication with this skill?

Authentication is typically managed through a ~/.bfabricpy.yml configuration file using your B-Fabric web service password, or via environment variables for CI/CD environments.

What is bfabricpy used for?

It is a Python client library used to interact with the B-Fabric laboratory information management system (LIMS), primarily for managing samples, workunits, and datasets programmatically.

Is there a way to run bfabricpy commands from the terminal?

Yes, by installing the bfabric-scripts package, you gain access to the 'bfabric' command-line interface for reading and managing entities.

Does it support relational data access?

Yes, bfabricpy features an Entity API that supports lazy loading, allowing you to easily access related objects like an application linked to a workunit.

BfabricPy LIMS Integration

Name: BfabricPy LIMS Integration
Author: CodingKaiser

byCodingKaiser

0•

Data Science & ML

Facilitates seamless Python-based interaction with the B-Fabric Laboratory Information Management System for managing research data and workflows.

bfabricPy is a specialized Claude Code skill designed for bioinformaticians and developers working with the B-Fabric LIMS. It provides a robust Python interface for performing CRUD operations on critical laboratory entities such as samples, workunits, datasets, and resources. By bridging the gap between Python scripts and the LIMS API, this skill enables automated sample tracking, lazy-loading of relational data, and the creation of standardized laboratory applications. Whether you are automating an 'omics' pipeline or building a custom research dashboard, bfabricPy streamlines data management within the FGCZ ecosystem.

Key Features

01Full CRUD operations for B-Fabric entities including Samples and Workunits

02Base64-encoded resource management for uploading files directly to workunits

03Comprehensive CLI utilities for quick terminal-based LIMS data access

04Relational Entity API with lazy loading for effortless relationship navigation

05Standardized App Runner framework for building consistent LIMS applications

060 GitHub stars

Use Cases

01Developing custom data processing applications that integrate with B-Fabric workunits

02Automating sample registration and status updates in high-throughput pipelines

03Exporting laboratory metadata directly into pandas DataFrames for research analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add codingkaiser/kaiser-skills bfabricpy

For use in Claude.ai and ChatGPT

Download Skill