openbis

Repository containing the masterdata definitions of the BAM Data Store project

A conversational AI assistant for the openBIS research data management system. Uses RAG with Ollama to provide natural, accurate responses to queries about openBIS. Scrapes documentation, processes it into semantic chunks, and delivers helpful answers through a simple command-line interface.

ETL scripts written in Jython 2.7 for openBIS dropboxes.

The official training material for pyBIS in BAM

Mapper script to convert SigmaBAM chemical inventory exports into openBIS-compatible format.

Upload Helper Tool and Parsers for OpenBIS in the BAM Data Store

Python package used to check the correctness of a given Masterdata definitions file with respect to the entities already registered in the BAM Data Store.

An example parser for openBIS using the bam-masterdata interface.

Datastore Advanced Label App

A set of utility functions to map Python schemas and parsers between 2 database platforms.

Data Collection Utility

instanceio

A template to create and work with data models in the BAM Data Store

An openBIS parser for creep testing data in BAM

A parser for Powder XRD data into openBIS.

A minimal cookiecutter template to generate repositories for BAM Masterdata definitions.

Fork of ETH sis openBIS

Parsers for automatically extracting metadata from measurement files and providing them for automatic upload to the OpenBIS ELN.

A Data Store upload helper with flexible choice of object types and their parents/children dependencies. Based on Bastian Rühles https://github.com/BAMresearch/openbis-upload-helper