We are pleased to announce the openBIS User Group Meeting 2025.

Date: 22-24 September 2025.

Location: BAM, Unter den Eichen 87, 12205 Berlin, Germany

Registration

You can register for the event here: https://express.converia.de/frontend/index.php?folder_id=10753&page_id=

Registration deadline: 07.09.2015 

Registration fees

Day 1 – 22.09.2025 – € 54.00

Day 2 – 23.09.2025 – € 54.00

Day 3 – 24.09.2025 – € 55.00

Contact

For any questions related to the event, please get in touch with the openBIS support: openbis-support@id.ethz.ch

Program

Day 1: 22.09.2025

09:30-10:00 Registration & coffee

10:00-10:10 Welcome & introduction, BAM, ETHZ Scientific IT Services

10:10-10:30 ChatBIS – an AI-powered conversational assistant for openBIS, Carlos Madariga, BAM

10:30-10:50 openBIS Schemas and Parsers in GitHub: Building an Open-Source Software Ecosystem for openBIS, Jose Pizarro Blanco, BAM

10:50-11:00 Short break

11:00-11:20  From custom openBIS solutions to a digital logbook prototype: Supporting digitalisation at Empa, Anusch Bachofner, Stefanie Hauser, Empa

11:20-11:40  Welding Process Data Management – openBIS workflows and lab integrations, Çağtay Fabry, BAM

11:40-12:00  Customizing openBIS for Optimized Materials Science and Engineering Workflows,  Rejiba, Khalil; Lee, Sang-Hyeok; Korte-Kerzel, Sandra; Kerzel, Ulrich, Aachen University

12:00 -13:00 Lunch

13:00-13:20 Enabling FAIR large-scale data analysis in HPC using openBIS – An Open Source-first strategy from a proteomics research infrastructure, Filip Årman, Swedish National Infrastructure for Biological Mass Spectrometry (BioMS)

13:20-13:40 openBIS for Evolutionary Biology, Kristian Ullrich, Carsten Fortmann-Grote, Max-Planck-Institute for Evolutionary Biology

13:40-14:30 openBIS roadmap, Caterina Barillari, ETHZ Scientific IT Services

14:30-14:50 Coffee break

14:50-17:30 Round table discussion, everyone

Day 2: 23.09.2025

09:30-12:00 WORKSHOP 1. How to migrate data: Introduction to AFS & migration of dropbox scripts – Part 1.  ETHZ Scientific IT Services

09:30-12:00 TRAINING 1. openBIS admin training, ETHZ Scientific IT Services

12:00-13:00 Lunch

13:00-17:00 WORKSHOP 1. How to migrate data: Introduction to AFS & migration of dropbox scripts – Part 2.  ETHZ Scientific IT Services

13:00-15:30 TRAINING 2. pyBIS. ETHZ Scientific IT Services

15:30-16:30 DEMO: DataStore Advanced Label App, Ingo Breßler, BAM

18:00 Group dinner

Day 3: 24.09.2025

09:30-10:00: Overview of Hackathon topics and organization. ETHZ Scientific IT Services, BAM

10:00-10:15 Coffee and room distribution

10:15-15:30 Locally deployed openBIS for all Developers. https://github.com/openbis/openBIS-UGM2025/blob/main/local-openbis-for-developers.md, Artur Pedziwilk, ETHZ Scientific IT Services.

10:15-15:30 Parsers to automatically instantiate objects, upload data, and fill property fields. https://github.com/openbis/openBIS-UGM2025/blob/main/parsers_for_data_upload.md Tara-Lakshmipathy, BAM

10:15-15:30 Data modelling consulting. ETHZ Scientific IT Services, BAM

15:30-15:45 Coffee

15:40-17:30 Wrap up, ETHZ Scientific IT Services, BAM

Talks abstracts

 
ChatBIS – an AI-powered conversational assistant for openBIS, Carlos Madariga, BAM
 
chatBIS is an AI-powered conversational assistant designed to simplify interactions with the openBIS research data platform. Using Retrieval-Augmented Generation and local LLMs, it guides the users through the system and explains complex system functions with natural language, reducing onboarding time and enhancing user productivity. Its architecture integrates with tools like PyBIS and currently supports documentation search and data retrieval. chatBIS aims to be integrated into the openBIS Electronic Lab Notebook to provide easy, real-time access to the tool and significantly improve the user experience.

 
 
openBIS Schemas and Parsers in GitHub: Building an Open-Source Software Ecosystem for openBIS, Jose Pizarro Blanco, BAM
 
We present a set of open-source tools developed in the Federal Institute for Materials Research and Testing (BAM) for openBIS. Our goal is to build a sustainable and open-source software ecosystem that extends and complements openBIS. These are designed to help streamlining and validating metadata schema definitions, as well as data injection into openBIS. Hosted on GitHub, they foster collaboration and community contributions, while building an ecosystem in which data stewards can create and extend the existing schemas and parsers with ease.

 
 
From custom openBIS solutions to a digital logbook prototype: Supporting digitalisation at Empa, Anusch Bachofner, Stefanie Hauser, Empa
 
At Empa, the Scientific IT team supports a wide range of projects and collaborations using openBIS. We maintain a documentation platform offering practical tips, use cases, and guidance to help users. In close exchange with laboratories, we develop tailored solutions such as chemical inventories, QR codes for inventory, and dynamic scripts to automate processes. In different projects, we help users managing sensitive or confidential data within openBIS. Our current focus is a prototype digital logbook integrated with ELN-LIMS, designed to support workflow-based data logging and tracking of complex experimental setups. It enables researchers to log workflow-based experimental data and complex setups in a structured and user-friendly way, with data automatically stored in openBIS.

 
 
Welding Process Data Management – openBIS workflows and lab integrations, Çağtay Fabry, BAM
 
Arc welding processes are an important manufacturing technology applied to a wide range of critical materials and components such as offshore constructions, pressure vessels and additive manufacturing. Data management for experimental arc welding research faces the challenge of constantly changing experimental setups, incorporating a wide range of custom sensor integrations. Measurements include timeseries process and temperature recordings, 3D-geometry data and video recordings of the process from a sub-millisecond scale to multiple hour-long experiments. In addition, various manual pre-processing steps of the workpieces need to be considered to track the complete manufacturing process and its analysis – from raw materials to final dataset and publication.

As a unified RDM system, the BAM Data Store offers the capability to incorporate all steps – albeit not without its own challenges.

The talk gives an overview of the different workflows and processing steps along the welding experiments together with their integration into the BAM Data Store. Current solutions and ongoing integration work is explained and discussed. This includes the direct integration and upload of automated processing steps into the Data Store from different machines and sensors using custom Python APIs.

Ultimately the complete processing chain across multiple internal steps should be represented in the Data Store.

 
 
Customizing openBIS for Optimized Materials Science and Engineering Workflows,  Rejiba, Khalil; Lee, Sang-Hyeok; Korte-Kerzel, Sandra; Kerzel, Ulrich, Aachen University
 

In today’s data-centric Materials Science and Engineering landscape, experiments routinely generate vast amounts of information—making adherence to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles essential for efficient laboratory management. At the Institute of Physical Metallurgy and Material Physics at RWTH Aachen University, we have reimagined our research workflows by using openBIS as an integrated Laboratory Information Management System (LIMS) and Electronic Laboratory Notebook (ELN) in everyday lab work and extended its functionalities beyond what is offered out of the box.

The introduction of openBIS has been pivotal in managing the heterogeneous data generated by large-scale collaborative projects like the Collaborative Research Centre (CRC) 1394, “Structural and Chemical Atomic Complexity – from Defect Phase Diagrams to Material Properties”. This multi-disciplinary project, which is a participant project in NFDI-MatWerk, focuses on the complexity of materials at the atomic level and requires seamless management of diverse data types, including experimental and simulation results. Through rapid prototyping, metadata schemata were developed covering a wide range of sample preparation techniques, characterization methods and simulation routines.

A key component of our approach is the development of a Companion App for openBIS. This user-friendly tool streamlines laboratory operations by simplifying data management tasks and enhancing daily research activities. By leveraging the companion app, researchers can more easily register and retrieve experimental details, leading to an overall smoother and more efficient research workflows. The companion app reduces the manual effort needed to fill metadata entries by automatically extracting key-value pairs from the data itself whenever possible and helps perform complex queries using a user-friendly interface suited to the needs of a material scientist.

 
 
Enabling FAIR large-scale data analysis in HPC using openBIS – An Open Source-first strategy from a proteomics research infrastructure, Filip Årman, Swedish National Infrastructure for Biological Mass Spectrometry (BioMS)
 
As a research infrastructure, we have been using openBIS for more than 10 years and highly value its robustness and versatility in the changing landscape of bioinformatic tools and software. Using openBIS support for web application plug-ins, we have integrated a software workflow submitter app that integrates with our local SLURM cluster to send data processing workflows using datasets from openBIS and uploading results to reproducible workflow objects. In this way, we can ensure FAIR and easy data processing with the complete data life-cycle contained and tracked in openBIS.

openBIS for Evolutionary Biology, Kristian Ullrich, Carsten Fortmann-Grote, Max-Planck-Institute for Evolutionary Biology
 
openBIS has become the central platform for electronic note taking, laboratory inventory management, and research data management at the Max Planck Institute for Evolutionary Biology. Initially run as multiple instances for various departments and research groups, we have now transitioned to one multigroup instance for the whole institute enabling sharing of resources where needed and encapsulation of research artefacts where desired. Besides the standard use-cases and applications of openBIS, we have implemented additional objects, controlled vocabularies and dynamic properties to support documentation of genetically modified organisms as required by law, automatic synchronisation with bacterial strain collections, and submission and tracking of Next Generation Sequence orders. Our openBIS instance is complemented by a dynamic mapping engine that translates the openBIS database backend to the resource description framework (RDF). We thereby turn openBIS into a linked data hub and enable federated queries against openBIS in combination with other linked data services such as wikidata, uniprot and domain specific knowledge graphs. In this presentation, we will describe our openBIS customizations, share some experiences from installation and service management and suggest mprovements of openBIS to beconsidered in future development efforts.

This work is partially supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI46/1 – 501864659.

Demo Abstract

 
DataStore Advanced Label App, Ingo Breßler, BAM
 
The web-based DataStore Advanced Label App is an evolution of the OpenBIS batch label generator. It has been developed to create printable sample labels featuring QR codes with additional information. The aim is to facilitate the seamless transition between digital data and physical samples in laboratory workflows. It supports custom label layouts and predefined label grids provided by users, such as those used for Herma sheets, thus enabling standardised, efficient batch label generation. The tool offers a user-friendly web interface that can be accessed on any PC with DataStore access and requires no software installation. It produces standard A4 PDF files that are suitable for printing on regular printers. Users can quickly select multiple sample objects for batch processing and extend the QR code generation to include additional information and various formats tailored to different sample container sizes or purposes. Implemented in JavaScript, this solution ensures cross-platform compatibility and ease of use for all employees. This approach streamlines sample labelling, enhancing the traceability of physical samples and their integration with digital records in everyday laboratory workflows.

Repo: https://github.com/BAMresearch/dalapp