openBIS UGM 2023

We are pleased to announce the openBIS User Group Meeting 2023.

 

Date: 12-14 September 2023.

Location: HG building, ETH Zurich. Rämistrasse 101, 8092 Zürich.

Google Maps

 

 

Registration

Registration for the event is now closed.

 

Registration fees

3-days attendance: 100CHF

2-days attendance: 70CHF

1-day attendance: 40CHF

 

 

Contact

For any questions related to the event, please contact the openBIS support: openbis-support@id.ethz.ch 

 

 

 

Program

 

Day 1: 12.09.2023

Location: ETHZ HG building, Room D5.2

  

10:00-11:00 Registration & coffee

 

11:00-11:10 Welcome & introduction, Dr. Bernd Rinn, ETHZ Scientific IT Services

 

11:10-11:35 Introducing openBIS at Empa with a focus on iPads, Anusch Bachofner and Stefanie Hauser, Empa

 

11:35-12:00 Web application development for openBIS using Windmill, Dr. Simone Baffelli and Dr. Matthias Rösslein, Empa

 

12:00-12:25 From Pilot to Rollout: Introducing the BAM Data Store for Institutional RDM in Materials Science, Dr. Rukeia El-Athman, Bundesanstalt für Materialforschung und –prüfung (BAM)

 

12:30 -13:30 Lunch

 

13:30-13:55 openBIS @ Fraunhofer IWM: Creating an Infrastructure for Digitization, Dr. Heiko Hafok, Fraunhofer-Institut für Werkstoffmechanik IWM

 

13:55-14:20 Large-File Raw Data Synchronization for openBIS Research Repositories, Friedemann Ringwald, Universitäts Klinikum Heidelberg

 

14:20-14:45 openBIS and pyBIS in a data management pipeline, Dr Guanghao You, NCCR Evolving Languages

 

14:45-15:10 Addressing Research Data Management Challenges in a Collaborative Material Science Project, Prof Ulrich Kerzel, RWTH Aachen University

 

15:15-15:45 Coffee break

 

15:45-16:05 openBIS roadmap, Dr. Caterina Barillari, ETHZ Scientific IT Services

 

16:05-17:15 Round table discussion, everyone

 

18:30 Dinner in Zurich town center

 

 

Day 2: 13.09.2023

On this day there will be 2 parallel workshops in the morning and 2 parallel workshops in the afternoon.

Each workshop has a limited number of spaces that are available on a first come first served basis.

 

09:00-12:30 Workshop 1: openBIS users training

Location: ETHZ HG building, Room E 33.1

 

25 places available.

 

In this workshop we will provide a general overview of openBIS followed by a practical training session.

 

Topics covered:

  • Working with Inventory of lab materials.
  • Working with Inventory of lab protocols.
  • Lab notebook: Registration of experiments and data upload.

 

Requirements & info:

  • Own laptop.
  • This course is designed for beginners and does not require any previous knowledge about openBIS.
  • A training server will be made available to participants on the day.
  • Information on training material will be sent out to participants before the training.

 

 

09:00-12:30 Workshop 2: Integrating with other systems: the openBIS V3 Java API

Location: ETHZ HG building, Room E 33.5

 

15 places available.

 

In this workshop we will look at how to use the V3 Java API to integrate openBIS with other systems.

 

Topics covered:

  • openBIS V3 API philosophy.
  • How to navigate the V3 API documentation.
  • How to create V3 Java applications that can be used from other systems to integrate with openBIS. Create entities and search entities.

 

Requirements & info:

  • Own laptop.
  • Java programming knowledge.
  • Git installed.
  • IntelliJ Community Edition IDE installed: https://www.jetbrains.com/idea/download/.
  • Java JDK 17 installed: https://adoptium.net/en-GB/temurin/releases/.
  • A training server will be made available to participants on the day.

 

 

12:30-13:30 Lunch

 

13:30-17:00 Workshop 3: openBIS instance admins training

Location: ETHZ HG building, Room E 33.1

 

25 places available.

 

In this workshop we will provide a general overview of the openBIS admin functionalities followed by a practical training session.

 

Topics covered:

  • Registration of openBIS types.
  • Customization of ELN Settings.
  • Dynamic property plugins.
  • Entity validation plugins.
  • User management.

 

Requirements & info:

  • Own laptop.
  • This course is designed for openBIS Instance Admins.
  • A training server will be made available to participants on the day.
  • Information on training material will be sent out to participants before the training.

 

 

13:30-17:00 Workshop 4: automating data imports: the dropbox core plugin

Location: ETHZ HG building, Room E 33.5

 

15 places available.

 

In this workshop we will look at how to use the dropbox functionality of openBIS for data ingestion.

 

Topics covered:

  • How to create openBIS dropboxes.
  • The dropbox lifecycle and rollback mechanism.
  • Registering openBIS entities from dropbox.
  • Use openBIS V3 API to search from dropbox.
  • Upload data from dropbox.
  • Parse files from dropbox.

 

Requirements & info:

  • Own laptop.
  • Python 2.7 programming knowledge.
  • Visual Studio Code.
  • A training server will be made available to participants on the day.

 

 

 

Day 3: 14.09.2023

On this day there will be 1 workshop in the morning and 1 workshop in the afternoon.

Each workshop has a limited number of spaces that are available on a first come first served basis.

 

09:00-12:00 Workshop 5: working with openBIS using Python, JupyterHub and pyBIS

Location: ETHZ HG building, Room E 33.1

 

15 places available.

 

In this workshop we will look at how to work with pyBIS for users’ and admins’ functionalities.

 

Topics covered:

  • Connect to openBIS and browse through its content
  • Create and modify openBIS master data and the ELN settings
  • Search, create, update and delete Objects and Datasets

 

Requirements & info:

  • Own laptop.
  • Python 3+ programming knowledge.
  • A training server will be made available to participants on the day.

 

 

12:00-13:00 Lunch

 

13:00-17:00 Workshop 6: developing your own openBIS webapps and extending the ELN-LIMS: the openBIS V3 Javascript API

Location: ETHZ HG building, Room E 33.1

 

 

15 places available.

 

In this workshop we will look at the V3 Javascript API for developing webapps.

 

Topics covered:

  • How to use the Javascript API from a web application with provided examples.
  • ELN Plugin system.
  • How to use the AS service plugins to create custom APIs usable from web applications.

 

Requirements & info:

  • Own laptop.
  • JavaScript programming knowledge.
  • Visual Studio Code.
  • A training server will be made available to participants on the day.