openBIS UGM 2019

The openBIS User Group Meeting 2019 will take place in the Main Building of ETH Zurich on 18th and 19th of June. During the first day, current users will present their experiences with openBIS in their daily work; during the second day there will be 3 parallel workshops and users will have the option to choose 2 of them. The detailed program can be found below.


The openBIS User Group Meeting 2019 will take place in the main building of ETH Zurich.

Details on how to reach the location can be found here:



Registration for the openBIS User Group Meeting 2019 is now open:


Registration deadline 

Registration will close on 31st of May 2019.


Registration Fee

A fee of 50 CHF will apply.

Employees of ETH Zurich are requested to provide their fund code during registration. Participants who are not employees of ETH Zurich will be requested to pay the registration fee on arrival. Please note that we are not able to accept credit card payments, only cash.



If you can no longer attend the event after registration, please send an email to



If you have any questions regarding the event, please contact


Day 1

Location: ETH Zurich Main Building, HG D3.2


10:00-10:30 Coffee and registration

10:30-10:45 Welcome and Introduction. Bernd Rinn, ETH Zurich Scientific IT Services

10:45-11:15 Building a FAIR data infrastructure for biomedical research. Sven Fillinger, QBiC, University of Tübingen

11:15-11:45 TX-MS:  Rapid determination of quaternary protein structures. Lars Malmström, S3IT, University of Zurich

11:45-12:15 Streamlined data management of shared laboratory resources with the openBIS Importer Toolset. Aaron Ponti, Single Cell Unit, ETH Zurich

12:15-13:30 Lunch

13:30-14:00 The RITE way: nuclear pore complexes moving into an ELN. Elisa Dultz, ETH Zurich

14:00-14:30 Complete lab record keeping using the openBIS Jupyter extension. Andreas Cuny/Fabian Rudolf, ETH Zurich

14:30-15:00 Experiences from Andreas Fürholz, ZHAW

15:00-15:30 Coffee break

15:30 -16:00 OpenNGS – managing Next Generation Sequencing data and analysis with openBIS. Tomasz Zielinski, SynthSys and SBS, University of Edinburgh

16:00-16:30 Latest openBIS developments and outlook. Caterina Barillari, ETH Zurich Scientific IT Services

16:30-17:00 Discussion


Day 2

Location:ETH Zurich Main Building, HG E 33.1; HG E 33.3; HG E 33.5


We will host three parallel workshops. The same workshops will run twice, so users have the option to choose one in the morning and one in the afternoon. It is also possible to attend only one workshop in the morning session.

Users are required to bring their own laptops for the workshop sessions.


Workshops schedule:

09:00-12:00 First workshop session (with coffee break)

12:00-13:00 Lunch

13:00-16:00 Second workshop session (with coffee break)


Workshop 1: User training on openBIS ELN-LIMS

The goal of this workshop is to familiarize new users with the ELN and LIMS functionalities of openBIS. We will also cover analysis of data stored in openBIS using Jupyter and MATLAB.


  • Defining an openBIS data model
  • Creation of an inventory of materials
  • Registration of laboratory protocols
  • Registration of experiments and data upload
  • Basic customisation of openBIS
  • Analysis of data stored in openBIS with Jupyter & MATLAB

Target audience

Master and PhD students, postdocs, staff scientists, data managers.


The workshop is intended for beginners and existing openBIS users who are not yet familiar with the ELN and LIMS functionalities of the software.


Workshop 2: Programming with openBIS.

The goal of this workshop is to provide users with an overview of the many options available to use openBIS programmatically.

This workshop will have four topics and users are requested to choose two of them at registration. If users are interested in all topics, they can choose two topics for the morning session and two for the afternoon session.


  • BigDataLink : Using obis with openBIS to manage your data outside the DSS
  • V3 API: Python. Programming against Jupyter for integrations and pipelines
  • V2 API: Jython. Dropboxes for data imports
  • V3 API: Java/Javascript. Writing client applications for integrations and pipelines

Target audience

Developers, openBIS system admins.


Programming knowledge in at least one of these languages: Python, Java, Javascript.


Workshop 3: Reproducible data analysis workflows

The goal of this workshop is to give the participants conceptual and practical knowledge on combining data analysis workflows and data management for their research projects. We will present current software solutions and best practices for reproducible and traceable data analysis workflows.


  • Overview of current workflow systems and their features related to data management
  • Introduction to conda and containers with hands-on examples
  • Quick introduction to snakemake as a popular workflow manager, openBIS-snakemake interfacing, examples from genomics with hands-on examples

Target audience

Master and PhD students, staff scientists, data managers, developers.


Familiarity with the terminal and openBIS. Python knowledge is an advantage.