openBIS User Group Meeting 2021

We are pleased to announce the openBIS User Group Meeting 2021, which will take place from 27th till 30th of September 2021.

Location

 

Online. Zoom links for the workshop sessions will be sent to registered participants a few days before the event.

Registration

 

Registration for the different sessions is now open.

The first day of the meeting is open to anyone who wants to join, but registration is mandatory. There is no registration deadline for the first day.

 

The workshops have limited places available. Place allocation is on a first-come, first-served basis.

Deadline for all workshops registrations: 20.09.2021

Cancellations

 

If you register for a workshop but are no longer able to attend, we would be grateful if you could inform us in advance, as soon as possible: sis.helpdesk@ethz.ch

 

This would allow us to give someone else the opportunity to join.

 

Program

 

27.09.2021

 

RegistrationZoom link registration

 

09:00-09:45 Welcome from SIS. Overview of latest developments and roadmap. Bernd Rinn, Caterina Barillari, SIS ETH Zurich

 

09:45- 10:15 Integrating imaging and omics data for biomedical research, Sven Nahnsen, QBiC Tübingen

 

10:15-10:45 Advancing Lab Operations with openBIS, Martin Hediger, University Hospital Zürich

 

10:45-11:00 coffee break

 

11:00-11:15 Structuring your research with openBIS, Tatiana Kochetkova, Empa

 

11:15-11:30 To the Data management and beyond: example of lab workflow in OpenBIS, Nikolajs Toropovs, Empa

 

11:30-12:00 Secure handling of confidential data, Diana Coman Schmid, SIS ETH Zurich

 

12:00-12:15 wrap up

 

12:15-14:00 lunch break

 

14:00-16:00 round table discussion

28.09.2021

 

The trainings on this day do not require any previous openBIS knowledge.

 

09:00-12:30 ELN user training

 

Registrationhttps://forms.gle/qTTKkGtGKffimpAV7

 

In this course we will provide a general overview of openBIS ELN/LIMS 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.

This course is designed for beginners and does not require any previous knowledge.

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.

 

Max number of places: 25

 

12:30-13:30 lunch break

 

13:30-16:30 Instance admin training

 

Registration: https://forms.gle/KrNz3jwNfEd97fsB8 

 

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

Topics covered:

Registration of openBIS types.

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

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.

 

Max number of places: 15

29.09.2021

 

The workshops on this day require familiarity with openBIS and programming.

 

09:00-09:30 Introduction to development workshops – openBIS Integrations Overview

 

Registration: https://forms.gle/qj8rkw4m2AZxiu14A

 

During this introduction we will explain how openBIS integrations for labs are done, with all the moving parts and openBIS extensions involved.

 

09:30-11:30 – Workshop 1 – Creating and Importing openBIS Data Models with Excel : The Excel Master Data Core Plugin

 

Registration: https://forms.gle/Y296VVdYBptpNhk87

 

Topics:

  • How to create data models for openBIS using the XLS master data plugin.

 

 

Max number of places: 15

 

11:30-13:00 lunch break

 

13:00-15:00 Workshop 2 – Automating data imports : The Dropbox Core plugin

 

Registration: https://forms.gle/GfLGGWeqFNnauXWp8

 

Topics:

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

 

 

Max number of places: 15

 

15:00-15:30 Coffee break

 

15:30-17:30 Workshop 3 – Integrating with other systems : The openBIS V3 Java API

 

Registration: https://forms.gle/QRgisqkd7JnYmbGw7

 

Topics:

  • 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.

 

Max number of places: 15

30.09.2021

 

The workshops on this day require familiarity with openBIS and programming.

 

09:00-11:00 – Workshop 4 – Developing your own openBIS Web apps and extending ELN-LIMS : The openBIS V3 Javascript API

 

Registration: https://forms.gle/f4XpitGWYunVy8Jg8

 

Topics:

  • 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.

 

Max number of places: 15

 

11:00-11:15  Coffee break

 

11:15-13:15 – Workshop 5 – Working with openBIS using Python, Jupyter Lab and pyBIS

 

Registration: https://forms.gle/PmtfnERQAizYHwsY9

 

Topics:

  • connect to openBIS and browse through its content
  • search, create, update and delete Samples and DataSets
  • create and modify openBIS master data and ELN-LIMS settings

 

Max number of places: 15