openBIS User Group Meeting 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
Registration: Zoom 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 Secure handling of confidential data, Diana Coman Schmid, SIS ETH Zurich
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 Digitalization of Sequencing Lab Workflows with OpenBIS LIMS, Martin Hediger, University Hospital Zürich
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
Registration: https://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