Introduction to openBIS

27 June 2023
Streamed
Application deadline:
20 June 2023
Cancellation deadline:
20 June 2023
Caterina Barillari, Rostyslav Kuzyakiv
Data management
Beginner
Academic: 100 CHF
For-profit: 500 CHF
0.25 ECTS credits
Course material




No future instance of this course is planned yet

Overview

This course provides a general overview of openBIS, followed by a practical training session.

openBIS is a combined data management platform, Electronic Laboratory Notebook, and Inventory Management System. openBIS helps scientists meet requirements from funding agencies, journals, and academic institutions to publish data according to the FAIR data principles. Scientists can use openBIS to document their daily experimental or computational work, store any related experimental raw and derived data, and link everything to materials, samples and protocols stored in the lab inventory. The system ensures safe data storage and provenance tracking.

openBIS is open-source software distributed under the Apache v2.0 licence, developed by ETH Zurich Scientific IT Services (ETH SIS). ETH SIS provides openBIS to academic research groups in CH as part of its openRDM.swiss service.

Audience

This course is intended for life scientists and bioinformaticians, such as PhD students, post-docs and staff scientists.

Learning objectives

At the end of the course, the participants are expected to:

  • use the openBIS inventory of material and samples
  • use the openBIS inventory of laboratory protocols
  • document projects and experiments in the openBIS lab notebook and upload data
  • analyse data stored in openBIS with Jupyter or MATLAB

Prerequisites

Knowledge / competencies

No previous knowledge is required.

Technical

This course will be streamed, you are thus required to have your own computer with an Internet connection.

An openBIS test server will be made available to participants on the day of the course. Test cases will be provided by the instructors; however you are invited to bring your own data for testing.

Application

The registration fees for academics are 100 CHF. Participants from non-academic institutions should contact us before applying. While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Deadline for registration and free-of-charge cancellation is set is set to 20/06/2023. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

The course will be only be held online via Zoom.

The course will start at 9:00 CET and end around 16:00 CET. Precise information will be provided to participants in due time.

Additional information

Coordination: Monique Zahn, SIB Training group.

We will recommend 0.25 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.