Introduction to openBIS

The video of the lecture can be found in the SIB YouTube channel.

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. The course will provide a hands-on user training and an overview of the analysis of data stored in openBIS.

openBIS is open-source software distributed under the Apache v2.0 licence, developed by ETH Zurich Scientific IT Services (ETH SIS). In addition, ETH SIS provides openBIS to academic research groups in CH as part of its openRDM.swiss service. openRDM.swiss received start-up funding from Swissuniversities' P-5 program from 2018-2020.

Audience

This course is intended for master and 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
• be able to analyse data stored in openBIS with Jupyter or MATLAB

Prerequisites

Knowledge / competencies

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

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 60 CHF. This includes course content material. Participants from non-academic institutions should contact us before application.

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 18/05/2021. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

This course will be streamed to the registered participants.

The course will start at 9:00 CET and end around 17:00 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.