Introduction to openBIS (lectures and practicals) - now on YouTube

A recording of the introduction to openBIS is available on YouTube.

Overview

This 0.5-day 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). ETH SIS provides a data management service to the entire Swiss scientific community based on openBIS, either as a cloud-hosted version or on local infrastructure, as part of the swissuniversities funded openRDM.swiss project.

Audience

This course is intended for master and PhD students, post-docs and staff scientists working in experimental labs.

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

If you are interested in attending only the lecture, apply here.

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 and coffee breaks. Participants from non-academic institutions should contact us before application.

Deadline for registration and free-of-charge cancellation is set is set to 22/04/2020. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

Venue and Time

This course will be streamed to the registered participants. More information will be sent in due time.

The course will start at 9:00 CET and end around 13:00 CET. Precise information will be provided to participants in due time.

Schedule

09:00-09:45 introduction to openBIS (C. Barillari)

10:00-13:00 openBIS training (C. Barillari, P. Bhoumik) + demo of data analysis with Jupyter notebooks and MATLAB (H. Lütcke)

Additional information

Coordination: Monique Zahn

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.

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