Topic outline

  • General

    Introduction to OpenBIS

    Streamed from Basel and Zurich, 1 June 2021

    This page is addressed to registered participants. To access the course description and the application form, please click here.

    For any assistance, please contact training@sib.swiss.


    During the training participants will have access to an openBIS instance for the exercises. Details and login credentials will be sent via email a couple of days before the training day.

    • Course Material


      openBIS user training

      The course material contains a tutorial (openBIS-tutorial.docx) with the exercises that will be done during the training. 

      In addition, some files that will be used during the training are also provided.

      Participants are required to download all the training material before the start of the course.


      Data analysis part

      In the last part of the hands-on tutorial, we will explore how to analyse datasets stored in openBIS with two popular tools: Jupyter notebooks and Matlab


      Jupyter notebooks

      For the Jupyter part, we will follow this online tutorial:

      https://gitlab.ethz.ch/sis-rdm-training/openbis-training/-/blob/master/2_data_analysis/jupyter/Data_Analysis_with_Jupyter_Tutorial.ipynb

      To run through the tutorial yourself during the training, you need to install and run Jupyter on your local computer. A quick guide can be found in the section "Install & run Jupyter" in the tutorial notebook.

      If you are not familiar with Jupyter notebooks at all, it will definitely be helpful to check out the Jupyter documentation (https://jupyter-notebook.readthedocs.io/en/stable/notebook.html) or run through a few of online tutorials (https://jupyter.org/try) before the training.


      Matlab

      For the Matlab part, instructions are provided here: 

      https://sissource.ethz.ch/hluetcke/matlab-openbis/-/wikis/home 

      Obviously, you should have Matlab installed on your machine if you want to follow along during this part of the training.