e-Science 2020: Computing for Biomedical Research

Computing infrastructures have become an essential ingredient of biomedical sciences. The variety and amount of data has significantly increased, and the typical researcher workstation is not longer sufficient. Large collaborations are necessary to carry out research, involving complex logistics for handling distributed data collection, analysis and management. New approaches (computers, software and methodology) are needed to tackle challenges regarding compute power, storage space, data management and collaboration. These new approaches enable and enhance science (e-science), and are increasingly relevant for biomedical research.

The aim of this course is to bring attention to new approaches (methods, infrastructures) that can be used for handling large-scale data in biomedical research, including processing, data management and collaboration. At the end of the course, the participant will (1) be familiar with new concepts and state of the art, (2) understand how these new approaches relate to his/her own research, and (3) have had basic experience with a few tools.


Silvia Delgado Olabarriaga
Department of Epidemiology and Data Science
Amsterdam UMC, Location AMC
Email: s.d.olabarriaga at,


  • Basic concepts of research infrastructures and e-science
  • Introduction to distributed computing (grids, clouds, clusters)
  • Introduction to research data management (concepts and examples)
  • Demo's and hands-on experience with e-infrastructure platforms available for AMC researchers

Schedule and Location

  • 26-29 October 2019, from 1pm to 5pm
  • zoom links announced below for each day

After the course

In Oct 2020 the e-Science course was for the first time totally on-line.
The Graduate School will ask your opinion about the course using a standard evaluation form. That form serves quality control for the Graduate School, so it is important that you complete that one.

In addition to that, I (Silvia) would like your feedback through this form about specifics of the ON-LINE edition.

Many thanks for your time!
Silvia Olabarriaga

Before the course

It is important to observe the preparations that will help target the classes and enable smooth practice. Please start early and ask the coordinator for clarification if necessary.

Answer questionnaire before Thursday 22 October

Please take a few minutes to answer a brief questionnaire about your background. Your answers will be useful to help the instructors prepare more adequate lectures:

click here for background survey

Preparation of individual introductions before 25 October

On the first day the students will pitch about their own research (2 min).
This can (optionally) be done with the support of a maximum of 1 slide (powerpoint or pdf without animations) that needs to be sent to the coordinator before 25 October.
Last-minute slides will not be presented.

Please include the following information in your pitch:
  • your background (medical, technical, education and current position)
  • introduction to your research (project, department, topic, main research question and approach)

Preparation of working environment before Monday 26 October

The classes will be online using ZOOM. The links will be published along with the classes below. Before the course, please
  • Install the Zoom desktop client on your computer. See more information
  • Get acquainted with Zoom:
  • If you never used zoom before, this is a test meeting where you can practice (coordinator needs to start the meeting manually, so please make appointment first)
We will also use a mind map tool for some exercises. This can be used directly from the Web browser, without the need to install anything. Before the course, please
  • Check GitMind:
  • Make sure you can login (create an account or use your existing google, facebook or twitter)
  • Get acquainted with GitMind

Program and Contents

Day #1, Oct 26: Introduction to computing and e-science

  • Zoom meeting
  • Introduction to the course (slides)
  • Basics of e-science, e-infrastructures, big data and open science (slides)
  • Basics of computing and research infrastructures (slides)
  • Terminology game: instructions
  • Invited lecture: Introduction to the Netherlands e-Science Center, Lars Ridder, NLeSC (slides)

Day #2, Oct 27: Large scale computing

  • Invited lecture: Introduction to AnDREa, Bob van Dijk, Amsterdam UMC (slides)

Day #3, Oct 28: Big research management

  • Invited lecture: Introduction to research data management with YoDa and iRODS, Paulo Heemskerk, Amsterdam UMC (slides)

Day #4, Oct 29: National and European infrastructures

  • Zoom meeting
  • Invited lecture: Introduction to the European infrastructures, Yin Chen, EGI (slides)
  • Invited lecture: Overview of the Virtual Imaging Platform (VIP), Sorina Pop, CREATIS)
  • Invited lecture: Introduction to National research infrastructure services, Carlos Teijeiro Barjas, SURF, (slides)
  • Exercise: Design 'best' infrastructure for your research: instructions
  • Wrap-up, end course (slides)

day1-intro-course.pdf (883 KB) Silvia Olabarriaga, 2020-10-23 23:11

day1-intro-escience.pdf (6.24 MB) Silvia Olabarriaga, 2020-10-23 23:15

day1-intro-computing.pdf (1.86 MB) Silvia Olabarriaga, 2020-10-23 23:16

day1-exercise.pdf (15.8 KB) Silvia Olabarriaga, 2020-10-23 23:16

day2-largeComputing.pdf (9.56 MB) Silvia Olabarriaga, 2020-10-23 23:25

day2-Bob-CloudcomputingAmsterdamUMC.pdf (6.96 MB) Silvia Olabarriaga, 2020-10-23 23:25

day2-VRE.pdf (2.57 MB) Silvia Olabarriaga, 2020-10-23 23:27

day3-dataManagement.pdf (3.73 MB) Silvia Olabarriaga, 2020-10-23 23:32

day3-collaborationManagement.pdf (746 KB) Silvia Olabarriaga, 2020-10-23 23:32

day3-versionControl.pdf (886 KB) Silvia Olabarriaga, 2020-10-23 23:32

day4-recap-course.pdf (882 KB) Silvia Olabarriaga, 2020-10-23 23:34

day1-NLeSC-intro-2020.pdf (1.79 MB) Silvia Olabarriaga, 2020-10-27 16:17

day3-iRODS_YoDa_28102020.pdf (370 KB) Silvia Olabarriaga, 2020-10-28 17:29

day4-VIP_eScience_2020.pdf (2.5 MB) Silvia Olabarriaga, 2020-10-29 15:13

day4-EGI_Infra 2020.pdf (6.2 MB) Silvia Olabarriaga, 2020-10-29 15:14

day4-SURFServices-GeneralPresentation.pdf (5 MB) Silvia Olabarriaga, 2020-10-29 16:40