e-Science 2018: 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 used a few tools.


Silvia Delgado Olabarriaga
Department of Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB), Room: J1B-210-1
Tel. +31 (0)20-5664660
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)
  • Introduction to Big Data and applications in biomedical research (concepts and examples)
  • Hands-on experience with e-science platforms available at the AMC

Schedule and Location

  • 19-23 April 2018, from 1pm to 5pm
Monday Tuesday Wednesday Thursday Friday
19 Nov 20 Nov 21 Nov 22 Nov 23 Nov
13:00-14:00 HvA, A2-28 visit L0-217 HvA, A2-24 HvA, A2-22
14:00-15:00 HvA, A2-28 to L0-217 HvA, A2-24 L0-230
15:00-16:00 HvA, A2-28 Science L0-230 HvA, A2-24 J1b-223
16:00-17:00 HvA, A2-28 Park L0-230 L0-227 J1b-223

Note: HvA is the building next to the AMC (see location). When no building is informed, the room is in the AMC.

Before the course

Answer questionnaire before 13 November

Please take a few minutes to answer a brief questionnaire about your background:

click here for background survey

This will be useful to help the instructors prepare more adequate lectures.

Preparation of individual introductions before 16 November

On the first day the students will pitch about their own research (2 min).
This can be done with the support of a maximum of 2 slides (powerpoint or pdf) that need to be sent to the coordinator before 16 November.
Last-minute slides on USB or email will not be presented.

Please include the following information in your pitch:
  • background (study, career)
  • introduction to your research (project, department, PI, topic, main research question and approach)
  • types of data used in your research
  • potential bottlenecks

Preparation for practical lectures before 16 November

We will have three practices in rooms L0-230 and L0-227. These rooms have computers that connect directly to your CDW.
Note: If you are an external student who does not have access to computers at the AMC CDW, please bring your own laptop or team up with a colleague during the practices.

Please make sure make sure in advance that you can login into the computers of this room (might need to visit helpdesk of ADICT next to the Albert Hein if you cannot login).
Alternatively, you can also use own laptop on the public or eduroam WiFi, but then you need to make sure that you check whether the public or eduroam WiFi is good enough in the used computer rooms.

Program and Contents

Day #1, Nov 19: Introduction to computing and e-science

  • Introduction to the course (slides, intro students)
  • Basics of e-science, e-infrastructures, big data and open science (slides)
  • Basics of computing and research infrastructures (slides)
  • Practice & Summary: reflection and discussion about own research project (slides)

Day #2, Nov 20: Visit to the Science Park Amsterdam

Invited speakers will tell about what is going on at the Science Park of the University of Amsterdam
Address: Science Park 904, 1098 XH Amsterdam, room A1.04

  • 12:50 Arrival at Science Park 904, Building A, reception on ground floor
  • 13:00 Guided tour of Faculty of Sciences by Mieke van den Berg.
  • go to room A1.04
  • 13:30 Introduction to SURF
    • SURF and SURFnet services for research, Peter Hinrich, SURFnet (slides)
    • Introduction to SURFsara and national infrastructure for research, Raymond Oonk, SURFsara (slides)
  • 16:00 Introduction to the European Open Science Cloud (EOSC), Yin Chen, EGI (slides)
How to get to Science Park
  • train to Science Park Station. Walk 8-10 minutes from station to UvA Science Park 404.
  • bus from Amstel Station or Muiderpoort station, stops at Science Park.
  • park your car at parking P03. Note: paid parking!
  • From the main hall take the stairs or elevator to the 1st floor to reach to room A1.04

Day #3, Nov 21: Research data management

  • Introduction to research data management (slides)
  • Invited: Introduction to TraIT, Rita Azevedo, Lygadure (slides)
  • Invited: Workshop about tranSMART, Menno de Vries, NKI (instructions)

Day #4, Nov 22: Large scale computing

  • Large scale computing (slides)
  • Invited: Research ICT Infrastructure at the AMC, Hans van den Berg, ADICT (slides)
  • Practice: introduction to the national research cloud: Romy van der Beek, Sebastian Holt Bak (INFO.NL) and Martin Brandt, Ymke van den Berg (SURFsara)

Day #5, Nov 23: Research Management

  • Management tools: software, collaboration, project (slides)
  • Practice with githib (instructions)
  • Course wrap-up and final exercise (slides)

day1-intro-course.pdf (3.46 MB) Silvia Olabarriaga, 2018-11-19 12:16

day1-intro-escience.pdf (6.96 MB) Silvia Olabarriaga, 2018-11-19 12:18

day1-intro-computing.pdf (2.71 MB) Silvia Olabarriaga, 2018-11-19 12:18

day1-exercise-summaryDay1.pdf (3.82 MB) Silvia Olabarriaga, 2018-11-19 12:18

day2-surf.pdf (2.12 MB) Silvia Olabarriaga, 2018-11-21 15:04

day3-dataManagement-intro.pdf (3.99 MB) Silvia Olabarriaga, 2018-11-21 15:13

day4-AMC-ICTResearch.pdf (1.6 MB) Silvia Olabarriaga, 2018-11-21 15:25

day2-EOSC.pdf (2.71 MB) Silvia Olabarriaga, 2018-11-21 15:53

day4-largeComputing.pdf (4.56 MB) Silvia Olabarriaga, 2018-11-21 18:41

day3-TraIT.pdf (7.4 MB) Silvia Olabarriaga, 2018-11-22 17:57

day2-surfsara.pdf (7.59 MB) Silvia Olabarriaga, 2018-11-22 18:15

day5-management.pdf (1.47 MB) Silvia Olabarriaga, 2018-11-22 21:40

day5-recap-course.pdf (831 KB) Silvia Olabarriaga, 2018-11-22 21:40

day1-intro-students.pdf (880 KB) Silvia Olabarriaga, 2018-11-23 11:55