e-Science: Computing for Biomedical Research

This page is about the FIRST e-SCIENCE course offered for AMC GRADUATE STUDENTS in 2013.

See elsewhere actual information on the e-Science course.

Have you ever thought that your computer has become too small for your data processing needs?
Do you feel overflowed by a tsunami of data?
Do you have the impression that you spend more time arranging computers to run data analysis than actually doing the research that the data is supposed to support in the first place?

If this sounds familiar, dont’ worry. You are not alone. Come and join the e-science course on March 26-28, where you can learn how others are addressing the modern challenges of data analysis for biomedical research.

Silvia Delgado Olabarriaga
Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, J1B-206
Tel. +31 (0)20-5664660
Email: s.d.olabarriaga @ amc.uva.nl
https://wiki.bioinformaticslaboratory.nl, https://www.ebioscience.amc.nl


Computing infrastructures have become an essential ingredient of biomedical sciences. The variety and amount of data has significantly increased, and the typical desktop 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, and collaboration. These new approaches enable and enhance science (e-science), and are increasingly used in (AMC) biomedical research.

The aim of this course is to bring attention to new approaches that can be used for handling large-scale data in biomedical research, including processing, storage 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) be able to apply some of these technologies and tools in practice.

When, Where

See also: A4 with course summary


  • Basic concepts of research infrastructures and e-science
  • Introduction to distributed computing (grids, clouds, clusters)
  • Scientific workflow management (concepts and examples)
  • Hands-on experience with the AMC e-science platform


Note that all rooms are in the ground floor (01) of building "L", below the floor where the main entrance is located. Ask directions at the reception if you are not familiar with the building.

Date Time Room Topic
Tuesday, 26-3-2013 09:00 - 11:00 L01-211-2 Introduction to e-science and e-infrastructures
  11:00 - 12:00 L01-211-2 Invited lecture: Dutch e-science infrastructures, Jan Bot, SURFSara
  12:00 - 13:00 L01-243 Group discussion and presentations
Wednesday, 27-3-2013 09:00 - 11:00 L01-211-2 Introduction to workflow management
  11:00 - 13:00 L01-243 Hands-on exercises with WS-PGrade workflow management system
Thursday, 28-3-2013 09:00 - 10:00 L01-211-2 Advanced workflow management
  10:00 - 12:00 L01-243 Hands-on exercises with WS-Pgrade
  12:00 - 13:00 L01-211-2 Invited talk: Science Gateways, Shayan Shahand, KEBB (AMC)
    L01-211-2 Closing

Program and Contents

Click on the lectures for downloading the slides

Day 1

Additional Reading: The slides contain several links to on-line materials and articles related to the topic of the lectures. In addition, the following materials are related to the topics of day 1:

Day 2

Additional Reading:

Day 3

Additional Reading:


Registration is closed.

Contact and information


For more info about the course or registration, contact Silvia D. Delgado (s.d.olabarriaga amc.uva.nl).
Topic revision: r3 - 27 May 2020, UnknownUser

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