Information Technology Reference
In-Depth Information
The targeted learning outcome of these hands-on tutorials is to have students
understand the basic processes and principles of accessing distributed computing
infrastructures, and to give them direct experience in designing applications that
utilize grid or cloud resources for more ef
cient execution.
16.2.2 Introduction to e-Science for Students of the Academic
Medical Center of the University of Amsterdam
The AMC provides education for medical and medical informatics professionals at
undergraduate, master and graduate levels. Since 2010, the topic of
has
been introduced in the curriculum in the form of lectures, seminars and courses for
the bachelor and master programs in Medical Informatics, as well as at the AMC
Graduate School for medical students. The goal of these courses is to familiarize the
students with modern information technologies for large-scale data analysis, which
is becoming a prominent topic in both medical informatics and medical biosciences.
The students of medical informatics courses have a strong background in infor-
mation management with programming skills mainly in Java, but they are not very
familiar with command-line interfaces. The AMC graduate school students, on the
other hand, have a very diverse pro
“
e-science
”
le, ranging from medical background and
totally naive in programming, up to skilled capabilities for scripting to implement
data analysis tools and pipelines using bash, R and MATLAB scripts. Both medical
informatics and graduate school students typically have no experience with dis-
tributed computing.
In these courses we use WS-PGRADE as a web-based platform from which the
students can have hands-on experience with distributed computing. The assign-
ments include executing existing workflows on diverse infrastructures,
imple-
menting small modi
cations to these workflows, programming new workflow
components, and composing new simple workflows. The goal is to bring distributed
computing closer to these students, by providing them a
first e-science experience
in a simple and easy manner.
The assignments using WS-PGRADE are carried out during practical lessons of
2 h on different levels varying from basics to advanced topics. At the basics level
only simple
-like workflows are executed locally, on clusters and on
the grid using data that is uploaded to the portal. At the advanced level, the
workflows include data on grid storage and the use of generator-collector ports. The
medical informatics students only follow the basics level using Java components,
whereas the AMC graduate students use bash scripts on both levels.
An introduction to WS-PGRADE is presented prior to the lab exercises. The
students receive printed instructions for the assignments, and all materials are also
available online, including sample
“
hello world
”
files and the introductory presentation. The
students are assisted by instructors during the lesson (one instructor for each group
of five to six students). In these courses the assignments are performed on the AMC
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