Fundamentals of Bioinformatics

Course code:
Period 1
Language of tuition:
Faculty of Science
dr. ir. K.A. Feenstra
dr. ir. K.A. Feenstra
dr. ir. K.A. Feenstra
prof. dr. J. Heringa
dr. D. Molenaar
dr. S. Abeln
Teaching method(s):
Lecture, , Computer lab

Course objective

Interested in Bioinformatics?
Or you want to find out how biology can make an exciting application
Or you want to learn how what more you could do with your data, and with
less effort? Enter here to start!

Fundamentals of Bioinformatics (FoB) is the starting course of the
Bioinformatics master. It aims to give a broad overview of important
topics relevant to the field, with a focus on current open problems.
Students will be made aware of these open problems during practical
sessions that aim to let the student ‘stumble upon’ these problems by
themselves. Based on their background, students will be assigned to
separate classes where they will be working to fill gaps in their
background knowledge in programming and/or biology.

• To make the students aware of gaps in their own background knowledge.
• The student will be aware of the major issues, methodology and
available algorithms in bioinformatics.
• To work together in a group of diverse backgrounds.
• To gain hands-on experience in scripting and handling basic
mathematical equations as a means of solving bioinformatics problems.
• To develop a basic understanding of major concepts in genomics and
molecular cell biology that are relevant to current topics in

Course content

• Evolution, Genomes, Sequences, Blast/PSI-Blast, Semantic Web,
Multi-omics, Next-generation Sequencing

• Exercises during/in between lectures
• Project in groups to solve a major bioinformatics problem. The groups
will be composed to include each of the three major background areas:
bioinformatics, biology and computer science. Success of the group
project will depend on the level of cooperation!

Form of tuition

• 12 Lectures (two hour lecture in the morning, two days per week)
• 12 Computer practicals (two hour sessions following the morning
lectures, two days per week), partially supervised.
• Project work
Feedback (theoretical and practical) will be given during the project
and computer practical sessions.

Type of assessment

• [30%] Programming or Biology classes
• [30%] Project and group work
• [40%] Oral or written exam (depending on number of course students) to
◦ Exercises
◦ Project results (individual)
◦ Lecture topics

Course reading

• course material (slides, scientific papers) on
• Marketa Zvelebil and Jeremy O. Baum Understanding Bioinformatics
Garland Science 2008 ISBN-10: 0-8153-4024-9

Entry requirements

Bachelor in any science discipline (including medicine), or strong
programming background.

Recommended background knowledge

An interest in algorithmics approaches to biological problems.

Target audience

mAI, mBSB (JD), mCS, mMNS, mBMol

© Copyright VU University Amsterdam
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