Fundamentals of Bioinformatics

2019-2020

Course Objective

Interested in Bioinformatics?
Or you want to find out how biology can make an exciting application
domain?
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.

Goals:
• 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
bioinformatics.

Course Content

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

Practical:
• 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!

Teaching Methods

• 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.

Method of Assessment

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

Entry Requirements

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

Literature

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

Target Audience

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

Recommended background knowledge

An interest in algorithmics approaches to biological problems.

General Information

Course Code X_405052
Credits 6 EC
Period P1
Course Level 400
Language of Tuition English
Faculty Faculty of Science
Course Coordinator P. Schmidt
Examiner P. Schmidt
Teaching Staff dr. ir. K.A. Feenstra
prof. dr. J. Heringa
dr. D. Molenaar
dr. S. Abeln
B. Stringer MSc
L. Hoekstra

Practical Information

You need to register for this course yourself

Last-minute registration is available for this course.

Teaching Methods Lecture, Computer lab
Target audiences

This course is also available as: