TU Delft
Year
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NEDERLANDSENGLISH
Organization
2015/2016 Applied Sciences Bachelor Nanobiology
NB2161
Bioinformatics
ECTS: 4.5
Responsible Instructor
Name E-mail
Prof.dr.ir. M.J.T. Reinders    M.J.T.Reinders@tudelft.nl
Dr. J. de Ridder    J.deRidder@tudelft.nl
Instructor
Name E-mail
A.M.E.T.A. Mahfouz    A.Mahfouz@tudelft.nl
Contact Hours / Week x/x/x/x
0/0/0/0/0/0/12/0
Education Period
4A
Start Education
4A
Exam Period
4A
5AB
Course Language
English
Course Contents
Bioinformatics is increasingly important to help answer biological questions, to deal with large volumes of measurement data which are now easily generated in the lab in the light of the vast amounts of prior knowledge already present in biological literature and stored in databases. In this course, the student will learn how to use computer methods as tools for biological research. An overview of core application software, databases and online applications will be provided, as well as in-depth knowledge on key algorithms and procedures to process and analyze sequence data and quantitative measurements. The course offers both theoretical insight and practical experience, in lab courses and small projects to be performed.
Study Goals
At the completion of this course the student will be able to:
- be aware of the existence of a range of bioinformatics tools and databases;
- analyze a given simple biological data analysis problem, discuss which tools/databases can help solve it;
- apply and use bioinformatics tools and databases, both interactively and in an automated way, and reflect on the results obtained;
- explain in detail a number of core bioinformatics algorithms, for sequence alignment, statistical testing, clustering.
Education Method
- Lectures
- Computer lab work
- Project

The course will be taught in five blocks of two week, each dealing with a specific topic. Each block consists of 2 full days, one in each week. The first day includes 2 lectures and 2 computer lab courses (2h lecture + 2h computer lab course + 2h lecture + 2h computer lab course). The second day is divided between working on an implementation assignment and a small project in which the topics discussed will be explored on a small real-world problem.
Books
- Marketa J. Zvelebil, Jeremy O. Baum, “Understanding bioinformatics”, Garland, 2007, 798p
- selected papers on next-gen sequencing, made available through Blackboard
Assessment
The course includes 2 exams each of 3 hours. The first exam covers Modules 1 and 2. The second exam covers all 5 modules. Moreover, you will need to hand in: (1) your lab-work, (2) the code produced for the programming assignment and (3) the scientific poster explaining your solution to the project.
- Assignments and lab-work are given Lab points: 2 points if completed sufficiently and on time, 1 point if completed sufficiently but not on time and 0 points if not sufficient or not on time.
- The Project grade is an average of the poster grades.
- A final grade is obtained only if the Exam grade is a 5 or higher and a total of 12 Lab points are obtained.
The final grade is calculated by a weighted average of the Exam grade (60%) and the Project grade (40%).


A single resit (spanning the entire course material) is possible in August following the course. This will consist of a 3 hour exam. The resit exam grade will only replace the final exam grade (60% of the total grade).
Location
Delft