BIF-31306 Algorithms in Bioinformatics

Course

Credits 6.00

Teaching methodContact hours
Individual Paper0
Lecture16
Tutorial34
Course coordinator(s)dr. S Smit
Lecturer(s)dr. S Smit
prof. dr. ir. D de Ridder
dr. M Suarez Diez
Examiner(s)prof. dr. ir. D de Ridder

Language of instruction:

English

Assumed knowledge on:

INF-22306 Programming in Python.

Continuation courses:

BIF-80336 MSc Thesis Bioinformatics.

Contents:

Modern biology routinely generates huge amounts of data: sequences, from NGS experiments; quantitative data, from -omics experiments; and graphs, representing molecular interactions. At the heart of many bioinformatics applications are algorithms that handle such types of data in time- and memory-efficient ways. Almost invariably these algorithms optimize some criterion - e.g. alignment quality, energy function or probability measure - using the data available.
In this course, the main types of algorithms will be discussed, aiming to gain a deeper understanding of the computational strategies underlying these algorithms. This will allow students to recognize which type of algorithm will be applicable in the development of new bioinformatics tools to help answer new questions in (computational) biology.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- identify the algorithmic design technique and the underlying optimization criterion in bioinformatics algorithms;
- explain in detail the working of a number of fundamental bioinformatics algorithms;
- implement a given bioinformatics algorithm in python;
- analyse algorithms discussed in state-of-the-art bioinformatics/computational biology literature.

Activities:

- study theory and program practice problems.
- read and present literature.

Examination:

Students will be graded based on reports handed in on the practical assignments (60%), on the literature presentations/discussions given (30%) and on participation (10%). Each component needs a minimum mark of 5 to pass.

Literature:

Literature and exercises are made available in electronic form during the course.

ProgrammePhaseSpecializationPeriod
Restricted Optional for: MBFBioinformaticsMSc6AF