Principles of Bioinformatics

Doel vak

Are you interested in bioinformatics? Would you like to know how huge

amounts of data can be analyzed in order to discover new biology? Would

you like to solve open questions in scientific research? This course is

open for any Bachelor student in a Science Degree (including Biology or

Biochemistry).

Principles of Bioinformatics is the concluding course for the minor Bioinformatics and Systems Biology. The lectures provide a comprehensive overview of key topics in the field. In practical sessions, you'll work on a bioinformatics benchmark, gaining hands-on experience with current algorithms and uncovering areas for further advancement in this rapidly evolving research field

Learning goals

The student:

• is aware of the major issues, methodology, data resources, and

available algorithms in bioinformatics. [Knowledge and understanding]

• can collaborate on a project in a group of diverse backgrounds.

[Communication]

• gains hands-on experience in scripting and handling basic mathematical

equations as a means of solving bioinformatics problems. [Applying and

understanding]

• To ask a question about something that is unclear. [Communication]

• Knows what biological databases contain and how to use them. [Applying

and understanding]

• Understands and can explain what a bioinformatics methods benchmark is

and why it is relevant. [Knowledge and understanding]

Inhoud vak

The following topics are covered:

• Evolutionairy profiles

• Data resources in for the Life Sciences, including the Gene Ontology

Database (GO)

• Homology Searching ( BLAST / PSI-BLAST )

• Genomics, Massively Parallel Sequencing (MPS)

• Benchmarking

• Computational Analysis of Genome Sequencing (Genome Assembly)

• Differential gene expression

• Clustering, machine learning and pattern recognition

There are practical sessions that aim to show you existing solutions

within the field of Bioinformatics. In the practicals you will use

existing databases and (web-server) solutions to solve biological

problems. You will also use python scripts to automate queries to

databases and web servers to investigate the value of current

Bioinformatics Algorithms.

Practical work:

One individual assignments:

• Homology searching

One group assignment in Python including:

• Running (PSI-)BLAST in Python, using the GO database, creating a ROC plot

Aanvullende informatie onderwijsvormen

• 6 lectures together with 'Introduction to Bioinformatics' (2 hours per lecture)

• 2 lectures specific to 'Principles of Bioinformatics'

• 6 group practical sessions (two hour sessions), partially supervised.

• 1 small assignments of which one together with 'Introduction to Bioinformatics'.

Toetsvorm

• [pass/fail] One individual assignment

• [~10%] One individual assignment

• [~40%] Group assignment consisting of three graded parts

• [~50%] Digital exam to assess: lecture topics

You are allowed to resit one part of the course if that makes you able

to pass the course. The resit will be either oral or written after the

end of the course.

Vereiste voorkennis

Programming in Python, Molecular Biology

Literatuur

• Course material (slides, scientific papers) on canvas
Background reading:
• Essential Bioinformatics, Jin Xiong, Cambridge University Press,
ISBN978-0-521-60082-8 (this is a very basic book, for BSc level only)
• Marketa Zvelebil and Jeremy O. Baum Understanding Bioinformatics
Garland Science 2008 ISBN-10: 0-8153-4024-9 (if you are planning to take
any further courses in bioinformatics, we would advise you to get this
book)

Aanvullende informatie doelgroep

This course is available for students in the minor 'Bioinformatics and
Systems Biology' and students from the major Biomedical Mathematics.

Overige informatie

This course is part of the Minor Bioinformatics and Systems Biology.
Most of the lectures of this course will be given together with the BSc
course "Introduction to Bioinformatics".

Aanbevolen voorkennis

An interest in programming and biological problems.