BIF-30806 Advanced Bioinformatics

Course

Credits 6.00

Teaching methodContact hours
Lecture8
Tutorial36
Practical70
Course coordinator(s)dr. ing. H Nijveen
Lecturer(s)dr. MH Medema
dr. S Smit
dr. ing. H Nijveen
Examiner(s)prof. dr. ir. D de Ridder

Language of instruction:

English

Assumed knowledge on:

BIF-20306 (Introduction to Bioinformatics) or SSB-20306 (Bioinformation Technology) and BIF-50806 (Practical Computing for Biologists) or INF-22306 (Programming in Python)

Continuation courses:

BIF-80336 MSc Thesis Bioinformatics

Contents:

This course covers the process of bioinformatics data analysis and the interpretation of the results in a biological context. The following topics will be addressed in the course:
- command line usage;
- programming/scripting;
- current bioinformatics data analysis tools;
- automated analysis pipelines;
The first part of the course will cover command line usage (linux), bioinformatics script programming (perl/python), as well as the theory and tools required to analyse data produced by current sequencing technologies and interpret the results. Topics include genome assembly, sequence annotation, gene expression, biological networks, and comparative genomics. During the second part of the course, students - in teams - will apply their knowledge in a small research project. Given a specific biological question and the required data, the goal is to build a data analysis pipeline and describe the biological interpretation.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- be proficient in command line usage;
- run existing data analysis tools using the command line;
- write computer scripts for data analysis;
- design and implement an automated data analysis pipeline connecting multiple tools;
- work with large data volumes (big data from NGS technologies);
- interpret the results of (NGS) data analysis;
- describe a data analysis process;
- describe the biological interpretation and implication of the analysis results.

Activities:

Hands on course, lectures, and study of relevant literature.

Examination:

Practical assignments (40%), a written report and oral presentation on the research project (60%).
The practical assignments need a 5 and the report and presentation need a 5.5 to pass.

Literature:

Recommended reading: 'Practical Computing for Biologists' - Haddock & Dunn, ISBN-13: 978-0878933914.

ProgrammePhaseSpecializationPeriod
Restricted Optional for: MPBPlant BiotechnologyMScA: Functional Plant Genomics2MO
MBFBioinformaticsMSc2MO
MinorPeriod
Restricted Optional for: WUBIFBSc Minor Bioinformatics2MO