General Information
| Course Code | X_401094 |
|---|---|
| Credits | 6 EC |
| Period | P3 |
| Course Level | 300 |
| Language of Tuition | English |
| Faculty | Faculty of Science |
| Course Coordinator | dr. E. Bosdriesz |
| Examiner | dr. E. Bosdriesz |
| Teaching Staff |
dr. J.M. Urtasun Elizari dr. E. Bosdriesz dr. S. Abeln prof. dr. J. Heringa dr. ir. K.A. Feenstra |
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Part of programme(s)
Premaster
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Practical Information
You need to register for this course yourself. The (de)registration deadlines can be found on VU.nl
| Teaching Methods | Computer lab, Practical, Lecture |
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Target audiences
This course is also available as:
Course Objective
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]
Course Content
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
Additional Information Teaching Methods
• 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'.
Method of Assessment
• [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.
Entry Requirements
Programming in Python, Molecular BiologyLiterature
• Course material (slides, scientific papers) on canvasBackground 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)
Additional Information Target Audience
This course is available for students in the minor 'Bioinformatics andSystems Biology' and students from the major Biomedical Mathematics.
Additional Information
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".