Applied Bioinformatics

ECTS Credits

10 ECTS

Level of Study

Bachelor

Teaching semester

Autumn.

This course has a limited capacity, enrolment is based on application. The application deadline is Wednesday in week 33 for the autumn semester. Please see this page for more information. You will receive confirmation of whether you received a seat in Studentweb no later than Monday the week after the deadline.

It is compulsory to attend the first lecture/orientation meeting, or you risk losing your seat. If you are unable to attend the first lecture, you must contact the Study Section (studie.bio@uib.no). The time of the first lecture/orientation meeting can be found in the schedule on the course website or on Mitt UiB.

Objectives and Content

The course provides an introduction to the use of bioinformatics tools, including analysis of protein sequences,retrieval of information from databases, pairwise and multiple sequence alignments, phylogenetic trees, visualization and analysis of protein structures, as well as an introduction to the use of Python and Unix for bioinformatics analyses. The theoretical basis for selected methods, such as dynamic programming, is studied in detail. The course consists of lectures, exercises and a PC lab.

Learning Outcomes

On completion of the course the student should have the following learning outcomes defined in terms of knowledge, skills and general competence:

Knowledge

• The student can explain which type of data is available from the most common protein sequence and structure databases (UniProt, GenBank, Protein Data Bank, CATH).
• The student can explain the theories underlying the most common methods for sequence searches and sequence alignments, and in particular knows the principle and main steps for pairwise and multiple sequence alignments;
• The student can explain and is able to apply the main steps of dynamic programing for/to simple alignments of short sequences;
• The student can explain the principles behind reconstruction and interpretation of phylogenetic trees;
• The student can list methods to uncover structure-function relationship in proteins and knows their underlying principles;
• The student can explain the main advantages and limitations of methods for the prediction of secondary structure and 3D prediction from sequence.
• The student has a basic understanding for how to use unix commands to parse files with biological information. 
• Know the main principles of metagenomic and metatranscriptomic analysis

Skills

The student is able to:

• select and apply the most appropriate bioinformatics sequence or structure database to retrieve or search data given a specific question in molecular biology;
• select and apply the most appropriate method for aligning sequences, reconstructing evolutionary relationships, visualizing and analyzing protein structures.
• use python and unix to do simple bioinformatic analyses

General competence

• The student is able to reflect using its knowledge and skills in bioinformatics so as to decide whether a given molecular biology problem could benefit from a bioinformatics approach, and which methods to use.
• Using their theoretical knowledge about the most commonly used bioinformatics methods, the student is able, if encountering a new online tool, to get a general understanding of its underlying principle

Required Previous Knowledge

MOL100 and INF100

Recommended Previous Knowledge

INF100 Introduction to programming

Credit Reduction due to Course Overlap

BINF100: 5 ECTS,

KB207: 10 ECTS

Teaching and learning methods

Lectures and exercises.

Compulsory Assignments and Attendance

Lectures and practical tasks, together with approved reports.

The first lecture/orientation meeting is compulsory.

Completed activities are valid for 6 semesters.

Forms of Assessment

Written, possibly oral exams depending on number of candidates; approved reports

Examination support materials: Non- programmable calculator, according to model listed in faculty regulations

Examination Support Material

None

Grading Scale

The grading scale used is A to F. Grade A is the highest passing grade in the grading scale, grade F is a fail.

Reading List

The reading list will be available within June 1st for the autumn semester and December 1st for the spring semester.

Programme Committee

The Programme Committee is responsible for the content, structure and quality of the study programme and courses.

Course Administrator

The Mathematics and Natural Sciences - Department of Biological Sciences has the responsibility for the course and programme.