Print Syllabus

Syllabus

BK0001 Bioinformatics, 15.0 Credits

Bioinformatik

Subjects

Bioinformatics Bioinformatic

Education cycle

Master’s level

Advanced study in the main field

Second cycle, has only first-cycle course/s as entry requirements
Master’s level (A1N)

Grading scale

Language

English

Prior knowledge

180 credits at first cycle, of which

• 60 credits biology of which 15 credits cell biology or molecular genetics or genetics

or

• 60 credits animal science of which 15 credits cell biology or molecular genetics or genetics

or

• 60 credits agricultural sciences of which 15 credits cell biology or molecular genetics or genetics

or

• 60 credits equine science of which 15 credits cell biology or molecular genetics or genetics

or

• 60 credits veterinary nursing of which 15 credits cell biology or molecular genetics or genetics

or

• 60 credits veterinary medicine of which 15 credits cell biology or molecular genetics or genetics

or

• 60 credits computer science and 7,5 credits cell biology or molecular genetics or genetics



and English 6

Objectives

The course aims to give a solid basis in basic bioinformatic methods. It covers the theories, algorithms and practical applications of computer-based methodology for the analysis of DNA/protein sequences, protein structures, and data produced by large-scale methods for understanding interactions of different biomolecules.

On completion of the course, the student should be able to:

• account for the fundamental concepts within bioinformatics

• independently carry out homology analyses of both protein - and DNA sequences and interpret the results

• use the most common commands in Unix/Linux,

• use the most common commands in R,

• independently build a "workbench" for bioinformatics with publically available softwares suited to the own needs,

• use biological databases

• describe technologies within High Troughput Sequencing (HTS or NGS) and methods for the analysis of expression data that have been retrieved with RNAseq technology,

• management and anlalysis of large scale data sets,

• manage the use of software solutions in computer clusters and cloud services.

Content

The course covers bioinformatic methods such as theories, algorithms and practical applications in computer-based methodology for the analysis of DNA/protein sequences, protein structures, annotation of genomes, metagenomics. The course also covers theories for the analysis of RNAseq expression data and different analytical methods within High Troughput Sequencing (sometimes called NGS).

Topics to be covered includes: biological databases, biostatistics, homology analyses, gene analyses (emphasis on open source softwares), web-based analytical tools, Unix OS, R, comparative genomics, functional genomics, metagenomics, molecular evolution, RNAseq expression analysis, management of large amounts of data, principles for the use of computer clusters, and cloud services and annotation of new genomes.

The course is based on lectures, exercises, project work and laboratory sessions. Apart from the written and the oral examination, compulsory components occur within e g exercises, project work and laboratory sessions.

Grading form

The grade requirements within the course grading system are set out in specific criteria. These criteria must be available by the course start at the latest.

Formats and requirements for examination

Passed written and oral examination. Passed participation in compulsory course modules.

• If a student has failed an examination, the examiner has the right to issue supplementary assignments. This applies if it is possible and there are grounds to do so.

• The examiner can provide an adapted assessment to students entitled to study support for students with disabilities following a decision by the university. Examiners may also issue an adapted examination or provide an alternative way for the students to take the exam.

• If this syllabus is withdrawn, SLU may introduce transitional provisions for examining students admitted based on this syllabus and who have not yet passed the course.

• For the assessment of an independent project (degree project), the examiner may also allow a student to add supplemental information after the deadline for submission. Read more in the Education Planning and Administration Handbook.

Other information

• The right to participate in teaching and/or supervision only applies for the course instance the student was admitted to and registered on.

• If there are special reasons, students are entitled to participate in components with compulsory attendance when the course is given again. Read more in the Education Planning and Administration Handbook.

Responsible department

Department of Animal Breeding and Genetics