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BK0001

Bioinformatics

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.

Information from the course leader

Dear students,

The course will start with an introduction about the course schedule, introduction to the online system that will administer and contain all modules of the course and present practical details how to work.

The course will start the 30 August 2021 at 10 CET. All materials, including recorded lectures and tutorials will be available through the course management system Canvas.

Due to COVID19 the course will be an online course with some opportunities for hybrid solutions depending on the pandemic situation.

There is now a published schedule for the course, some very minor changes may occur and the final schedule with more detailed information will be published just before the start.

A Zoom link will be distributed to all registered students in due time.

In the name of all teachers and personnel working with the course:

Welcome to an exciting adventure together!

Professor Erik Bongcam-Rudloff

Course evaluation

The course evaluation is now closed

BK0001-10005 - Course evaluation report

Once the evaluation is closed, the course coordinator and student representative have 1 month to draft their comments. The comments will be published in the evaluation report.

Additional course evaluations for BK0001

Academic year 2021/2022

Bioinformatics (BK0001-M1005)

2021-08-30 - 2021-11-01

Syllabus

BK0001 Bioinformatics, 15.0 Credits

Bioinformatik

Subjects

Bioinformatic

Education cycle

Master’s level

Modules

Title Credits Code
Project 5.0 0102
Exam 10.0 0103

Advanced study in the main field

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

Grading scale

5:Pass with Distinction, 4:Pass with Credit, 3:Pass, U:Fail The requirements for attaining different grades are described in the course assessment criteria which are contained in a supplement to the course syllabus. Current information on assessment criteria shall be made available at the start of the course.

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.

Formats and requirements for examination

Passed written and oral examination. Passed participation in compulsory course modules.
  • If the student fails a test, the examiner may give the student a supplementary assignment, provided this is possible and there is reason to do so.
  • If the student has been granted special educational support because of a disability, the examiner has the right to offer the student an adapted test, or provide an alternative assessment.
  • If changes are made to this course syllabus, or if the course is closed, SLU shall decide on transitional rules for examination of students admitted under this syllabus but who have not yet passed the course.
  • For the examination of a degree project (independent project), the examiner may also allow the student to add supplemental information after the deadline. For more information on this, please refer to the regulations for education at Bachelor's and Master's level.

Other information

  • The right to take part in teaching and/or supervision only applies to the course date to which the student has been admitted and registered on.
  • If there are special reasons, the student may take part in course components that require compulsory attendance at a later date. For more information on this, please refer to the regulations for education at Bachelor's and Master's level.

Responsible department

Department of Animal Breeding and Genetics

Further information

Determined by: Programnämnden för utbildning inom veterinärmedicin och husdjur (PN - VH)
Replaces: Ersätter: BI1324

Grading criteria

There are no Grading criteria posted for this course

Litterature list

  1. Bioinformatics Kommentar: The literature will be presented at each course module as books in the subject are quickly outdated.

Course facts

Tuition fee: Tuition fee only for non-EU/EEA/Switzerland citizens: 38054 SEK Cycle: Master’s level
Subject: Bioinformatic
Course code: BK0001 Application code: SLU-10005 Location: Uppsala Distance course: No Language: English Responsible department: Department of Animal Breeding and Genetics Pace: 100%