Welcome to the MVE510 - Introduction to bioinformatics. This is the course home page and it contains all the information you need to participate and complete the course.

The course will be held at Chalmers campus with physical lectures and computer exercises.

 

Teachers

Erik Kristiansson, examiner, course administrator, lecturer
Anna Johnning, computer exercise assistant
David Lund, computer exercise assistant

 

Student representatives

Amir Ali Barani
Jenny Marie Dean
Houshi He
Hugo Hilmersson
Lin Zhang

 

The course aims, schedule, and plan

Syllabus with course aims

Course schedule

Course plan 

 

Course material

Please refer to the course plan for lecture-by-lecture reading instructions.

Lecture notes

• Lecture 1 (updated 2024-11-06)
• Lecture 2 (updated 2024-11-07)
• Lecture 3 
• Lecture 4 (updated 2024-11-18)
• Lecture 5 (updated 2024-11-18)
• Lecture 6
• Lecture 7
• Lecture 8, Linear models in RNA-seq
• Lecture 9
• Lecture 10
• Lecture 11
• Lecture 12
• Lecture 13, Guest lectures
• Lecture 14, repetition and bonus lecture (suggestion: AI and large language models in bioinformatics and its relation to the Nobel Prize in Chemistry 2024)

Papers

The following scientific papers are a part of the literature of this course. These papers provide an alternative view of the topics discussed in the course. 

• Lecture 2: The Third Revolution in Sequencing Technology, van Dijk EL, Jaszczyszyn Y, Naquin D,  Thermes C. Trends in Genetics, 34(9) 2018.
• Lecture 4: A beginner's guide to SNP calling from high-throughput DNA-sequencing data, Altmann A, Weber P, Bader D, Preuss M, Binder EB, and Müller-Myhsok B. Human Genetics, 131(10) 2012.
  Lectures 5 and 6: Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. Schbath S, Martin V, Zytnicki M, Fayolle J, Loux V, and Gibrat JF. Journal of Computational Biology, 19(6) 2012.
• Lectures 7 and 8: Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis, Finotello F and Di Camillo F. Briefings in Functional Genomics, 14(2) 2014.
• Lecture 9: Clustering. Naomi Altman and Martin Krzywinski. Nature Methods, 14(6) 2017.
• Lecture 9: Principal component analysis. Jake Lever, Martin Krzywinski, and Naomi Altman. Nature Methods, 14(7) 2017.
• Lecture 11: Integrative analysis of omics data, Österlund T, Cvijovic M, and Kristiansson E. Systems Biology, 6(1) 2017.
• Lecture 11-12: The road to metagenomics: from microbiology to DNA sequencing technologies and bioinformatics, Escobar-Zepeda A, de León AVP, and Sanchez-Flores A. Frontiers in Genetics, 6 2015.

Extra exercises

• Lecture 5

Optional course book

Xinkun Wang, Next-Generation Sequencing Data Analysis, CRC Press, ISBN 9781482217889. The course covers chapters 2-5, 7-9, and 13. 

 

Computer exercises

The course contains four compulsory computer exercises. Computer exercise 1 is examined at the scheduled exercise. Computer exercises 2, 3, and 4 should be handed in as written reports. The computer exercises should be done in groups of a maximum of two persons.

• Computer exercise 1
• Computer exercise 2 (deadline December 8th)
• Computer exercise 3 (deadline December 22nd)
• Computer exercise 4 (deadline January 19th)

 

Software you need to install if you work from your own computer

• RStudio (https://rstudio.com/) or R (https://www.r-project.org/)
• IGV (http://software.broadinstitute.org/software/igv/)

Note that you can connect to the computers at Chalmers from remote. Please refer to this page for full details. All software should be available for the computers in SalA as well as the computer rooms in the Chemistry and Math building.

 

Guidelines for writing and submitting reports

The reports should be submitted as a group (of a maximum of two persons) through the Canvas course page. The report should be either in PDF or Word format. All of the code necessary should be included at the end of the report as an Appendix. Please double-check that the submitted code works as intended. Don't forget to add the names and Swedish social security numbers of all persons in the group on the front page. You only need to submit one report per group.

The reports should contain answers to all the questions posed in the exercise sheet. The answers should almost always have some motivation, meaning that even though the question could be answered with a yes or a no, we require a motivation why. Example question: "Do you see any differences?" Describe the observed differences (if the answer is yes), and not only a yes or a no. When you have been asked to generate a figure, this figure should be included in the report. The reports do not need an introduction, method, results, or discussion section, but should include some information about what has been done. Example: “When doing the quality assessment using fastqc, we saw that…”.

Good luck!

Exam

• 11 January 2024, morning (08:30-12:30)

Previous exams

• April 6, 2018
• August 29, 2018
• January 17, 2019, solutions
• April 26, 2019
• August 28, 2019, solutions
• January 16, 2020, solutions
• April 8, 2020
• January 13, 2021 (note that the year on the exam is wrong!)
• April 13, 2022
• January 12, 2023
• April 5, 2023
• August 23, 2023

Examination
This course is examined based on,

• Written exam: 08:30 on January 16, 2024. This gives you 5 points and determines your grade in the course.
• Four compulsory computer exercises. When you have passed all four of them you earn 2.5 points.