MVE510 Introduction to bioinformatics Autumn 26

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On this page and in the course PM, you will find all the information about the course! All relevant files are collected under Files and linked below, and the reports for the computer exercises are submitted under Assignments. Questions are primarily answered during classes, but you can also post questions on the course website under Discussions. Specific coding questions about the computer exercises are answered by the teaching assistants during the scheduled computer labs. The information on the page will be updated continuously during the course, so please activate notifications for Announcements.

If you find any errors on the course website, please notify Anna.

 

Syllabus, Schedule & Course PM

 

Teachers

Lecturer & course administrator: Anna Johnning
Examiner: Erik Kristiansson
Teaching assistants: Sophia Axillus, James Butler & Laleh Varghaei

 

Course material

The course is based on the following material that is available to download from the Canvas course page,

  • Lecture notes
  • Eight academic papers
  • Exercises on sequence alignment

There is also an optional course book, where the course covers chapters 2–5, 7–9, and 13. A few copies are available from the Chalmers library.

  • Next-Generation Sequencing Data Analysis by Xinkun Wang. 
    • Hardback: ISBN 9780367349899
    • Ebook: ISBN 9780429329180

 

Lectures* Content Additional Material

Tuesday, week 1

Friday, week 1

Tuesday, week 2

Friday, week 2

Tuesday & Friday,
week 3
  • Sequence alignment

Tuesday & Friday,
week 4
  • Transcriptome sequencing (RNA-seq)

Friday, week 4
  • Linear models

Tuesday, week 5
  • Multiple testing

Deadline for submitting the report for Computer Exercise 2

Friday, week 5
  • Unsupervised data exploration

Tuesday & Friday, week 6 
  • Metagenomics

Friday, week 6
  • Examples from research

Tuesday, week 7
  • AI in the Life Sciences

Fri, week 7
  • Repetition
  • Old exam questions
  • Repetition_2020, Repetition_2021, Repetition_2022, Repetition_2024

Guest lectures
  • Date TBD: IRLAB Therapeutics
  • Date TBD: AstraZeneca

Deadline for submitting the report for Computer Exercise 3

Deadline for submitting the report for Computer Exercise 4

Written exam

* These timings are approximate, as some material might spill over to the next scheduled lecture. 

 

Examination

This course is examined based on,

  • Written exam (5 hp, grade U–5)
  • Four compulsory computer exercises (2.5 hp, U/G) 

The course has no elements that generate bonus points for the written exam.

 

Written Exam

A passed exam is worth 5 credits and determines your grade in the course. The maximum score is 40 points; a pass requires at least 18 points, a grade of 4 requires 26 points, and a grade of 5 requires 34 points. No aids are allowed during the exam. Shortly after the exam, suggested solutions will be posted on Canvas. Old exams, along with some answers/solutions, can be found here.

This year's exams will be given on,

  • Thursday morning, January 14th
  • Wednesday morning, March 31th
  • Friday morning, August 27th. 

 

Computer exercises

The course contains four compulsory computer exercises. The purpose of the computer exercises is to,

  • Gain hands-on experience in bioinformatic analyses
  • Apply concepts covered by the lectures in realistic situations
  • Interpret and critically evaluate the results
  • Practice programming

Computer Exercise 1 is examined during the scheduled computer labs by the teaching assistants. Computer Exercise 2–4 are examined through written reports. Each exercise should be done in groups of a maximum of two students. 

It is highly recommended to submit the reports at your earliest convenienvce, but no lated than the deadlines listed under Assignments. Make sure you plan your work so that you can utilise the help from the teaching assistants during the scheduled computer labs.

Here is a suggested time plan where "X" marks the deadlines and the scheduled computer labs are marked at the bottom (high bar = 4 h lab, low bar =  2 h lab),

gantt.png

If you want to complete the exercises on your own computer, you can either access the relevant software through https://apps.chalmers.se/ or install the following:

All software are available on the computers in computer rooms HB105, HB110, KD1, KD2, M10, and MT11.

More information about the computer exercises – including instructions, deadlines, and the format of the reports – is found under Assignment.

 

Use of AI tools

During the studies, the students are free to use AI tools to support their learning, but it is not permitted to use generative AI to generate all code or write report text for computer exercises. No AI tools are permitted on the exam. The purpose of the computer exercises is to increase the knowledge and understanding of bioinformatics, which in turn increases the chance of passing the exam. It is, therefore, strongly recommended to write and debug your code without AI help. For those who still want to use generative AI, the following examples are allowed, but the student should be aware that they cannot blindly trust the answers generated by AI.
  • Identify where in the code there is a bug, but without debugging it
  • Interpret error messages when coding
  • Correct grammatical errors in your report text

 

Course evaluation

Please feel free to discuss with us, the teachers, how the course can be improved at any time during the course! You can also provide feedback through the student representatives listed below, particilarly before the mid-course meeting on Thursday, November 26, at 12:00 (study week 4), and before the course board meeting (date TBD). At the end of the course, we would greatly appreciate your completing the course survey. Your feedback helps us identigy what works well and what should be improved for futer course iterations.

Ebba Ebenfelt (MPBIO)
Celina Hörnquist (MPBIO)
Rebecka Öhman (MPBIO)
Albin Jonsson (MPENM)
Philip Ohlsson (MPIDE)

Course summary:

Course Summary
Date Details Due