Bioinformatics

This is the repository for the course “Bioinformatics”. You will find lectures, practicals and more here. Everything is publicly accessible.

You can clone the repository and later update it any time with a single click / command to make sure that you have the newest version of all files.

You can click on the links below to directly view the HTML presentations.

• Lecture 1, 2024-04-05 - Introduction
• Lecture 1, part 2, 2024-04-05 - Introduction
• Lecture 2, part 1 - Sequence searches and alignments
• Lecture 3, 2024-04-22 - Protein sequences and protein similarity
• Lecture 4, 2024-04-29 - Multiple sequence alignments, logos, PSSMs
• Lecture 5, 2024-05-13 - Reproducible bioinformatics
• Lecture 6, 2024-05-27 - Sequence evolution
• Lecture 7, 2024-06-03 - Omics
• Lecture 8, 2024-06-10 - Transcription profiling
• Lecture 9, 2024-06-17 - Gene set enrichments
• Lecture 10, 2024-06-24 - Machine learning
• Lecture 11, 2024-07-05 - Beginning of life
• Lecture 12, 2024-07-12 - Visualizations

Practicals

• Practicals, 2024-04-12: Intro
• Practicals 1, 2024-04-12: Sequence searches Exercises and Homework
• Practicals 2, 2024-04-19 and 2024-04-26: Sequence logos and MSA Exercises and Homework
• Practicals 3, 2024-05-03: Sequence structures Exercises
• Practicals 4, 2024-05-10, 2024-05-31: Introduction to R and programmingExercises
• Practicals 5: R and programming, statistical tests, visualizations Exercises and Homework
• Practicals 6: Phylogenies with R Exercises and Homework
• Practicals 7: Transcriptomics and clustering Exercises and Homework
• Practicals 8: Differential gene expression analysis Exercises
• Practicals 9: Machine Learning Exercises + Homework

Additional resources

• Installing R and Rstudio
  • Guide for all platforms
  • How to install R packages
  • Please install also the package colorDF
  • Windows users might need to install the RTools package
  • My own installation instructions
• Writing report
• Editing files – this guide tells you more about how to edit text files (not only in bioinformatics!)

Marking

The final mark consists of three parts:

• Exam (multiple choice and free answers), 20 questions each for 2 points: maximum 40 points
• Homeworks, 6 homeworks each rewarded with 5 points, total maximum 30 points
• Report: maximum 30 points

In addition, you can get up to 15 bonus points for

• active participation in the practicals and lectures; in especially, for asking questions and helping others
• extra effort on homeworks and report
• coming up with own, original ideas and implementing them during practicals or in the report

However, any sign of plagiarism will result in zero points for the respective part of the exam. Plagiarism includes both copying from your colleagues (in which case both of you will receive 0 points) or from the internet.

You are permitted to use large language models (LLMs, such as ChatGPT) and other resources to learn and train your skills, and even to check spelling or grammar. During the course, I will provide you with advice, instructions and caveats on how to use these tools safely and efficiently.

However, you are not allowed to use any of these resources to straight out write the report, the homeworks or the exam. Any evidence of this will result in zero points for the respective part of the exam. Please keep in mind that detecting plagiarism or LLM use is much easier than you think.

Any questions? Please ask!