Please follow the steps in the Preparation Page before the course starts.

A two-day course for students and other life scientists who are just starting with bioinformatics.

Prerequisites for this course: Although not required, familiarity with python or a coding language is recommended. Participants should bring laptops.

We’ll start by exploring the most used bioinformatics resources for variety of different data sets, continue with a genomics practice on mutations. We’ll cover the best practices and common challenges in this practice as a foundation to the understanding of bioinformatics pipelines. Rest of the course, you’ll be working in smaller project groups. You’ll be able to choose projects on clustering, immunobiology, and cancer genomics. As you can see, majority of the course will be hands-on allowing you to practice your acquired knowledge.

At the end students will

• realize the wealth of bioinformatics database structures and the -omic tools

• understand how to download and use data from bioinformatics databases

• learn best practices and common challenges in genomics

• explore downstream analyses approaches for bioinformatics datasets

• work on a project to practice acquired knowledge on a topic of interest

• work in groups on datasets provided by real life science researchers on clustering, immunobiology, molecular biology, and cancer genomics

• present their findings

Please note that the program below is the schedule, we aim for. Things may take more time, and our hours may be somewhat extended. The rooms are reserved until 18h. In case needed, your flexilibily would be appreciated. :)

09:00 - 09:30 introductions

09:30 - 10:30 introduction to bioinformatics and databases (UCSC Genome browser, biomart, oma, string and others from SIB)

10:30 - 11:00 coffee break

11:00 - 12:00 introduction to genomics, HPC, command line, conda, biopython

12:00 - 13:00 lunch break

13:00 - 14:00 cancer genomics and repeat mutations

14:00 - 16:00 practice on genomics

16:00 - 16:30 coffee break

16:30 - 17:00 project selection and meet up with project leaders

09:00 - 09:30 Q&A, reflections

09:30 - 12:00 project work

12:00 - 13:00 lunch break

13:00 - 15:00 project work

15:00 - 16:30 presentations

16:30 - 17:00 wrap-up, conclusions, feedback

The module will consist of lectures and practical exercises. In addition to lectures, students will be required to self-study selected topics. Students will work in groups on a data challenge and present their results at the end of the course.

Exercises during the course: 50% Data challenge: 50% The course is taught in English. We’ll be working in bash. You may also use python, R etc. depending on the projects. No prior knowledge in coding is required although familiarity with a coding language will be helpful. Please bring laptops. If you have questions, feel free to email Tugce.

There are two days of classes on the last two Fridays of May. Some preliminary reading and preparation materials are provided. First day includes theory introduction and hands-on exercises. The second day includes practical guided work on the group projects, discussions and final presentations.

Copy the presentations from here:

cp /cfs/earth/scratch/icls/shared/bioinfo4beginners/'Practice Slides.pdf' .