All courses funded by this research school will make all of its material freely available online to everyone in the world using the Creative commons 3.0 license. Lectures may be recorded on video and put online.
Compulsory courses (3-5 hp)
The basis for this research school is two compulsory courses per year for the students. The courses are progressive, i.e. the learning outcomes from the first course are a necessary requirement for the next course. The earlier courses are aimed at teaching important computational methods, while the later courses are aimed at relevant high-throughput methods for medical bioinformatics.
1. Applied Bioinformatics, 5 hp (Lars Arvestad, SU). In this course the students will be taught a good working habits for bioinformatics. They will learn to work in Unix, using Python for scientific code development and learn about good practices for scientific programming. Tentative maximum enrollment of 30 students.
- Includes pre- and post-course assignments.
- Last ran online, 9:00 to 17:30, on 11-12 and 15-17 June 2020.
- The interactive part of the course will run on Zoom 14-18 June 2021.
2. Statistics in Bioinformatics, 3HP. Replaces Algorithms in Bioinformatics, 5HP. We are currently organizing this course and will provide more detail later.
- First given 19 to 23 October 2020. Next edition will run 22-26 November 2021.
3. Machine Learning in Medical Bioinformatics, 5HP (Björn Wallner, LiU). In this course the students will learn statistical and machine learning methods that are widely used in medical bioinformatics today. Last ran from 13:00 on 20 May to 12:00 on 24 May, 2019. Due to the pandemic the 2020 edition ran online from 13:00 on 11 May, to 12:00 on 15 May. The next edition will run 17-21 May 2021. Older course materials are published — Click here for publicly available course materials.
4. Experimental design for high-throughput technologies, 3 HP (Carsten Daub, KI). In this important course the students will learn how to design the bioinformatics analysis of high throughput experiments. Given the background from the three earlier methods they should be able to design a pipeline that can easily be extended for more advanced analysis. Click here for publicly available course materials from the 2018 edition, or here for the 2019 edition.
- Last ran from 12:00 on September 2 to 16:00 on September 6, 2019, in Solna. It did not run in 2020 for Covid related reasons.
- 2021 edition: count on 18-22 October for at-home prep work, and 25-29 October for in-person teaching in Solna.
5. Variation interpretation and structural bioinformatics, 5HP (Mauno Vihinen, LU). In this course the student will learn how to use information from personal genomics studies to interpret the effects of small and large variations. The students will also learn how to use structural bioinformatics tools predictions and analyses of variant effects and mechanisms.
- Click here for publicly available course materials from the 2019 edition.
- Last ran 18-22 January 2021. 2022 dates to be announced later this year..
6. Computational Systems Biology (Mika Gustafsson, LiU). Students will study basic systems biology and its application in biomedical research and medical problems. The course introduces basic concepts and mathematics underlying modern systems biology. You will understand the differences between small-scale and large-scale models using examples from biomedical research. The course will emphasise large-scale systems biology methods.
- Click here for publicly available course materials.
- We ran for the first time from 10:15 AM on 20 May to 15:00 on 24 May, 2019.
- Due to the Covid19 crisis, the 2020 edition ran online from 10:15 AM on 11 May to 15:00 on 15 May
- The 2021 edition will run on Zoom on the following days: 5, 11, 18, 20, and 26 May.
Taking courses in an alternative order due to parental leave or other reasons:
If you an enrolled student taking parental leave, first of all, congratulations, and enjoy! Secondly, naturally any courses you missed can be taken after you return if they are still offered. The caveat is that enrollments would not be automatic, rather you would be responsible for contacting the teacher to request admission.
If you wish to take any courses earlier than suggested, this is OK if you and the teacher feel you are ready. We don’t recommend delaying courses, because later in your PhD you will have less time for courses, and also less time to apply the training to your thesis. However there are many situations in which it makes sense to delay a course, and it is typically possible to accomodate you.
Rebecka Jörnsten’s course “Modern large-scale factorization and dimension reduction methods” has unfortunately been cancelled, but the topics have been absorbed into the new “Statistics in Bioinformatics” course. We are also considering additional courses.
The second (usually compulsory) part of the research school is the Annual Meeting. This year it will be much shorter than usual and run by Zoom on 19 May — students and PIs should have received an invite and schedule by now. This will be limited to student meeting, students reporting to the PIs, and a PI meeting.
The next offline meeting will probably be at Varbergs Kusthotell near Göteborg — the dates for this are to be discussed on 19 May.
In addition to increasing the communication between the medical and informatics community the Annual Meeting is also an important part of the education of the Ph.D. students. The Annual Meeting under ordinary circumstances includes:
1. Training in presentation skills.
2. Posters — required of all students
3. Individual mentoring by the bioinformatics mentor.
4. Social activities
5. Research talks by students and PIs.
6. Unstructured time for discussions.
Some photos from the 2018 meeting are here.
We will provide a completion certificate to students that fullfill either of the following requirements:
- Four of the required courses and two Annual Meetings
- Five of the required courses and one Annual Meeting
The Studierektor can, upon student request, review a sufficiently-similar non-MedBioInfo course and determine whether it can be counted toward the above course requirement. The certificate outlines the school’s goals and obligatory elements, and describes the competitive acceptance criteria. This certificate is not a degree and does not itself confer any additional ECTS points.
There are of course many fine courses available outside the Research School, in Sweden, abroad, or online, which we encourage students to take as appropriate. Programming courses are important for first-year students who have not had them (or the equivalent experience). SciLifeLab offers courses — the Python may be particularly appropriate. Watch for the registration deadline for this programming course. Some of the core courses require programming, and students are responsible for meeting all prerequisites in time to take courses. Some advanced students may find other NBIS courses such as Single-Cell Analysis useful.
One of the aspects of this program is to improve the supervision of the students. Here, we propose to use a modified version of the idea used in Gothenburg some time ago with two supervisors for each student, one bioinformatician and one medical scientist. Our goal is that this program each student will be assigned a mentor from the Swedish bioinformatics community. The mentor should be from another research constellation than the student. The role of the mentor will be to help the student identify and solve computational bottlenecks in their research project, and also to provide more general career advice. The student will discuss with the mentor at least twice per year, either via electronic meetings or by short visits. We suggest using this Student-Mentor-meeting-form to guide student-mentor discussions.