Enabling Research in Evolutionary Biology
Bioinformatics courses are taught by Alexis at the Karlsruhe Institute of Technology with the occasional help of his PostDocs and PhD students from the Heidelberg Institute for Theoretical Studies. See here for contact details.
As of winter 2023/24 the lectures on "Introduction to Bioinformatics for Computer Scientists" will be taught jointly and simultaneously at KIT and the Univesrity of Crete (see below for further information).
At KIT A 20 minute oral exam at the end of the semester, dates will be scheduled via doodle.
The exam modalities at UoC will be announced later on.
Write an email to Alexis such that he can add you to the course mailing list, very important!
The Master level course on “Introduction to Bioinformatics for Computer Scientists” deviates substantially from the standard course schemes at KIT (Karlsruhe Institute of Technology) and UoC (University of Crete) as your lecturer (Prof. Alexandros (Alexis) Stamatakis) is currently setting up a second research lab in Crete while maintaining his lab and position in Germany.
The course will be taught simultaneously at both Universities. Live lectures will either take place at UoC or at KIT (exact schedule for live lectures to be determined) and be streamed via Zoom to the respective other university. Keep in mind the time difference between Greece and Germany - Greece is one hour ahead!
Further, because winter semester lecture periods between Greece and Germany deviate substantially, the course has been condensed into 9 lectures of three hours each to fit the time period during which the respective winter semesters do overlap.
The exams will take place during the standard exam periods of the respective universities (to be discussed with the KIT students).
As far as your lecturer knows this is the first time a course is being taught in this form at KIT and UoC, so he is really looking forward to this experiment.
Live Lectures at KIT will take place in Room: -120 in building 50.34
Live lectures at UoC will take place in Multimedia Room: K.206
KIT Students: Please register properly for the course via the KIT campus system.
KIT & UoC Students: send an Email to Alexandros.Stamatakis@h-its.org to make sure to be added to the course mailing list.
UoC Students: The UoC course web-site can be found here.
Course material from previous semesters including links to the video lectures on youtube is available on-line; updated slides will be provided shortly after the course.
Lecture day & time: Mondays at 08:45 German local time / 09:45 Greek local time
Lecture Block duration: 2 hours 30 minutes (1:15 of lecture, 15 mins break, 1 hour of lecture)
Lecture Schedule - University Acronym after block number indicates where the lecture will be given live (subject to change) and in parentheses it is indicated who will be teaching this lecture.
Lecture SCHEDULE, subject to change
You will need to select papers to present, give a presentation and write a report.
This main seminar allows students to understand and present the contents of current papers in Bioinformatics such as published for instance in the journals Bioinformatics, BMC Bioinformatics, Journal of Computational Biology etc. or at conferences such as ISMB or RECOMB.
We will provide a list of interesting papers but students can also propose papers they are interested in. Students may also chose to cover broader topics of more general interest such as multiple sequence alignment, Bayesian phylogenetic inference, read assembly etc.
Each student will be assigned a lab member (a PhD student or PostDoc) for help with understanding the article and preparing the slides as well as the report.
Students should give a 35 minute presentation on their topic of choice and write a report (Seminararbeit) comprising 8 pages (including references)!
Below you will find some useful material on writing reports in English:
Latex template for reports: We are going to use the Springer LNCS (Lecture Notes in Computer Science) Latex template available here.
Please make sure to download file: llncs2e.zip!
Here are some examples from well-written reports of previous years. Note that in earlier years we had a higher report page limit!. The current page limited is reflected by the 2021 example.
Here are some examples of nice slides from previous years:
The seminar on "Hot topics on Bioinformatics" is only intended for students that attended the lecture taught in winter 2022/23 and passed the exam. It will be taking place on Thursdays from 09:45 - 11:15 in room SR236.
There is a limited number of 10 places available for this seminar: students must register via the KIT campus system and will receive places (or not) on a first come first served basis. Please also drop Alexis an email once you have registered to be included in the seminar mailing list! In case of difficulties with the registration please contact Alexis via Email.
Room ATIS Seminar Room SR010, final presentation times, see below.