Enabling Research in Evolutionary Biology
Bioinformatics courses are taught by Alexis in Karlsruhe with the occasional help of his PostDocs and PhD students from the Heidelberg Institute for Theoretical Studies. See here for contact details.
Please send Alexis an email to be added to the course mailing list and thereby obtain access to the course slides.
A 20 minute oral exam at the end of the semester, dates will be scheduled via doodle.
Write an email to Alexis such that he can add you to the course mailing list, very important!
We will try to go for course beers with the entire course at least once. All drinks will be on Alexis.
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 an Exelixis lab member 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!
Below you will find some general material for the Bioinformatics seminar:
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:
Here are some examples of nice slides from previous years:
In the practical we will try to implement something "useful" as open source tool in C or C++.
Here are some old slides by Alexis covering some aspects of C programming:
Make sure to use all tools/mechanisms at your disposal to produce high quality code, for instance:
-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
The practical will be graded.
The seminar on "Hot topics on Bioinformatics" only for students that attended the lecture taught in winter 2020/21, will take place virtually on Thursdays from 12:00 - 13:30.
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. In case of difficulties with the registration please contact Alexis via Email. Also make sure you have been included in the seminar mailing list!
You can find the contact data of your supervisors here.
Note that the deadlines reported in the above video are those for 2020 and are hence invalid. This summer topics need to be fixed by April 30, presentation slots will be announced later on, and the report submission deadline is on September 30.
Kick-off meeting on April 15 LIVE at 10:00 via MS Teams (see Ilias page of the course for the link).
Kick-off meeting slides:
Related slides from the lecture during the winter term:
Test datasets can be downloaded here.
This practical will be supervised together with Alexis' PhD students Lukas Hübner and Ben Bettisworth
We will have a total of 3 individual milestone meetings during the semester with each of the two teams and one final meeting after the end of the summer term teaching period (date to be coordinated).
Re-implement and optimize (the shit out of) the modified Robinson-Foulds distance described in this paper here
Please have a look at the associated software framework Ben prepared for you to parse phylogenetic trees and extract their bipartitions here.
The student team that will write the fastest, correct code on a reference system to which you will be given access to will be invited by Alexis for dinner.