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, the pandemic permitting. 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 lectures will either take place in the classrom or on-line. The exact schedule (i.e., classroom versus on-line lectures) will be announced via email but is also available and will be updated on this page here further below.
All lectures will also be available as pre-recorded videos on youtube.
Please register properly for the course via the KIT campus system, but also send an Email to Alexandros.Stamatakis@h-its.org to make sure to be added to the course mailing list.
When a lecture takes place on-line you are expected to watch the respective lecture on youtube before Thursday. During the lecture slot on Thursday and starting at 12:30, we will then hold a Question and Answer session via Zoom (instead of MS Teams) as Zoom has shown to be more stable. The Zoom meeting link is available in the "Detailinformationen" box of the class under "Organisatorisches" on the KIT campus system.
Lectures and slides will be provided beforehand (in general one week before the actual lecture slot), that is, before the actual course hours from 12:00-13:30 on Thursdays.
If the lecture does not take place in the class room, we will meet via Zoom at 12:30 to discuss the contents of the last lecture together for about 30 minutes. Please turn your video on to yield this more interactive. The last lecture (course wrap up and exam preparation) will be LIVE either in the class room or via Zoom.
The course material including links to the video lectures on youtube is available here.
Lecture plan, subject to change