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 15 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.
Q: Will both the programming practical and the seminar be offered in the summer semester?
A: This depends on how many students would like to do either of them, if there are too few participants for either class, the majority will decide.
Q: Can I validate both, the programming practical and the seminar?
A: This is feasible. You will then either have to validate the seminar or the programming practical as part of the so-called gneral CS containers (CS seminar 1-3 or CS Practical 2).
Lectures will take place in room 301 of the main computer science building 50.34 on Thursdays from 11:30 - 13:00.
Lecture plan, subject to change
The seminar on "Hot topics on Bioinformatics" for the students that attended the lecture taught in winter 2017/18, will take place on Thursdays from 11:30 - 13:00 in room 301.
You can find the contact data of your supervisors here.
Kick-off meeting on April 19 at 14:00 in room ATIS-SR 010.
Kick-off meeting slides:
This practical will be supervised together with Alexis' PhD student Benoit Morel and Sebastian Schlag (a PhD student at the chair of Prof. Sanders)
We will have a total of 3 individual milestone meetings during the semester with each of the two teams and one final meeting/coordination after the end of the summer term teaching period.
Described in this PDF here.