The Exelixis Lab


Enabling Research in Evolutionary Biology

Bioinformatics

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.

Course Evaluation Results (Learning Quality Indices)

  • Winter 2012/13: 100 out of 100. PDF
  • Summer 2014: 97.9 out of 100. PDF
  • Winter 2014/15: 100 out of 100. PDF
  • Winter 2015/2016: 100 out of 100. PDF
  • Winter 2016/2017: 100 out of 100. PDF
  • Winter 2017/2018: 100 out of 100. PDF

Practical Evaluation results (Learning Quality Indices)

  • Summer 2015: 100 out of 100. PDF
  • Summer 2017: 100 out of 100. PDF

Teaching Awards

  • Alexis and Michael Hamann (PhD student from the chair of Prof. Wagner at KIT) received a certificate for teaching excellence from the dean of the CS faculty at the Karlsruhe Institute of Technology for their programming practical "Hands-on Bioinformatics Practical" tought in summer 2017 based on the practical evaluation by the students. This practical also resulted in a peer-reviewed publication in the high quality journal Bioinformatics.
  • The three former students of the programming practical (Michael Hoff, Stefan Orf and Benedikt Riehm) will receive a prize from KIT on October 14, 2016, for research work conducted by students, since they published a peer-reviewed paper presenting the results of the practical.
  • Alexis and Tomas received a certificate for teaching excellence from the dean of the CS faculty at the Karlsruhe Institute of Technology for their programming practical "Hands-on Bioinformatics Practical" tought in summer 2015 based on the practical evaluation by the students.
  • Alexey, Alexis, Andre, Kassian, Mark Holder, and Tomas received a certificate for teaching excellence from the dean of the CS faculty at the Karlsruhe Institute of Technology for the course "Introduction to Bioinformatics for Computer Scientists" tought in winter 2014/15 based on the course evaluation by the students.

General Information

Course Slides

Please send Alexis an email to be added to the course mailing list and thereby obtain access to the course slides.

Lecture

Knowledge Quiz Answers:

Reading List and on-line material

Exam

A 20 minute oral exam at the end of the semester, dates will be scheduled via doodle.

Course Mailing List

Write an email to Alexis such that he can add you to the course mailing list, very important!

Course beers

We will try to go for course beers with the entire course at least once. All drinks will be on Alexis.

Seminar: Bioinformatics

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:

Practical

In the practical we will try to implement something "useful" as open source tool in C or C++.

Some notes about C programming

Here are some old slides by Alexis covering some aspects of C programming:

Code quality assessment

Make sure to use all tools/mechanisms at your disposal to produce high quality code, for instance:

  • Use as many assertions as you can, as provided by
  • Use the valgrind tool to detect and remove memory leaks, segmentation faults, etc.
  • Enable all compiler warning flags you can think of and fix all warnings! In my lab we typically activate the following flags:
    -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
    
  • use the clang compiler instead of gcc it generated and detects many more warnings.
  • Keep in mind that the argument for malloc is size_t and not an integer!
  • Play with the compiler optimization flags to see which ones generate the fastest code!
  • Use a version control management system like git for code development, in my lab we typically use github

Grading

The practical will be graded.

FAQs

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).

winter 2017/18 course

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

  • Lecture 1 (Alexis): Introduction
  • Lecture 2 (Alexis): Basic Molecular Biology
  • Lecture 3 (Benoit): Pair-wise Sequence Alignment
  • Lecture 4 (Alexey): BLAST & Genome Assembly
  • Lecture 5 (Alexis): Multiple Sequence Alignment
  • Lecture 6 (Alexis): Introduction to Phylogenetics
  • Lecture 7 (Alexis): Phylogenetic Search Algorithms
  • Lecture 8 (Alexis): Statistical Models of Evolution I
  • Lecture 9 (Alexis): Statistical Models of Evolution II
  • Lecture 10 (Lucas): Discrete Operations on Trees
  • Lecture 11 (Alexis): Bayesian Phylogenetic Inference
  • Lecture 12 (Alexis): Advanced Bayesian Inference
  • Lecture 13 (Alexis): Introduction to Population Genetics
  • Lecture 14 (Alexis): Advanced Population Genetics
  • Lecture 15 (Alexis): Course wrap-up and exam preparation

summer 2018 courses

Main Seminar: Hot Topics in Bioinformatics

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.

Paper & Supervisor Assignments

You can find the contact data of your supervisors here.

Deadlines & Dates

Intro slides

  • general intro slides
  • writing papers and giving talks slides

Programming Practical

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)

Student teams:

    team 1
  • Ivo
  • Sabine
    team 2
  • Adrian
  • Peter
  • Lukas

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.

Milestone Meetings

  • Meeting 1: May 24
  • Meeting 2: June 21
  • Meeting 3: July 19

Topic

Described in this PDF here.

Please have a look at the associated software tools by Benoit and Sebastian.

Deadlines

  • Final code submission deadline July 31st
  • Report submission (if we don't write a paper together) September 15