Algorithms for Sequence Analysis

Dear all,

if you want to take the exam in the first round in two weeks(!), please be sure to register in the LSF! If you do not achieve the qualifications, your registration will be voided (you will not get a fail grade!). The exam number is 10135. The exact date (25./27./28.7.) and time will be distributed by a doodle. The link will be made availablein the Materials section. Please be sure to register in both places, the LSF and in the doodle! Everything else will cause problems.

If you decided to wait for the second round of exams, then you need not do anything now.

Dear all,

the slides and recording of lecture 19 (from Monday July 4), as well as a pre-recording of the next lecture (of Thursday July 7) are now online. I will not be able to give a live lecture on Thursday, unfortunately, as I am attending a funeral of a friend and former colleague in Berlin.

(In fact, the Thursday lecture briefly introduces the BLOSUM62 score matrix, and with this colleague I worked on non-symmetric score matrices a long time ago; it was one of my first papers: Non-symmetric score matrices and the detection of homologous transmembrane proteins.)

So please take the time on Thursday morning to watch the pre-recorded lecture, which should be easy going (in comparison to previous topics like the FM index), as it expands on well known topics (pairwise alignments).

Some other notes about the course:

1. Please evaluate the course, both lecture and tutorial (separately) before July 14. Evaluation links are provided on top of the Materials page (administrative section). It will be most helpful if you can provide free-text comments on what was good and what to do better next time.
2. The last regular assignment (#10) will be published on Thursday. There may be a (small) bonus assignment the week after just in case people are missing one or two points in one category. It will not be possible to catch up a lot of points by this bonus assignment.
3. First exam dates have been changed to Monday, Wednesday, Thursday (with a few more slots on Tuesday), July 25, 27, 28. A doodle will be sent around shortly.

- Sven Rahmann

Hello,

we have received multiple request (with good and less good reasons) to move the deadline of the current assignment.

The assignment would be due on Thursday (June 16), but we are moving the deadline by 1 week to June 23!

As I am back now, I will provide a recording of Monday's lecture by tomorrow. There will be no new problem assignments this week. Assignments relating to Monday's lecture will be part of the next set that will be published on June 23.

So, the schedule is:

• Assignment 08: June 23 -> June 30
• Assignment 09: June 30 -> July 07
• Assignment 10: July 07 -> July 14

Thus, assignment 10 will be the official last assignment. There may be an 11th which may allow you to get a few bonus points. This is intended for people who may be short just a few points.

Hopefully this helps with your planning. The safe strategy is to get >= 50% on every assignment.

 

Good morning,

unfortunately due to child care constraints, I cannot give a live lecture this morning. I have pre-recorded the lecture about the BWT, however. The temporary links are here, and later they will also (and only) be in the materials section (it is in two parts because I was looking for a slide that did not exist):

1. Part I: https://cs-uni-saarland-de.zoom.us/rec/share/eOZpqnJxyp_VlNPYaIA3wP2s0vl7vSH0r23rPChtvKrTbkhRXwvxsXnO90hSLMZR.J3wl1WM5ELvmW02d?startTime=1654720517000

2. Part 2: https://cs-uni-saarland-de.zoom.us/rec/share/eOZpqnJxyp_VlNPYaIA3wP2s0vl7vSH0r23rPChtvKrTbkhRXwvxsXnO90hSLMZR.J3wl1WM5ELvmW02d?startTime=1654724047000

The total length is a little less than 90 min. Also, remember to visit the next campus fair today after the lecture!

 

The first exam period this semester will be July 25 - July 27. This will be an oral exam on campus. Time slots will be assigned using a doodle-like system soon.

We are aware of the AI exam on July 27 and the computational epigenomics block course on August 1-15. If you also take the AI exam, you should get a time slot on Monday July 25. If not, you should take a time slot on July 27.

The second exam period will be in late September (probably Sep 26, 27, 28).

 

Dear all,

please note first that next Monday is a holiday (no lecture, no classes at all in fact).

Also note that next Thursday's lecture will introduce the extremely important BWT (Burrows-Wheeler transform).
On the same day (June 09), the career fair "next" takes place on campus. If this interests you, please prepare for it (https://www.uni-saarland.de/en/institution/career-center/next.html).

Third, we have just released Assignment 07, which runs over two weeks and is due on June 16.
It contains two programming tasks, but only one is required. You can get bonus points if you do both. (The github will be open soon.)
It also contains some tasks about the BWT, which you should solve next week after the June 09 lecture.

Dear all,

here is a quick update:

- Lecture 10 (from today, SAIS) is online. 

- A new assignment (06) is also online. You have till next Thursday to complete it. This time, there is no programming task.

- You still have time till Thursday (May 26) to finish your implementation of Ukkonen's linear-time suffix tree construction algorithm!

 

Soon, the annual career fair "next" will take place. Please find some information below.

Link: http://www.next.saarland 
Resources: https://www.uni-saarland.de/einrichtung/career-center/next/ressourcen.html
FAQ: https://www.uni-saarland.de/einrichtung/career-center/next/vorbereitung-tipps-faq.html

Note: The following online lecture series is open to women only! It is not organized by UdS!

Are you interested in a scientific career as a woman in bioinformatics? You have questions and worries regarding how to get there?

The online lecture series "Women in Bioinformatics" provides the answers. Successful female scientists present their research, their career path and answer your questions.

Registration is now open for the talk by Prof. Dr. Alice McHardy on 14.6.2022, 14:00 – 15:30  (CEST) (rescheduled from 10.05.22). Prof. Dr. McHardy holds a diploma in biochemistry and a doctoral degree in bioinformatics, both from Bielefeld University in Germany. From 2005 to 2007 she first was a postdoc and then a permanent staff member in the Bioinformatics and Pattern Discovery Group at the IBM T.J. Watson Research Center in Yorktown Heights, USA. She then became the head of the independent research group for Computational Genomics and Epidemiology at the Max Planck Institute for Computer Science in Saarbrücken. In 2010, she was appointed Chair of Algorithmic Bioinformatics at Heinrich Heine University in Düsseldorf. In 2014, she became head of the Department of Computational Biology of Infection Research at the Helmholtz Centre for Infection Research in Braunschweig and was appointed as a full professor at TU Braunschweig.

Participation is free but registration is required for every talk. Details can be found at: https://www.bio.ifi.lmu.de/women-in-bioinformatics. Please note that the time of the lecture may vary.

For further updates on upcoming talks please register for our Newsletter (https://lists.lrz.de/mailman/listinfo/wbioinformatics) or follow us on Twitter (https://twitter.com/WBioinformatics).

Dear all,
the registration for the tutorials is open now.
To use the github classroom you need a github account (it doesn't matter if it was created trough university mail or another one).

Tuesday and Wednesday I plan to briefly show you how github classroom works, the tasks are structured and how you can run the tests. If you don't have any experience with git yet, you can find a tutorial in the material section.

Dear all,

after zoom took some time to process the recordings, the videos of today's lecture are online now (00: administrative business; 01: first lecture) and can be accessed from the Materials section. Assignment 01 is also online. Please 1) download and read the PDF, and 2) access the link to github classroom, where you must accept the assignment. You will also need a github account. If you have any questions, please contact Jens Zentgraf (see Team).

Next week, we will look in detail at the average time analysis of the naive algorithm (and how to derive it), and will get to know a vastly faster algorithm. Note that Monday is a holiday, and there will be no lecture on Monday. Tutorials will start next week, and you will receive instructions on how to express your preferences. In case of any doubts about the situation, we suggest to go to the online tutorial first and maybe later switch to the on-campus tutorial.

Happy holidays!