Algorithms for Sequence Analysis

Dear all, if you enjoyed the Algorithms for Sequence Analysis lecture last semester, you may be interested in the "Current Topics in Sequence Analysis" seminar this semester, which discusses advanced topics that build on the material of the lecture. You cannot register for the seminar directly, but need to go through the SIC seminar assignment system at https://seminars.cs.uni-saarland.de/. You will get a high priority though if you passed the exam. Note: Today (Tue Oct 19) is the last day for seminar registration and assignment!

 

Dear successful participants of Algorithms for Sequence Analysis (Summer 21),

the second exam day for the course is October 5 (all day). Please find instructions on how to register on top of the Materials section.

The same rules as for the first exam apply (registration/un-registration up to one week before exam day, two-step process: reserve a time slot AND register in the LSF). Only successful participants (whose matriculation number is on the list in the Materials section) will be admitted to the exam.

IMPORTANT: Today is the last day where you can register or unregister for the exam in the LSF.

The exam is an online oral exam. After the registration deadline, all registered students will receive a zoom link for the exam.  Please remember that you need to register in a two-step process (in any order):

1. pick a date in the doodle (link in Materials)

2. register officially for the exam in the LSF / HISPOS.

Doing only one of these will not yield a complete registration.

Sven Rahmann

 

First of all, the course has finished! Congratulations to all of you who stayed till the end!

The list of those who have qualified to take the exam has been published in the Materials section.

The exams will be ONLINE (Zoom) oral exams.

The first exam period consists of 14 possible time slots on Aug 17 and Aug 18, 2021:

09:00 - 09:45
09:45 - 10:30
10:30 - 11:15
11:15 - 12:00
--- lunch break
13:00 - 13:45
13:45 - 14:30
14:30 - 15:15
 

IMPORTANT: If you would like to participate in the exam, you have to do two things.

1. Register in the LSF (HISPOS), exam number 10135. Registration AND un-registration is possible till ONE WEEK before the exam. This is an OFFICIAL registration. If you are not registered here, I will not do an exam with you. If you are registered and do not show up for the exam, you have FAILED the exam.

2. In order to plan the exam times, please also reserve one and only one time slot at https://terminplaner4.dfn.de/algorithms-for-sequence-analysis-2021. For this, you need a password that is given in the Materials section. Please always keep this in sync with the LSF registration, so if you un-register in the LSF, please also free up your time slot! As a recommendation, please take the first free time slot where you are available.

We will check the list of registrations after August 11 and email you with further information (Zoom link, final time slot, etc.).

All the best,
Sven Rahmann

Dear all,

the scores of all those who might have a chance to be admitted to the exam have been published on the Materials page.

If one of the final scores has a *red* background, you have not achieved 50% yet. Plese check whether everything was scored correctly and email me any questions, and be sure to obtain additional points on assignment 13.

 

Hello everyone,

the link to the bonus assignment 13 has been posted on the Materials page.

Please use it if you might just be a few points short of the required 50% in theory and/or programming, or just for fun.

Also, if you haven't done it, there is still time to evaluate the lectures and the tutorial (separately); links are also on the Materials page.

All the best,

Sven Rahmann

 

As of today, you'll find your (archived) scores for assignments 1-6 and a separate sheet with scores for assignments 7-11 and current totals on the Materials page. Assignment 12 is due on Monday, as usual. There will be an Assignment 13 with bonus points next week (i.e., you can get additional points, which you should do if you are just below the 50% threshold).

There are also two links on the Materials page for evaluating the lecture and the tutorial (separately). Please use these links until July 15. After that, the evaluation forms will be deactivated.

Thank you!
Sven Rahmann

 

Please evaluate the course using the provided links to the Qualis evaluation system (see Materials section). Lecture and Tutorial should be evaluated separately; there are two different links. I will also remind you in the lecture. The evaluation period ends on July 15, so please provide your feedback before that date.

Also, the link to the repository for Assignment 11 (due July 5) has been published in the Materials section.

 

Scores up to assignment 7 are now available on the Materials page.

Please note: There will be approx. 12 assignment sheets; there may be bonus problems (counting zero towards the required total, but offering the possibility to increase your points). Clearly, programming is a bigger problem than theory, so there will be some easy programming problems on the remaining sheets.

Assignment 9 has been published on the Materials page; the assignment sheet is also on the website. It is due on June 21.

Also, there are now new solutions for older assignments (up to 7). In particular, you can now take a look at the complete solution for the +-1RMQ programming task. Links to lecture videos have been added, too. Everything is linked on the Materials page.

Bonne continuation!

Dear all,

the university asks us to spread this information (in German) about the upcoming (online) career day to all students:

 

Auch in diesem Jahr bieten wir vom Career Center der Universität des Saarlandes die Campusmesse „next“ digital an – und zwar am 17. Juni 2021, 11.00–17.00 Uhr.

Wichtig: Bei dieser Messe sollten die Studierenden bereits frühzeitig vor dem Messetag ihre Profile anlegen, damit sie mit interessierten Unternehmen gematcht werden und für den Messetag Gespräche vereinbaren können.

* Präsentation: https://www.uni-saarland.de/fileadmin/upload/einrichtung/career-center/next/next-digital_2021/Downloads/nextdigital-2021_Praesentation.pdf

* Tipps zur Vor- und Nachbereitung: https://www.uni-saarland.de/fileadmin/upload/einrichtung/career-center/next/next-digital_2021/Downloads/next-digital_Tipps-zur-Messevorbereitung.pdf

* ENGLISH version of hints for preparations: https://www.uni-saarland.de/fileadmin/upload/einrichtung/career-center/next/next-digital_2021/Downloads/next-digital_Tips-Fair-Preparation_EN.pdf 

* Karrieremesse „next digital“: www.next.saarland

* Karriereportal zur Stellensuche: www.jobs.uni-saarland.de

 

Dear all,

this may be relevant to you if you are really interested in sequence analysis and maybe consider writing a Master's thesis in the topic, or doing some research later. As you may know, each (even very special) field has its own research meetings. For string algorithms / pattern matching, several formats exist, and one is the CPM conference (Combinatorial Pattern Matching). It is quite theoretical.

This year, because of the pandemic, it is online (although you could attend in person), and registration is free.

I invite you to look at the program and decide whether you want to listen to some of the talks. This lecture should have given you a good foundation to understand some of the current research topics in the field. Note that most of this is not directly relevant to bioinformatics, but on a more theoretical level.

Here is the information:

=======================================
=== CPM 2021 Call for PARTICIPATION ===
=======================================

32nd Annual Symposium on Combinatorial Pattern Matching
Wrocław, Poland, July 5-7, 2021
https://cpm2021.ii.uni.wroc.pl/

Due to the Covid-19 pandemic, the conference will be run in a hybrid
mode: online over Zoom and offline in Wrocław. In both cases, there
are NO participation fees, but you need to register here:
https://cpm2021.ii.uni.wroc.pl/registration.shtml
(registration also allows you to participate in the summer school on July 4).

At the moment, citizens/residents of EU/EFTA countries and UK/Ireland
can freely enter Poland, and citizens/residents of Japan, Canada,
South Korea, Australia are allowed to enter by air. You do not need to
quarantine when you show proof of vaccination or negative test
(antigen or RT-PCR, you can take it before arrival or after arrival).
The exact rules are complicated and keep changing, so we strongly
advise verifying them on your own.

Due to not having any participation fees and local regulations, the
social program will be minimal, with lunches on your own. However,
there will be coffee and a walking tour of the center.

We will be happy to answer any questions concerning the local
arrangements at cpm2021@cs.uni.wroc.pl.

KEYNOTE SPEAKERS
Hideo Bannai (Tokyo Medical and Dental University, Japan)
Michal Koucký (Charles University, Czech Republic)
Nadia Pisanti (University of Pisa, Italy & Erable Team INRIA, France)

SUMMER SCHOOL SPEAKERS
Martin Farach-Colton (Rutgers University)
Jakub Radoszewski (University of Warsaw)

HIGHLIGHT SPEAKERS
Panagiotis Charalampopoulos (Interdisciplinary Center Herzliya)
Travis Gagie (Dalhousie University)

ACCEPTED PAPERS
https://cpm2021.ii.uni.wroc.pl/accepted.shtml

 

Dear all,

a new score table has been published, including your current scores (up to sheet 5).

Please remember to submit your answers to assignment sheet 6 by Monday, and keep up the good work. Note: The programming task can be submitted the week after (June 7) with assignment 7.

In addition, assignment sheet 7 has been published (due June 7). You can accept it here:
https://classroom.github.com/a/SA3-eszk

Enjoy the problems!

Your assignments are now graded up to sheet 4. Please review your scores and let me know if something does not seem right.

I am gradually publishing solutions for all exercises on the Materials page. For some programming tasks, you can obtain complete working solutions in Python. Be sure to study them if the problem in the assignment wasn't clear to you.

Have a nice weekend!

I have only started my appointment at UdS, and this will be my first lecture. Because of the pandemic, I have not yet moved to Saarbrücken and will provide the lectures and tutorials from my home office. In case of problems of questions, please contact me by email (see contact information on the Teams page).

I am actively looking to buy a family home in or near Saarbrücken. Please contact me if you know someone who is selling or wants to sell. Thanks!