News
Reminder: Exam round #2Written on 19.09.22 by Sven Rahmann Dear all, a short reminder: these are the last days to register (or unregister!) in LSF for exam round #2 next week. Please remember to also update the doodle if you change your mind (see last news). All the best,
|
Algorithms for Sequence Analysis exams round #2Written on 05.08.22 by Sven Rahmann Dear all, a doodle has been published (in the Materials section) for the second round of exams for Algorithms for Sequence analysis. Please reserve your time slot, if Dear all, a doodle has been published (in the Materials section) for the second round of exams for Algorithms for Sequence analysis. Please reserve your time slot, if Note that there will be no further opportunities for this exam in this year. For next year, you'll have to re-qualify by doing the assignments again. Also, remember to register in the LSF up to ONE WEEK before the exam date. After that, it is too late. (As of today, the exam does not seem to be available in LSF, but this will change shortly.) Enjoy the summer!
|
Exam schedule publishedWritten on 23.07.22 by Sven Rahmann Dear all, please check the exam schedule and find you time slot. Most of you got the time slot they chose. Sometimes, we had to move around some times (to avoid gaps, and to accommodate a department meeting), but everyone is on the DAY they selected. The schedule is on the Material page on… Read more Dear all, please check the exam schedule and find you time slot. Most of you got the time slot they chose. Sometimes, we had to move around some times (to avoid gaps, and to accommodate a department meeting), but everyone is on the DAY they selected. The schedule is on the Material page on the very top. Please either confirm (by email to rahmann@cs.uni-saarland.de re: exam confirmation) or report a problem. If you need/want to withdraw now, you will need a medical certificate (or take the 5,0). In addition, the collected "possible exam questions" have been made available as a collected slide set (last among lectures), in addition to all lecture slides and videos. |
Consequences of plagiarismWritten on 18.07.22 by Sven Rahmann Dear all, an alarming and increasing number of you have recently submitted plagiarized solutions to assignments. In the very first lecture I made the clear statement that this will not be tolerated. On the first occasion, you receive a warning. On the second occasion, you are out of the course,… Read more Dear all, an alarming and increasing number of you have recently submitted plagiarized solutions to assignments. In the very first lecture I made the clear statement that this will not be tolerated. On the first occasion, you receive a warning. On the second occasion, you are out of the course, i.e. not admitted to the exam. We also report you to the examination office. If you cannot solve an assignment, don't do it. You only need 50%. This is very little (if you actually aim for 100%, as you should. If you try to optimize = minimize your work for this course, this is the wrong attitude, and you will get problems in the exam.) Because of the alarmingly high rate of plagiarized solutions that we found, we will now be taking an even closer look. Some of you will be informed shortly that you have not met the examination criteria. Plagiarism goes against every academic honor code. If you understand this, you don't copy. If you do not understand this, you are in deep trouble. I suggest you quit university before you actually ruin your life. |
Tutorial todayWritten on 13.07.22 by Jens Zentgraf Dear all, today's (15.07.) tutorial will take place online. The link can be found in the material section. |
URGENT: Exam registrationWritten on 13.07.22 (last change on 13.07.22) by Sven Rahmann 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… Read more 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. |
Important UpdatesWritten on 05.07.22 by Sven Rahmann 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… Read more 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:
- Sven Rahmann |
Assignment 09 releasedWritten on 30.06.22 by Sven Rahmann Assignment 09 is now online. It is due in one week on July 07. The github repository will be made available tomorrow. This is the second-to-last assignment. Assignment 10 next week will be the last assignment. |
No tutorials this weekWritten on 21.06.22 by Jens Zentgraf Hello, |
Deadline moved one week / following assignmentsWritten on 14.06.22 by 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… Read more 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:
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.
|
No lecture today, but uploaded later this weekWritten on 13.06.22 by Sven Rahmann Good morning., I am travelling this week, and the internet connection here is quite slow/unstable, so it does not allow me to give the lecture right now. I will attempt to record it and upload it later as soon as I find a spot with good bandwidth. I'm very sorry for the hassle. |
Pre-recorded lecture todayWritten on 09.06.22 by Sven Rahmann 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… Read more 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!
|
Exam datesWritten on 02.06.22 by Sven Rahmann 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… Read more 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).
|
Next career fair; Assignment 07Written on 02.06.22 by Sven Rahmann 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). 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). Third, we have just released Assignment 07, which runs over two weeks and is due on June 16. |
Assignment 06: no programming assignmentWritten on 24.05.22 by Sven Rahmann Dear all, in the first version, there unfortunately a programming assignment on Assignment 06. This should have appeared in Assignment 07. We have now removed it from Assignment 06. Sorry for the confusion! Please have another look at Assignment 06 in the Materials section now. |
Updates and career fair "next'Written on 23.05.22 by Sven Rahmann 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… Read more 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 |
No assignment this week, but on Monday (May 23)!Written on 20.05.22 by Sven Rahmann Because of the long programming assignment, there will be no new assignment today. As also next week's Thursday is a holiday, we will release an assignment early next week, after the Monday lecture, with 1.5 weeks time to work on it. The topic of that assignment will be suffix arrays. |
TutorialWritten on 17.05.22 by Jens Zentgraf Since there is currently no internet available at the university, we will discuss the exercise next week. |
No recording, the lecture will be skippedWritten on 09.05.22 by Sven Rahmann Dear all, please disregard the previous email. Due to technical quality issues with recordings from my laptop, there is no lecture available from today. I will give the lecture on Thursday. I'm very sorry for these issues. Enjoy the free time!
|
No live lecture today; recording available laterWritten on 09.05.22 by Sven Rahmann Dear all, please note that there will be no live lecture this morning. A recording of the conclusion of Ukkonen's Algorithm for suffix tree construction will be available later today. Thursday, we will have a regular lecture introducing suffix arrays and their properties and applications.
|
Announcement - Women in Bioinformatics Talk SeriesWritten on 21.04.22 by Sven Rahmann 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… Read more 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). |
TutorialsWritten on 17.04.22 by Jens Zentgraf Dear all, Dear all, |
Recordings and first assignment online!Written on 14.04.22 by Sven Rahmann 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… Read more 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! |