News

The re-exam schedule

Written on 23.03.25 (last change on 23.03.25) by Alexey Gurevich

The re-exam will occur on 26.03.2025 (Wed) in Alexey's office, Room 3.03 in the CBI building (E2.1). Below is the schedule and bonus points sorted by Matriculation number.

Please arrive about 5 minutes before your scheduled slot and be prepared for a small delay. There's an open waiting area next… Read more

The re-exam will occur on 26.03.2025 (Wed) in Alexey's office, Room 3.03 in the CBI building (E2.1). Below is the schedule and bonus points sorted by Matriculation number.

Please arrive about 5 minutes before your scheduled slot and be prepared for a small delay. There's an open waiting area next to R3.02 where you can sit and relax. You will be invited in — please don't knock, as there may be another student currently taking their exam.

Good luck! 

Matr. Nur. Exam Slot Bonus (p.p.)
2568636 11:20 9
7015544 12:00 10
7025890 10:40 11
7028747 13:00 13
7034245 10:00 13
7055732 11:00 28
7059084 10:20 24
7061868 13:40 14
7069891 13:20 19
7069908 11:40 13

The final exam schedule

Written on 10.02.25 (last change on 13.02.25) by Alexey Gurevich

Below is the table with the exam time slots and bonus points (from 0 to 30 percentage points). The exam will be in Prof. Alexey Gurevich's office: E2.1 (CBI)Room 3.03 (third floor), not in the lecture room! 

Please arrive about 5 minutes before your scheduled slot and be prepared for a small… Read more

Below is the table with the exam time slots and bonus points (from 0 to 30 percentage points). The exam will be in Prof. Alexey Gurevich's office: E2.1 (CBI)Room 3.03 (third floor), not in the lecture room! 

Please arrive about 5 minutes before your scheduled slot and be prepared for a small delay. There's an open waiting area next to R3.02 where you can sit and relax. You will be invited in — please don't knock, as there may be another student currently taking their exam.

Good luck! 

Matr. Num.

Exam slot       

Bonus (p.p.)

2568636 11.2 at 10:40 9
2578704 12.2 at 11:00 28
7006911 11.2 at 11:20 16
7010962 12.2 at 12:00 21
7011464 11.2 at 12:00 25
7015544 26.3 10
7025186 11.2 at 10:20 17
7025890 12.2 at 11:40 11
7025958 12.2 at 11:20 14
7028747 26.3 13
7037198 11.2 at 11:00 28
7055732 13.2 at 12:20 28
7056551 26.3 11
7056944 13.2 at 13:40 18
7059084 12.2 at 14:00 24
7059086 13.2 at 14:40 16
7061868 12.2 at 13:00 14
7062341 12.2 at 10:40 29
7062946 13.2 at 13:00 21
7064862 12.2 at 13:40 14
7068679 13.2 at 14:20 26
7069632 12.2 at 13:20 16
7069891 13.2 at 12:40 19
7069908 26.3 13
7072654 11.2 at 11:40 19
7072659 13.2 at 13:20 8

 

Assignment 6 Now Available

Written on 06.01.25 by Alexey Gurevich

Check it out on Cogniterra!

The submission deadline is at 23:59 CET on 19.01.2025.

Note: This assignment corresponds to Lecture 11, scheduled for 15.01.2025, with the related tutorial session taking place on the same day. Unlike previous assignments in 2024, this one is published well in… Read more

Check it out on Cogniterra!

The submission deadline is at 23:59 CET on 19.01.2025.

Note: This assignment corresponds to Lecture 11, scheduled for 15.01.2025, with the related tutorial session taking place on the same day. Unlike previous assignments in 2024, this one is published well in advance, but the deadline will follow shortly after the tutorial session, rather than the usual 1.5 weeks. To support problem-solving, the assignment includes detailed textual explanations of the main concepts.

Assignment 5 Now Available

Written on 19.12.24 by Alexey Gurevich

Check it out on Cogniterra!

The submission deadline is at 23:59 CET on 06.01.2025.

Assignment 4 Now Available

Written on 03.12.24 by Alexey Gurevich

 Check it out on Cogniterra!

The submission deadline is at 23:59 CET on 16.12.2024.

Assignment 3 Now Available

Written on 18.11.24 by Alexey Gurevich

Check it out on Cogniterra!

The submission deadline is at 23:59 CET on 02.12.2024.

Assignment 2 Now Available

Written on 04.11.24 (last change on 13.11.24) by Alexey Gurevich

Check it out on Cogniterra. This is the first coding assignment, so please read the introduction step carefully!

The submission deadline is at 23:59 CET on 18.11.2024.

Note the submission deadline for Assignment 1 expires tomorrow!
 

Assignment 1 Now Available

Written on 22.10.24 (last change on 13.11.24) by Alexey Gurevich

Check it out on Cogniterra!

The submission deadline is at 23:59 CET on 05.11.2024.

Hands-on Course Component on Cogniterra Now Available

Written on 21.10.24 by Alexey Gurevich

The hands-on complement to the course is now accessible on the Cogniterra platform. This includes all tutorial assignments, such as tool usage and coding problems. Each module will be released shortly before the corresponding tutorial session, giving you two weeks from the moment the module opens to… Read more

The hands-on complement to the course is now accessible on the Cogniterra platform. This includes all tutorial assignments, such as tool usage and coding problems. Each module will be released shortly before the corresponding tutorial session, giving you two weeks from the moment the module opens to submit your solutions.

Currently, only the introductory module is available, with the first tutorial coming soon. Separate announcements will be made as each new tutorial module opens.

To enroll in the course, please register an account on the Cogniterra platform. Make sure to use your real name to ensure your performance is tracked correctly. After registering, log in and join the course at https://cogniterra.org/511.

If you have any questions, feel free to ask—preferably via MS Teams.

 

 

Show all

Microbiome Data Analysis

The microbiome, a complex community of microorganisms, plays a crucial role in the life of the environment it inhabits, including the human body. For example, patients with Alzheimer's disease have substantially different gut microbiomes compared to healthy individuals. The recent biotechnology advances enabled the generation of large amounts of microbiome-related data across different omics levels, such as genomics, transcriptomics, proteomics, and metabolomics. However, effectively analyzing and interpreting this data to fully realize its promise and shed light on the role of microbiome requires the development and application of specialized computational methods.

This course covers cutting-edge bioinformatics tools and techniques for analyzing microbiome data (all omics levels). Students get hands-on experience by applying these tools to sample datasets. They also explore the computational principles that underlie these methods and implement some basic algorithms on their own.


Registration

The course is intended for Bioinformatics students (MSc and BSc) who are competent (== not beginners) in command line (Linux/macOS) and programming (preferably Python, but any language should work).

If you are eligible and want to enroll, please send an email to gurevich@cs.uni-saarland.de entitled "Enrollment MDA (WiSe 24/25)" and containing (i) a brief motivation to join the course (not more than 250 words), (ii) written confirmation the two key requirements are met: competent command-line (Linux/macOS) and programming skills. You will be added to the course MS Teams group after that.

The deadline for registration is 27.10.2024 at 23:59.

For the final exam in February, you will need to additionally register in LSF (the registration will open close to the exam date).

For the hands-on component of the course (practical and coding assignments), register om the Cogniterra platform and join the course.


When / Where / Who

Lectures: Wed, 10:15 – 11:45, E2.1 (CBI) R0.07 -- small seminar room (weekly, from 16.10.2024) by JProf. Dr. Alexey Gurevich

Tutorials: Wed, 14:00 – 15:30, E2.1 (CBI) R0.03 -- CIP pool (bi-weekly, from 23.10.2024) by JProf. Dr. Alexey Gurevich, with assistance from Dr. Azat Tagirdzhanov and Aleksandra Kushnareva from the HMSB group.

Both events will be held in presence. However, if/when we have more active students than available seats (ca. 25), a hybrid connect option will be available (via MS Teams; max until the midterm exam in early December).


Content and Exam 

The course comprises 12 lectures on (meta)genomics, transcriptomics, proteomics, and metabolomics data analysis and 7 assignments on practical (running state-of-the-art data analysis tools, 4) and algorithmic (implementing the underlying algorithms, 3) aspects. There will be a written midterm exam covering the first half of the course and (supposedly) an oral final exam covering the entire course theory.

Exam admission criteria

  • Practical and Coding assignments (each ≥ 50%)
  • Midterm exam (≥ 50%)

Grading

  • You should score at least 50% in the final exam to pass it but this grade constitutes only 70% of the final course grade (e.g., 50% in the final exam transforms into 35% of the final course grade).
  • The remaining 30% could be obtained via completing practical and coding assignments and midterm exams above 90% (10% for each of the three modules; for results between 50% and 90%, pro rata value is added)
  • The final percentage is converted into the German grade scale using this online calculator, with thresholds set to 100 and 50, and rounded to the closest valid grade (1.50 --> 1.3, 1.51 --> 1.7, etc.).

Course Syllabus (subject to change)

 Date  Type  Major Topic  Title  Slides 
16.10.2024 lecture other  Microbiome Data Analysis: Introduction (general info about the course content and grading)   MDA_L01 
23.10.2024 lecture amplicon seq.   Amplicon Sequencing: Part 1 (from raw reads to ASVs/OTUs)   MDA_L02
23.10.2024 tutorial (run) amplicon seq.  Basic 16S Data Analysis (see L02)  assignments 
30.10.2024 lecture amplicon seq.  Amplicon Sequencing: Part 2 (comparing samples' taxonomical content)   MDA_L03
06.11.2024 lecture metagenomics  Metagenomics: Introduction and Read-Based Analysis  MDA_L04
06.11.2024 tutorial (code) metagenomics  Burrows-Wheeler transform (BWT) and Sequence Alignment (see L04)  assignments
13.11.2024 lecture metagenomics  Metagenomics: Assembly-Based Analysis Part I (from reads to contigs)  MDA_L05
20.11.2024 lecture metagenomics  Metagenomics: Assembly-Based Analysis Part II (from contigs to MAGs)  MDA_L06
20.11.2024 tutorial (run) metagenomics  Metagenomics: from Reads to MAGs (see L05-L06)  assignments
27.11.2024 lecture functional ann.  Taxonomical and Functional Annotation  MDA_L07
04.12.2024 lecture functional ann.  Annotation of Secondary Metabolite Clusters (functional annotation part II)  MDA_L08
04.12.2024 tutorial (code) functional ann.  Hidden Markov Models (HMM) and Genome Annotation (see L08)  assignments
11.12.2024 midterm exam
(group 1) 
other  Intermediate Exam (during the lecture slot 10:15 -- 11:45; in presence; written)  questions
 answers
18.12.2024 lecture transcriptomics  (Meta)transcriptomics: Introduction and Common Tools  MDA_L09
18.12.2024 tutorial (run) transcriptomics  (Meta)transcriptomics Data Analysis (see L09)  assignments
08.01.2025 lecture proteomics  (Meta)proteomics and Mass Spectrometry Basics  MDA_L10
15.01.2025 lecture proteomics  Computational Mass Spectrometry  MDA_L11
15.01.2025 tutorial (code) proteomics  Basic Computational Mass Spectrometry Problems (see L11)  assignments
15.01.2025 midterm exam
(group 2) 
other  Intermediate exam (12:00 -- 13:30, i.e., right after the lecture; in presence; written)  questions
 answers
22.01.2025 lecture metabolomics  Metabolomics Intro and Data Analysis  MDA_L12
29.01.2025 lecture metabolomics  Computational Questions in Metabolomics Identification  MDA_L13
29.01.2025 tutorial (run) metabolomics  Metabolomics Data Analysis (see L12-13)  canceled
05.02.2025 consultation other  Q & A session (during the lecture slot 10:15 -- 11:45)  MDA_QA
12.02.2025  final exam other  Final exam (oral)  
26.03.2025  final exam other  Re-exam (oral)  

Contact

Feel free to send your questions, suggestions, and concerns directly to JProf. Dr. Alexey Gurevich (gurevich@cs.uni-saarland.de).

Privacy Policy | Legal Notice
If you encounter technical problems, please contact the administrators.