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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

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.

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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

The final exam constitutes 70% of the final 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 (corresponds to the L02 content)	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	assignments
13.11.2024	lecture	metagenomics	Metagenomics: Assembly-Based Analysis Part I (from reads to contigs)	MDA_L05
20.11.2024	lecture	metagenomics	Metagenomics: from reads to MAGs	assignments
20.11.2024	tutorial (run)	metagenomics	Metagenomics: Assembly-Based Analysis Part II (from contigs to MAGs)	MDA_L06
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	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 (corresponds to the L09 content)	assignments
08.01.2025	lecture	proteomics	(Meta)proteomics and Mass Spectrometry Basics	TBA
15.01.2025	lecture	proteomics	Computational Mass Spectrometry	TBA
15.01.2025	tutorial (code)	proteomics	Computational Mass Spectrometry (corresponds to the L11 content)	TBA
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 vs Metaproteomics (overview of specifics and challenges)	TBA
29.01.2025	lecture	metabolomics	Metabolomics Software	TBA
29.01.2025	tutorial (run)	metabolomics	Metabolomics Data Analysis	TBA
05.02.2025	consultation	other	Q & A session (during the lecture slot 10:15 -- 11:45)
10-14.02.2025?	final exam	other	Main exam (oral if ~<20 students left)
03-15.03.2025?	final exam	other	Re-exam

Contact

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