News
Assignment 3 Now AvailableWritten 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 AvailableWritten 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 AvailableWritten 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 AvailableWritten 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.
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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 Genome Annotation | TBA |
| 04.12.2024 | lecture | functional ann. | Annotation of Secondary Metabolite Clusters | TBA |
| 04.12.2024 | tutorial (code) | functional ann. | Hidden Markov Models (HMM) and genome annotation | TBA |
| 11.12.2024 | midterm exam | other | Intermediate exam (during the lecture slot 10:15 -- 11:45; in presence; written) | |
| 18.12.2024 | lecture | transcriptomics | (Meta)transcriptomics: Introduction and Common Tools | TBA |
| 18.12.2024 | tutorial (run) | transcriptomics | (Meta)transcriptomics Data Analysis (corresponds to the L09 content) | TBA |
| 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 |
| 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 <15 students left) | |
| 17-21.02.2025? | final exam | other | Re-exam (if needed) |
Contact
Feel free to send your questions, suggestions, and concerns directly to JProf. Dr. Alexey Gurevich (gurevich@cs.uni-saarland.de).