News
Currently, no news are available
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 will cover cutting-edge bioinformatics tools and techniques for analyzing microbiome data. Students will get hands-on experience by applying these tools to sample datasets. They will 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. Also, register in LSF.
The deadline for registration is 27.10.2024 at 23:59.
When / Where / Who
Lectures: Wed, 10:00 – 11:30, 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 HSMB 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 tutorials 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 |
| 16.10.2024 | lecture | other | Introduction to the course system and microbiome data analysis |
| 23.10.2024 | lecture | amplicon seq. | TBA |
| 23.10.2024 | tutorial (run) | amplicon seq. | TBA |
| 30.10.2024 | lecture | amplicon seq. | TBA |
| 06.11.2024 | lecture | metagenomics | TBA |
| 06.11.2024 | tutorial (code) | metagenomics |
TBA |
| 13.11.2024 | lecture | metagenomics | TBA |
| 20.11.2024 | lecture | metagenomics | TBA |
| 20.11.2024 | tutorial (run) | metagenomics | TBA |
| 27.11.2024 | lecture |
functional ann. |
TBA |
| 04.12.2024 | lecture | functional ann. |
TBA |
| 04.12.2024 | tutorial (code) | functional ann. | TBA |
| 11.12.2024 | midterm exam | other | Intermediate exam (written) |
| 18.12.2024 | lecture | transcriptomics | TBA |
| 18.12.2024 | tutorial (run) | transcriptomics | TBA |
| 08.01.2025 | lecture | proteomics | TBA |
| 15.01.2025 | lecture | proteomics | TBA |
| 15.01.2025 | tutorial (code) | proteomics | TBA |
| 22.01.2025 | lecture | metabolomics | TBA |
| 29.01.2025 | lecture | metabolomics | TBA |
| 29.01.2025 | tutorial (run) | metabolomics |
TBA |
| 05.02.2025 | consultation | other | Q & A session |
| 12.02.2025? | final exam | other | Main exam (oral if <15 students left) |
| 19.02.2025? | 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).