Sunagawa Lab Block Course Fall 2025: 551-1119-00L Microbial Community Genomics

Contents

Sunagawa Lab Block Course Fall 2025: 551-1119-00L Microbial Community Genomics#

General information#

Course location: HCI F441
Course dates: 04.11.2025 - 26.11.2025
- First day (Tue 04.11): 12:45 - 16:30
- Rest:
  - Tuesdays:
    - 13:10–14:40 — Session 1 (90 min)
    - 14:40–14:50 — Break (10 min)
    - 14:50–16:30 — Session 2 (100 min)
  - From Wednesday to Friday:
    - 09:00–10:30 — Session 1 (90 min)
    - 10:30–10:40 — Break (10 min)
    - 10:40–12:10 — Session 2 (90 min)
    - 12:10–13:10 — Lunch (60 min)
    - 13:10–14:40 — Session 3 (90 min)
    - 14:40–14:50 — Break (10 min)
    - 14:50–16:50 — Session 4 (120 min)
Tutors:
Technichal Support:
Coordinator:
- Shinichi Sunagawa - ssunagawa@ethz.ch

Evaluation#

Presentations: 26.11.2025, 9:00 - 15:00
Report: Hand in by 10.12.2025 (23:59)
- Submission format: PDF via email with subject “551-1119-00L_Fall2025_Report_YourName”
- Send a copy by email to smiravet@ethz.ch, martin.sperfeld@biol.ethz.ch, francisco.zorrilla@biol.ethz.ch, ssunagawa@ethz.ch

Useful resources#

Jupyter introductions
- Jupyter: https://lovelace-jupyter.ethz.ch//
Zoom room
Slack group
Drive folder

Student Projects#

Project Number (Student 1 & 2): Title
Project Number (Student 3 & 4): Title

…

Useful links:

Find more details in the project presentation and examples for reports and presentations in the shared folder

Data availability#

Some studies to use as reference:

Main resources from where genomes come from:

Agenda#

Week 1#

W1.01	04.11	12:45 - 14:15	`Introductory lecture`
W1.02	04.11	14:30 - 16:30	`Lecture on cooperation and competition in microbial communities`
W1.03	05.11	09:00 - 10:30	`Lecture on microbial community genomics`
W1.04	05.11	10:40 - 12:10	Setup infrastructure and Using Bash/UNIX
W1.05	05.11	13:10 - 14:40	Introduction to Python Programming, Data Analysis and Data Visualization
W1.06	05.11	14:50 - 16:50	Hands-on tutorial on genome mining methods
W1.07	06.11	09:00 - 10:30	Hands-on tutorial on genome mining methods (continuation)
W1.08	06.11	10:40 - 12:10	Hands-on tutorial on genome mining methods (continuation)
W1.09	06.11	13:10 - 14:40	Hands-on tutorial on genome mining methods (continuation)
W1.10	06.11	14:50 - 16:50	Hands-on tutorial on genome mining methods (continuation)
W1.11	07.11	09:00 - 10:30	`Introduction to the Ocean Microbiome Database (exercise)`
W1.12	07.11	10:40 - 12:10	Introduction to the Ocean Microbiome Database (continuation)
W1.13	07.11	13:10 - 14:40	Invited speaker lecture: Prof. Dr. Shinichi Sunagawa
W1.14	07.11	14:50 - 16:50	`Introduction to group projects`

Week 2#

W2.01	11.11	13:10 - 14:40	`Lecture on best practices for bioinformatic projects`
W2.02	11.11	14:50 - 16:50	`Explanation, selection and planning of projects`
W2.03	12.11	09:00 - 10:30	Invited speaker lecture: Dr. Olga Schubert
W2.05	12.11	10:40 - 12:10	Student projects
W2.04	12.11	13:10 - 14:40	Student projects
W2.06	12.11	14:50 - 16:50	Student projects
W2.07	13.11	09:00 - 10:30	Student projects
W2.08	13.11	10:40 - 12:10	Student projects
W2.09	13.11	13:10 - 14:40	Student projects
W2.10	13.11	14:50 - 16:50	Student projects
W2.11	14.11	09:00 - 10:30	Student projects - Prepare presentation
W2.12	14.11	10:40 - 12:10	Present progress & Discussion
W2.13	14.11	13:10 - 14:40	Present progress & Discussion
W2.14	14.11	14:50 - 16:50	Present progress & Discussion - Wrap-up and plan W3

Week 3#

W3.01	18.11	13:00 - 14:30	`Lecture on writing and presentations` (check `examples`)
W3.02	18.11	14:45 - 16:30	Student projects
W3.03	19.11	09:00 - 10:30	Student projects
W3.05	19.11	10:40 - 12:10	Student projects
W3.04	19.11	13:10 - 14:40	Student projects
W3.06	19.11	14:50 - 16:50	Student projects
W3.07	20.11	09:00 - 10:30	Student projects
W3.08	20.11	10:40 - 12:10	Student projects
W3.09	20.11	13:10 - 14:40	Student projects
W3.10	20.11	14:50 - 16:50	Student projects
W3.11	21.11	09:00 - 10:30	Student projects - Prepare presentation
W3.12	21.11	10:40 - 12:10	Present progress & Discussion
W3.13	21.11	13:10 - 14:40	Present progress & Discussion
W3.14	21.11	14:50 - 16:50	Present progress & Discussion - Wrap-up and plan W4

Week 4#

W4.01	25.11	13:00 - 14:30	`Lecture on writing and presentations` (check `examples`)
W4.02	25.11	14:45 - 16:30	Student projects
W4.03	26.11	09:00 - 10:30	Presentations (15 min. presentation + 5 min. questions)
W4.04	26.11	10:40 - 12:10	Presentations (continuation)
W4.05	26.11	13:10 - 14:40	Presentations (continuation)
W4.06	26.11	14:50 - 16:00	Discussion for writing the project
W4.07	26.11	16:00 - 16:30	Block Course wrap-up