Sunagawa Lab Block Course Fall 2022: 551-1119-00L Microbial Community Genomics¶
General information¶
Course dates: 08.11.2022 - 30.11.2022
Week 1: Tue 1:00PM - 4:30PM, Wed - Fri 8:30AM - 4:30PM
Week 2: Tue 1:00PM - 4:30PM, Wed - Fri 8:30AM - 4:30PM
Week 3: Tue 1:00PM - 4:30PM, Wed - Fri 8:30AM - 4:30PM
Week 4: Tue 1:00PM - 4:30PM, Wed - Wed 8:30AM - 4:30PM
Exam: 30.11.2021, 13:00 - 15:00
Presentations: 01.12.2021, 13:00 - 14:00
Tutors:
Samuel smiravet@ethz.ch
Guillem guillems@ethz.ch
Technichal Support:
Chris fieldc@biol.ethz.ch
Useful resources¶
RStudio-Workbench introduction site: https://sunagawalab.ethz.ch/share/teaching/home/551-1119-00L_Fall2022/contents/0_Setup.html
ZOOM room: https://ethz.zoom.us/j/66212792717
Slack group: https://join.slack.com/t/blockcourse55-3bk9609/shared_invite/zt-1io2akt7r-1E_34MrF8E5VAN8HGr7KnQ
Student Projects¶
Project 1 (unassigned): Visualization of genomes with auxiliary data such as phylogenetic, metabolic, or environmental information
Project 2 (Mina): Diversity within a mOTU: exploring the coherence of all MAGs assigned to single mOTUs
Project 3 (Colin): Comparison of closely related MAGs with contrasting environmental patterns
Project 4 (unassigned): Relation between genome-level features and environmental conditions
Project 5 (unassigned): Relation between genetic- and genome-level features with bacterial growth rate
Project 6 (unassigned): Relationship between optimal temperature with bacterial growth rate
Project 7 (Pierce): Auxotrophy from MAG exploration: amino acid synthesis pathways and their distribution across biological groups
Project 8 (unassigned): Pathway reconstruction and niche estimation based on genome annotations
Find more details in the Project presentation
Data availability¶
The main study used as reference of this course can be found here:
Agenda¶
Week 1¶
W1.1 |
08.11 |
13:00 - 14:30 |
|
W1.2 |
08.11 |
15:00 - 16:30 |
|
W1.3 |
09.11 |
08:30 - 10:00 |
|
W1.4 |
09.11 |
10:30 - 12:00 |
|
W1.5 |
09.11 |
13:00 - 14:30 |
|
W1.6 |
09.11 |
15:00 - 16:30 |
|
W1.7 |
10.11 |
08:30 - 10:00 |
|
W1.8 |
10.11 |
10:30 - 12:00 |
|
W1.9 |
10.11 |
13:00 - 14:30 |
|
W1.10 |
10.11 |
15:00 - 16:30 |
|
W1.11 |
11.11 |
08:30 - 10:00 |
|
W1.12 |
11.11 |
10:30 - 12:00 |
|
W1.13 |
11.11 |
13:00 - 14:30 |
Introduction to the Ocean Microbiome Database (cont.) |
W1.14 |
11.11 |
15:00 - 16:30 |
Introduction to the Ocean Microbiome Database (cont.) |
Week 2¶
W2.1 |
15.11 |
13:00 - 14:30 |
|
W2.2 |
15.11 |
15:00 - 16:30 |
|
W2.3 |
16.11 |
08:30 - 10:00 |
|
W2.5 |
16.11 |
13:00 - 14:30 |
Student projects |
W2.4 |
16.11 |
10:30 - 12:00 |
Student projects |
W2.6 |
16.11 |
15:00 - 16:30 |
Student projects |
W2.7 |
17.11 |
08:30 - 10:00 |
Student projects |
W2.8 |
17.11 |
10:30 - 12:00 |
Student projects |
W2.9 |
17.11 |
13:00 - 14:30 |
Student projects |
W2.10 |
17.11 |
15:00 - 16:30 |
Student projects |
W2.11 |
18.11 |
08:30 - 10:00 |
Student projects |
W2.12 |
18.11 |
10:30 - 12:00 |
Student projects |
W2.13 |
18.11 |
13:00 - 14:30 |
Present progress & Discussion |
W2.14 |
18.11 |
15:00 - 16:30 |
Wrap-up and plan W3 |
Week 3¶
W3.1 |
22.11 |
13:00 - 14:30 |
Student projects |
W3.2 |
22.11 |
15:00 - 16:30 |
Student projects |
W3.3 |
23.11 |
08:30 - 10:00 |
Student projects |
W3.4 |
23.11 |
10:30 - 12:00 |
Student projects |
W3.5 |
23.11 |
13:00 - 14:30 |
Student projects |
W3.6 |
23.11 |
15:00 - 16:30 |
Student projects |
W3.7 |
24.11 |
08:30 - 10:00 |
Student projects |
W3.8 |
24.11 |
10:30 - 12:00 |
Student projects |
W3.9 |
24.11 |
13:00 - 14:30 |
Student projects |
W3.10 |
24.11 |
15:00 - 16:30 |
Student projects |
W3.11 |
25.11 |
08:30 - 10:00 |
|
W3.12 |
25.11 |
10:30 - 12:00 |
Draft for project presentation |
W3.13 |
25.11 |
13:00 - 14:00 |
Discussion on presentation draft |
W3.14 |
25.11 |
14:00 - 16:30 |
Last analyses for projects |
Week 4¶
W4.1 |
29.11 |
13:00 - 14:30 |
Exam |
W4.2 |
29.11 |
14:00 - 16:30 |
Prepare presentation |
W4.3 |
30.11 |
08:30 - 10:00 |
Prepare presentation |
W4.4 |
30.11 |
10:30 - 12:00 |
Prepare presentation |
W4.5 |
30.11 |
13:00 - 15:00 |
Prepare presentation |
W4.6 |
30.11 |
15:00 - 16:00 |
Presentations (15 min. presentation + 5 min. questions) |
W4.7 |
30.11 |
16:30 - 16:30 |
BlockCourse wrap-up |