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 |