Sunagawa Lab Block Course Fall 2020: 551-1119-00L Microbial Community Genomics

Sunagawa Lab Block Course Fall 2020: 551-1119-00L Microbial Community Genomics#

General information#

  • Course dates: 15.09.2020 - 07.10.2020

    • Week 1: Tue 1PM - 5PM, Wed - Fri 8:30AM - 5PM

    • Week 2: Tue 1PM - 5PM, Wed - Fri 8:30AM - 5PM

    • Week 3: Tue 1PM - 5PM, Wed - Fri 8:30AM - 5PM

    • Week 4: Tue 1PM - 5PM, Wed - Wed 8:30AM - 5PM

  • Microbiology Seminars (attendance highly recommended): every Wed, 5:15PM via ZOOM: https://ethz.zoom.us/j/95255381852

  • Exam: 06.10.2020, 13:30 - 15:00

  • Presentation: 07.10.2020, 13:30 - 16:00

  • Tutors:

Agenda#

Week 1#

1.1

15.09

13:30 - 15:00

Introductory lecture

1.2

15.09

15:30 - 17:00

Setup infrastructure & introduction to UNIX

1.3

16.09

08:30 - 10:00

Lecture: The study of gut microbiota using the 16S rRNA gene

1.4

16.09

10:30 - 12:00

Scientific presentation on the data & project (via ZOOM: https://ethz.zoom.us/j/2798881349)

1.5

16.09

13:30 - 15:00

Introduction to R - basic R

1.6

16.09

15:30 - 17:00

Introduction to R - data transformation (tidyverse)

1.7

17.09

08:30 - 10:00

Introduction to R - data visualization (ggplot)

1.8

17.09

10:30 - 12:00

Pipeline for the analysis of 16S rRNA gene amplicon data

1.9

17.09

13:30 - 15:00

Pipeline for the analysis of 16S rRNA gene amplicon data

1.10

17.09

15:30 - 17:00

Describing microbial community structure - HMP data (Lecture)

1.11

18.09

08:30 - 10:00

Describing microbial community structure - HMP data (Tutorial)

1.12

18.09

10:30 - 12:00

Describing microbial community structure - data produced in session 1.5 & 1.6

1.13

18.09

13:30 - 15:00

Describing microbial community structure - data produced in session 1.5 & 1.6

1.14

18.09

15:30 - 17:00

Summary overview of RepFail metadata

Week 2#

2.1

22.09

13:30 - 15:00

Best Practices for Data/Project/Software Management

2.2

22.09

15:30 - 17:00

Work on group projects

2.3

23.09

08:30 - 10:00

Flash talk session by 3 members of the group

2.4

23.09

10:30 - 12:00

Work on group projects

2.5

23.09

13:30 - 15:00

Work on group projects

2.6

23.09

15:30 - 17:00

Work on group projects

2.7

24.09

08:30 - 10:00

Work on group projects

2.8

24.09

10:30 - 12:00

Work on group projects

2.9

24.09

13:30 - 15:00

Work on group projects

2.10

24.09

15:30 - 17:00

Work on group projects

2.11

25.09

08:30 - 10:00

Work on group projects

2.12

25.09

10:30 - 12:00

Work on group projects

2.13

25.09

13:30 - 15:00

Present progress by each group & Discussion

2.14

25.09

15:30 - 17:00

Wrap-up and plan W3

Week 3#

3.1

29.09

13:30 - 15:00

Work on group projects

3.2

29.09

15:30 - 17:00

Work on group projects

3.3

30.09

08:30 - 10:00

Journal Club

3.4

30.09

10:30 - 12:00

Work on group projects

3.5

30.09

13:30 - 15:00

Work on group projects

3.6

30.09

15:30 - 17:00

Work on group projects

3.7

01.10

08:30 - 10:00

Work on group projects

3.8

01.10

10:30 - 12:00

Lecture: Report writing (check also the Report example)

3.9

01.10

13:30 - 15:00

Work on group projects

3.10

01.10

15:30 - 17:00

Work on group projects

3.11

02.10

08:30 - 10:00

Discuss project results

3.12

02.10

10:30 - 12:00

Work on group projects (freeze results)

3.13

02.10

13:30 - 15:00

Work on group projects (freeze results)

3.14

02.10

15:30 - 17:00

Wrap-up

Week 4#

4.1

06.10

13:30 - 15:30

Lecture: Presentation and report format/content

4.2

06.10

16:00 - 17:00

Exam

4.3

07.10

08:30 - 10:00

Prepare presentation

4.4

07.10

10:30 - 12:00

Prepare presentation

4.5

07.10

13:30 - 16:00

Presentation

4.6

07.10

16:30 - 17:00

Wrap-up