Sunagawa Lab Block Course Fall 2023: 551-1119-00L Microbial Community Genomics

General information

• Course location: HCI E353

• Course dates: 07.11.2023 - 29.11.2023

  • First day (Tue 07.11): 12:45 - 16:30

  • Week 1: Wed - Fri 9:00 - 17:00

  • Week 2: Tue 13:30 - 17:00, Wed - Fri 9:00 - 17:00

  • Week 3: Tue 13:30 - 17:00, Wed - Fri 9:00 - 17:00

  • Week 4: Tue 13:30 - 17:00, Wed - Wed 9:00 - 17:00

• Presentations: 29.11.2023, 9:00 - 15:00

• Tutors:

  • Samuel Miravet Verde - smiravet@ethz.ch

  • Guillem Salazar Guiral - guillems@ethz.ch

• Technichal Support:

  • Chris Field - fieldc@biol.ethz.ch

Useful resources

• RStudio-Workbench and Jupyter introductions

  • Jupyter: http://cousteau-jupyter.ethz.ch/

  • R-Studio: http://cousteau-rstudio.ethz.ch/

• Zoom room

• Slack group

Student Projects

• Project 1 (Anja & Luca): Exploration of the effect of CarveMe stochastic component on GEM reconstruction

• Project 2 (Leah & Yongqi): Description of the metabolic capacities of a global collection of marine microbes

• Project 3 (Bella & Livio): Metabolic interaction analysis of marine communities across a depth gradient

• Project 4 (Jasmin & Noelia): Metabolic interaction analysis of marine communities across a latitudinal gradient

• Project 5 (Bella & Livio): Metabolic interaction analysis of marine communities across seasons

Useful links:

• Find more details in the project presentation and in the shared folder

Data availability

The data samples used during this course come from:

• Biosynthetic potential of the global ocean microbiome

The tools run in this course are described in the following articles:

• Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

• Metabolic dependencies drive species co-occurrence in diverse microbial communities

The study explored in the tutorial is presented here:

• Non-invasive monitoring of microbiota and host metabolism using secondary electrospray ionization-mass spectrometry

Agenda

Week 1

W1.1	07.11	12:45 - 14:15	Introductory lecture
W1.2	07.11	15:00 - 15:30	Setup infrastructure
W1.3	07.11	15:30 - 16:30	Using Bash/UNIX
W1.4	08.11	09:00 - 10:30	Lecture on genomics and metabolic modelling
W1.5	08.11	11:00 - 12:30	Lecture on tools for metabolic modeling in microbial communities
W1.6	08.11	13:30 - 15:00	Introduction to R
W1.7	10.11	15:30 - 16:45	Data transformation with R
W1.8	10.11	15:30 - 16:45	Data visualization with R
W1.9	09.11	09:00 - 10:30	Hands-on tutorial on GEM reconstruction
W1.10	09.11	11:00 - 12:30	Hands-on tutorial on GEM reconstruction (continuation)
W1.11	09.11	13:30 - 15:00	Hands-on tutorial on GEM reconstruction (continuation)
W1.12	09.11	15:30 - 17:00	Hands-on tutorial on GEM reconstruction (continuation)
W1.13	10.11	09:00 - 10:30	Introduction to the Ocean Microbiome Database (exercise)
W1.14	10.11	11:00 - 12:30	Introduction to the Ocean Microbiome Database (continuation)
W1.15	10.11	13:30 - 15:00	Introduction to the Ocean Microbiome Database (continuation)
W1.16	10.11	15:30 - 17:00	Explanation of potential group projects

Week 2

W2.1	14.11	13:30 - 15:00	Invited speaker lecture: Dr. Alan Pacheco (Vorholt Lab)
W2.2	14.11	15:30 - 17:00	Wrap-up and project planning
W2.3	15.11	09:00 - 10:30	Lecture on best practices for bioinformatic projects
W2.5	15.11	11:00 - 12:30	Student projects
W2.4	15.11	13:30 - 15:00	Student projects
W2.6	15.11	15:30 - 16:30	Student projects
W2.S	15.11	16:30 - 17:30	Institute seminar
W2.7	16.11	09:00 - 10:30	Student projects
W2.8	16.11	11:00 - 12:30	Student projects
W2.9	16.11	13:30 - 15:00	Student projects
W2.10	16.11	15:30 - 17:00	Student projects
W2.11	17.11	09:00 - 10:30	Present progress & Discussion
W2.12	17.11	11:00 - 12:30	Present progress & Discussion
W2.13	17.11	13:30 - 15:00	Present progress & Discussion
W2.14	17.11	15:30 - 17:00	Wrap-up and plan W3

Week 3

W3.1	21.11	13:30 - 15:00	Lecture on report writing (check also the report example)
W3.2	21.11	15:30 - 17:00	Student projects
W3.3	22.11	09:00 - 10:30	Student projects
W3.4	22.11	11:00 - 12:30	Student projects
W3.5	22.11	13:30 - 15:00	Student projects
W3.6	22.11	15:30 - 16:30	Student projects
W3.S	22.11	16:30 - 17:30	Institute seminar
W3.7	23.11	09:00 - 10:30	Student projects
W3.8	23.11	11:00 - 12:30	Present progress & Discussion
W3.9	23.11	13:30 - 15:00	Present progress & Discussion
W3.10	23.11	15:30 - 17:00	Present progress & Discussion
W3.11	24.11	09:00 - 10:30	Student projects
W3.12	24.11	11:00 - 12:30	Student projects
W3.13	24.11	13:30 - 15:00	Student projects
W3.14	24.11	15:30 - 17:00	Last analyses for projects

Week 4

W4.1	28.11	13:30 - 15:00	Prepare presentation
W4.2	28.11	15:30 - 17:00	Prepare presentation
W4.3	29.11	09:00 - 10:30	Presentations (15 min. presentation + 5 min. questions)
W4.4	29.11	11:00 - 12:30	Presentations (continuation)
W4.5	29.11	13:30 - 15:00	Presentations (continuation)
W4.6	29.11	15:30 - 16:00	Discussion for writing the project
W4.7	29.11	16:30 - 17:00	Block Course wrap-up