We are now accepting applications!
Application forms are available here! The application deadline is 1-May, 2024.
The 2024 Workshop on Microbial Community Multi-omics is being held 3-7th of June, 2024 in Český Krumlov, Czech Republic. This is the 1st time the Workshop of Microbial Community Multi-omics will be held in the Czech Republic. We have held similar courses through different venues for the previous five years but are really excited about teaming up with Evomics courses to host our course this year!
Our philosophy is to train participants in the most relevant topics in microbial community analysis in a vibrant, immersive, and inclusive environment. In this week-long workshop, members of the Huttenhower Lab and Harvard Chan Microbiome in Public Health Center (HCMPH) will provide an overview of bioinformatics methods for profiling the taxonomic structure (microbes and viruses) and function of microbial communities from high throughput ‘omics data, alongside statistical methods for associating those profiles with community metadata (e.g., host phenotypes). This course will focus on analyzing shotgun metagenomes, metatranscriptomes, and untargeted metabolomic data using the bioBakery: a computing environment containing reproducible methods for microbial community analysis. Participants will be expected to bring a laptop-style computer and have some basic familiarity with working at the command line.
The Workshop on Microbial Community Multi-omics 2024 is organized by:
The Huttenhower group, T.H. Chan School of Public Health, US
Daniel Kintzl, Český Krumlov Coordinator
Scott Handley, Evomics Director, Washington University, US
We also have a talented group of teacher assistants who help with the organization and preparation of the computer practicals.
Workshop Information
The Workshop registration fee is $850. We provide approximately 40 hours of teaching during the two-week workshop, so our price is approximately $22 an hour. Note that this amount does not cover travel, lodging, or boarding.
Other important details can be read on our FAQ page.
If you do not manage to attend the workshop on Microbial Community Multi-omics 2024, stay tuned for June 2025!
3-7 June, 2024
Note: This is the list of topics we plan to cover, timing and presenter may change closer to the date of the course.
| DATE | DAY | TIME | PRESENTER | TOPIC | LOCATION |
|---|---|---|---|---|---|
| 3rd Jun | Monday | 9-12 | Everyone
Curtis Huttenhower Jacob Nearing TBD |
Welcome and introductions
Introduction in microbial community analysis Experimental considerations in microbiome sequencing Tutorial: KneadData sequence QC |
|
| 3rd Jun | Monday | 2-5 | Kelsey Thompson
TBD Curtis Huttenhower |
Taxonomic profiling in microbial communities
Tutorial: Taxonomic profiling with MetaPhlAn 4 The human microbiome Projects (HMP1&II) |
|
| 3rd Jun | Monday | 7-9 | Everyone | Reception and networking | |
| 4th Jun | Tuesday | 9-12 | Kelsey Thompson
TBD TBD |
Identifying strain in community data
Tutorial: Tree visualization with GraPhlAn Tutorial: Strain profiling with StrainPhlAn 4 |
|
| 4th Jun | Tuesday | 2-5 | Curtis Huttenhower
Eric Franzosa TBD |
Study design for microbial multi-comic studies
Functional profiling in microbial communities Tutorial: Functional profiling with HUMAnN 4 |
|
| 4th Jun | Tuesday | 7-9 | Everyone | Lighting talks and networking | |
| 5th Jun | Wednesday | 9-12 | Kelsey Thompson
TBD TBD |
Metagenomic assembly and applications
Tutorial: Prioritizing bioactive genes with MetaWIBELE Tutorial: Detecting LGT with WAAFLE |
|
| 5th Jun | Wednesday | 2-5 | Curtis Huttenhower
TBD Eric Franzosa |
SGBs and microbial phylogenetics
Tutorial: Assembly and SGB creation tutorial Meta’omic visualization |
|
| 5th Jun | Wednesday | 7-9 | Everyone | Lighting talks and networking | |
| 6th Jun | Thursday | 9-12 | Jacob Nearing
TBD TBD |
Statistics for microbial multi’omics
Tutorial: Microbiome association testing with MaAsLin and Anpan Tutorial: Meta’omic visualization |
|
| 6th Jun | Thursday | 2-5 | Kelsey Thompson
TBD Eric Franzosa |
Metatranscriptomics (MTX)
Tutorial: Statistics for MTX with MaAsLin Viral profiling in microbial communities |
|
| 6th Jun | Thursday | 7-9 | Eric Franzosa
TBD |
Microbiome metabolomics
Tutorial: Prioritizing bioactive metabolites with MACARRoN |
|
| 7th Jun | Friday | 9-12 | Jacob Nearing
TBD |
Methods for multi’omic data integration
Tutorial: Data integration with HAllA |
|
| 7th Jun | Friday | 2-5 | Curtis Huttenhower
Everyone |
Reproducible microbial community analysis
Open time/QA |
Important information:
- Group photo! (We will add in person!)
- Online booking of your free time activities! (also available at the Info-Centre)
FIND YOUR WAY AROUND ČESKÝ KRUMLOV
- Český Krumlov town information
- Map of 2024 Český Krumlov – Check before arrival to choose the bus stop closest to your accomodation!!
- Map of the main locations in the schedule (Save to your Google Maps!)
- Map of some of the main Český Krumlov restaurants (Save to your Google Maps!)
- Map of some of the main Český Krumlov bars (Save to your Google Maps!)
- Map of Český Krumlov service points: shops, pharmacy, ATM, hospital (Save to your Google Maps!)
- Map of the historic City Centre of Český Krumlov
FACULTY AND GENOMICS
- Faculty Bios and Teaching Assistant Bios
- Suggested microbial community literature
- Instance Assignments
COMPETITIONS
- As a tradition we have a T-shirt design competition! Best T-shirt design will feature on the Workshop on Microbial Community Multi-omics 2024 T-shirts! Submit your design by EOD June 4th at the latest! (For inspiration, check out previous designs here!)
- BINGO!
CODE OF CONDUCT
- Code of conduct, contact people Kelsey Thompson ([email protected])