Oldenburg workshop - March 2025
We are planning a free, in-person workshop and early-career researcher symposium to discuss integrated microbial ‘omics and learn how to use anvi’o. The topics that we will cover during the workshop include,
- Genomics
- Metagenomics
- Genome-resolved metagenomics
- Pangenomics
- Phylogenomics
- Microbial population genetics
If you are interested in attending, please consider applying as soon as possible as we have limited number of seats in the workshop venue, and mark your calendars for March 3-7 2025.
Please feel free to share this page with anyone who may benefit from this workshop, and please note that we will cover travel and accommodation (as long as our funds last), so we strongly encourage applications from institutions with limited resources around the globe.
Feel free to write to any of us if you have any questions.
The application deadline was on Jan 10, 2025 and we are no longer accepting new applications.
The flyer for the workshop.
When and Where
From March 3, 2025 (Monday) to March 7, 2025 (Friday) at the Helmholtz Institute for Functional Marine Biodiversity (HIFMB) in Oldenburg, Germany. Here is a map for you:
Program
In addition to intense hands-on training sessions, this event includes an ECR symposium, during which all of the participants will give lightning talks about their research. We will send the details of lightning talks to each participant upon their invitation.
Here is a very preliminary overview of the workshop content:
Monday 3: Genomics
| 9:00 - 9:15 | Introduction to the workshop faculty & setting |
| 9:15 - 10:15 | Introduction to the anvi’o software ecosystem |
| 10:15 - 10:30 | Coffee & Tea Break |
| 10:30 - 12:00 | Genomics (gene calling, functional annotation, taxonomic characterization) |
| 12:00 - 13:00 | Group lunch at Bar Celona |
| 13:00 - 14:00 | Symposium talks |
| 14:00 - 15:30 | Genomics, continued |
| 15:30 - 15:45 | Coffee & Tea Break |
| 15:45 - 17:30 | Genomics, continued |
Tuesday 4: Metabolic reconstruction; Pangenomics
| 9:00 - 10:15 | Functions and metabolism (estimation of metabolic potential in genomes and metagenomes) |
| 10:15 - 10:30 | Coffee & Tea Break |
| 10:30 - 12:00 | Functions and metabolism, continued |
| 12:00 - 13:00 | Group lunch at Bar Celona |
| 13:00 - 14:00 | Symposium talks |
| 14:00 - 15:30 | Phylogenomics (theoretical introduction and hands-on session) |
| 15:30 - 15:45 | Coffee & Tea Break |
| 15:45 - 17:30 | Phylogenomics, continued |
Wednesday 5: Pangenomics; Phylogenomics
| 9:00 - 10:15 | Pangenomics (introduction to pangenomics, and its computational and biological underpinnings) |
| 10:15 - 10:30 | Coffee & Tea Break |
| 10:30 - 12:00 | Pangenomics (hands-on session) |
| 12:00 - 13:00 | Group lunch at Bar Celona |
| 13:00 - 14:00 | Symposium talks |
| 14:00 - 15:30 | Pangenomics (hands-on session), continued |
| 15:30 - 15:45 | Coffee & Tea Break |
| 15:45 - 17:30 | Pangenome graphs (theory + hands-on) |
Thursday 6: Metagenomics; Genome-resolved metagenomics
| 9:00 - 10:15 | Metagenomic read recruitment (theoretical introduction and hands-on session) |
| 10:15 - 10:30 | Coffee & Tea Break |
| 10:30 - 12:00 | Metagenomic read recruitment, continued |
| 12:00 - 13:00 | Group lunch at Bar Celona |
| 13:00 - 14:00 | Symposium talks |
| 14:00 - 15:30 | Genome-resolved metagenomics (a discussion on best practices in genome binning and refinement) |
| 15:30 - 15:45 | Coffee & Tea Break |
| 15:45 - 17:30 | Genome-resolved metagenomics, continued |
Friday 7: Microbial population genetics; Scalable bioinformatics
| 9:00 - 10:15 | Microbial population genetics (single-nucleotide variants, single-codon variants, single-amino acid variants, protein structures, and what we can learn from them) |
| 10:15 - 10:30 | Coffee & Tea Break |
| 10:30 - 12:00 | Microbial population genetics, continued |
| 12:00 - 13:00 | Group lunch at Bar Celona |
| 13:00 - 14:00 | Symposium talks |
| 14:00 - 15:30 | How to use automated, scalable, and reproducible bioinformatics workflows |
| 15:30 - 15:45 | Coffee & Tea Break |
| 15:45 - 17:30 | Bioninformatics workflows, continued |
How much does it cost?
We will cover your lunches and coffee/tea breaks. Travel support and accommodation is available upon request while the funds last. The rest is up to you.
We thank the Universitätsgesellschaft Oldenburg e.V. (UGO) and the Alfred-Wegener-Institute (AWI) for their financial support of this event.
Registration link
The application deadline was January 10, 2025.
List of participants
TBA.