Oldenburg workshop - March 2025
Table of Contents
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 | The anvi’o interactive interface |
| 12:00 - 13:00 | Group lunch at Bar Celona |
| 13:00 - 14:00 | Symposium talks |
| 14:00 - 15:30 | Genomics (gene calling, functional annotation, taxonomic characterization) |
| 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 |
Workshop materials
The lecture slides for the workshop can be downloaded from this Figshare link.
The table below shows the links to the tutorials used in each workshop session.
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 Faculty
The following individuals from the HIFMB were responsible for organizing, teaching, setting-up and running the workshop.
| Name | Role |
|---|---|
| Florian Trigodet | Primary Organizer & Faculty |
| Iva Veseli | Primary Organizer & Faculty |
| Meren | Organizer & Faculty |
| Alexander Henoch | Faculty, Teaching Assistant & Coffee Break Manager |
| Katy Lambert-Slosarska | Faculty, Teaching Assistant & Coffee Break Manager |
| Metehan Sever | Teaching Assistant, On-the-fly Bug Fixer |
| Raïssa Meyer | Coffee Break Assistant & Workshop Participant |
List of participants
The following 48 individuals attended the workshop.
| Full Name | University / Institution | |
|---|---|---|
| Abigail Turnlund | Helmholtz Institute for Functional Marine Biodiversity at the | niversity of Oldenburg (HIFMB) |
| Alberto Scarampi | University of Warwick | |
| Andrian P. Gajigan | University of Hawaii at Manoa | |
| Angela M. Marulanda G. | ICBM - Carl von Ossietzky Universität Oldenburg | |
| Ankish Arya | Indian Institute of Information Technology (Allahabad, Prayagraj) | |
| Archontis Goumagias | University Medical Center Groningen (UMCG) | |
| Balamurugan Sadaiappan | United Arab Emirates University | |
| Berna de Vries | University of Vienna | |
| Carolina Salvador Duque Estrada | Federal University of Rio de Janeiro | |
| Carolina Targon Tiberio | University of São Paulo | |
| Caroline Sophie Winther-Have | University of Copenhagen | |
| Claudia Pogoreutz | University of Perpignan Via Domitia | |
| Emeline Vidal | Marine Biological Laboratory | |
| Fabian Moye | Helmholtz Institute for Functional Marine Biodiversity at the Unive | sity of Oldenburg (HIFMB) |
| Fengqing Wang | Max Planck Institute for Marine Microbiology | |
| Garance Gauthier | Max Planck Institute for Marine Microbiology | |
| Ibrahim Cem Özsefil | Max Planck Institute for Marine Microbiology | |
| Joseane Aparecida Marques | Helmholtz Institute for Functional Marine Biodiversit | at the University of Oldenburg (HIFMB) |
| Judith Giel | Universität Bremen | |
| Keith Mluleki Dube | Stellenbosch University | |
| Kristina Weinert | Max Planck Institute for Marine Microbiology | |
| Laurice Beatrice Raphaelle dela Pena | University of the Philippines | |
| Manzoor Ahmad | United Arab Emirates University | |
| Mariana Martinez Noriega | National Autonomous University of Mexico | |
| Marianne Lalli | University of Helsinki | |
| Marie-Therese Fischer | University of Vienna | |
| Mertcan Esti | Max Planck Institute for Marine Microbiology | |
| Michael Dills | University of Tromsø - The Arctic University of Norway | |
| Mike Smykala | Carl von Ossietzky Universität Oldenburg | |
| Nathan Ernster | University of Innsbruck | |
| Nikita Rajkumari | Indian Institute of Science Education and Research Kolkata, In | ia |
| Nonsikelelo Precios Hlongwa | Stellenbosch University | |
| Paula García Martínez | King Abdullah University of Science and Technology | |
| Pedro Junger | Institut de Biologie de l’École Normale Supérieure (IBENS) | |
| Pranita Mishra | Max Planck Institute for Marine Microbiology | |
| Raïssa Meyer | Helmholtz Institute for Functional Marine Biodiversity at the Univ | rsity of Oldenburg (HIFMB) |
| Renato Gamba Romano | University of São Paulo / Oceanographic Institute | |
| Sabrin Abdelghany | ZMT Institute | |
| Samuel Huerten | ICBM - Carl von Ossietzky Universität Oldenburg | |
| Sergio Garcia Manogil Fernandez | IE University | |
| Shivang Pravin Bhanushali | University of Turku | |
| Shiyi Liu | Radboud University | |
| Siyu Mei | University of Groningen | |
| Thomas Klammsteiner | University of Innsbruck | |
| Vladimir Mikryukov | University of Tartu | |
| Xianghui Kong | Max Planck Institute for Marine Microbiology | |
| Xinyu Tang | Max Planck Institute for Marine Microbiology | |
| Yueqing Wang | Universität Bremen |