Welcome and Orientation
Conference Room A
Speaker: Ivica Dimkić and Đorđe Bajić
Introduction by organizers, workshop objectives, and participant
introductions.
About BiomeFUN 2025
Microbial communities promise to revolutionize many fields, from biotechnology and health to agriculture. Mathematical and computational modeling is key to fulfill this potential. In this workshop, we will learn techniques to quantitatively analyze, understand and engineer microbial communities and synthetic microbial consortia. We will cover a range of topics, from the analysis of metagenomic sequencing data, to building and simulating meta-genome-scale metabolic models and analyzing the function of synthetic consortia using cutting-edge statistical "structure-function landscape" methods.
What you will learn
- 16S and shotgun metagenomycs analysis
- Functional genomics, profiling and visualization
- Basic and advanced stoichiometric modeling with COBRA
- Meta-genome scale modeling of microbial communities
- Structure-function landscape modeling of microbial consortia
- Introduction to uses of machine learning in the field
Event Starts In:
Grants available!
Thanks to our main sponsor, the Federation of European Microbiological Societies (FEMS), we are thrilled to offer up to 10 grants - covering registration fee and accommodation - aimed at participants from low and middle income countries. Please state in your registration if you would like to apply for one of the grants!
1. Selection Criteria for FEMS Supported Participants
- Priority for FEMS-supported places will be given to PhD students and early-career postdoctoral researchers (within 5 years of PhD) working in microbiome analysis, SynCom communities and bioinformatics, or related fields.
- Selection will be based on a motivation letter with relevance of the workshop to the applicant’s current research, abstract and CV. Geographic and gender diversity will also be considered.
- Please note that the grants cover registration fee and accomodation. All participants are expected to cover their traveling expenses.
2. Criteria for selection of non-supported participants
- Scientists with a Masters degree or above who are currently involved in Life Science research/Industry are encouraged to apply.
Organizers
Speakers and teachers
Schedule
Day 1: Foundations in Bioinformatics and Data Processing
9:00 - 9:30
9:30 - 10:30
Metagenomic Sequencing Approaches for Microbial Communities
Conference Room A
Speaker: Marcel van den Broek
Introduction to sequencing methods (Illumina and long-read
technologies) and quality assessment techniques.
10:30 - 13:00
Practical 0.1: Python and R for Microbiome Analysis
Conference Room A
Speaker: Marcel van den Broek
Teaching: Katarina Kruščić
Basic programming skills tailored to microbiome data analysis,
covering essential syntax and data manipulation. Practical
exercises in sequence analysis and visualization.
Lunch Break
14:00 - 17:30
Practical 1.1: Data Import and Quality Filtering
Conference Room A
Speaker: Milan Dragićević and Alfonso Esposito
Teaching: Marcel van den Broek
Hands-on training using R/Python to import, preprocess, and
filter sequencing data.
Poster Session with Catering and Drinks
Conference Room B
Opportunity for participants to present their research and
network informally.
Day 2: Genome and Metagenome Analysis
9:00 - 12:00
Practical 1.2: Amplicon Data Analysis
Conference Room A
Speaker: Milan Dragićević
Teaching: Katarina Kruščić
Step-by-step processing and taxonomic classification of amplicon
sequencing data using bioinformatics tools.
12:00 - 13:00
Lecture Keynote
Conference Room A
Speaker: Alexandre Jousset
Lecture description
14:00 - 17:00
Shotgun Metagenomics and Functional Annotation
Conference Room A
Speaker: João Saraiva
Lecture on metagenomics for functional profiling and annotation
of microbial communities.
17:00 - 18:00
Practical 1.4: Metagenome Assembly and Functional Annotation
Conference Room B
Speaker: Alfonso Esposito
Hands-on training to assemble metagenomic data and annotate
functional genes within microbial communities.
Day 3: Genome and Metagenome Analysis
9:00 - 10:00
Functional Genomics
Conference Room A
Speaker: Gergely Maroti
Lecture on linking gene functions to overall community function,
using metagenomic and functional annotation tools.
10:00 - 13:00
Practical 1.5: Functional Profiling and Data Visualization
Conference Room A
Speaker: Gergely Maroti
Teaching: Katarina Kruščić
Hands-on work to visualize and interpret functional profiles
within microbial genomes and communities, focusing on
applications relevant to agriculture and environmental
microbiomes.
Lunch Break
14:00 - 15:00
Introduction to Stoichiometric Modeling of Metabolism
Conference Room A
Speaker: Timmy Paez Watson
Lecture covering foundational concepts in metabolic rates, mass
balances, and basic stoichiometric modeling.
15:00 - 18:00
Practical 2.1: Basic Stoichiometric Modeling
Conference Room B
Speaker: Timmy Paez Watson
Teaching: Minke Gabriels
Hands-on work on stoichiometric models.
Day 4: Genome and metagenome-scale metabolic modeling
9:00 - 10:00
COBRA and analysis of genome-scale metabolic models
Conference Room A
Speaker: Karel Olavarria
Theory of metabolic network models, focusing on community-wide
metabolic interactions and resource flows.
10:00 - 13:00
Practical 2.3. COBRA and analysis of genome-scale metabolic models
Conference Room A
Speaker: Karel Olavarria
Teaching: Minke Gabriels
Hands-on session using FBA to simulate microbial metabolic
networks and predict interspecies interactions.
Lunch Break
14:00 - 15:00
Metabolic modeling of microbial communities
Conference Room A
Speaker: Đorđe Bajić
Teaching: Minke Gabriels
Lecture on the application of metabolic modeling to microbial
communities.
15:00 - 18:00
Practical 2.4. Metabolic modeling of microbial communities
Conference Room B
Speaker: Đorđe Bajić
Teaching: Minke Gabriels
Hands-on work on the application of metabolic modeling to
microbial communities.
Day 5: Statistical approaches and AI for predicting and engineering microbial communities
9:00 - 10:00
Structure-Function Mapping for Microbial Consortia
Conference Room A
Speaker: Juan Diaz Colunga
Introduction to predictive models that map species composition
to community function, with applications in synthetic community
design.
10:00 - 13:00
Practical 3.1: Structure-Function Landscape Analysis and Prediction
Conference Room A
Speaker: Juan Diaz Colunga and Đorđe Bajić
Hands-on application of structure-function mapping to optimize
microbial communities for targeted functions in agriculture.
Lunch Break
14:00 - 15:00
Introduction to Machine Learning in Microbiome Science
Conference Room A
Speaker: Sascha Patz
Overview of machine learning applications in microbiome research
(no hands-on session).
Closing Discussion
Conference Room B
Reflection on workshop outcomes, future directions in microbiome
research, and opportunities for collaboration.
Closing Celebration with dinner and drinks
Register
Early Bird Registration
Regular/Professionals:
€350
Students and Early Career Scientists:
€250
Register before 30 June 2025
Regular Registration
Regular/Professionals:
€450
Students and Early Career Scientists:
€350
From 1 July to 1 August 2025
On-site Registration
Regular/Professionals:
€550
Students and Early Career Scientists:
€450
Important if you are applying to a fellowship:
Abstract, CV and motivation letter are required for fellowship applicants. Please submit these in the corresponding section in the registration form.
Abstract submission deadline: May 25
Abstract and grant status confirmation: May 30
What's included?
- 9 talks from leading experts in bioinformatics
- Access to 9 workshops
- Amazing after-parties
- Coffee & Snacks breaks, Lunches, Workshop dinner
- Visit to the Botanical Garden
- Certificate of attendance on course completion
- Materials and comprehensive resources, including access
to relevant datasets and online tools for extended learning
Venue
Hotel Palace
Adress: Topličin Venac 23, 11000 Belgrade
About Hotel
Palace Hotel Belgrade is located in the very heart of Belgrade, in the immediate vicinity of the main pedestrian area of Knez Mihailova Street. It has a very convenient location in a quiet part of the city, close to historical and cultural sights, city and state institutions, museums, theaters, cinemas, numerous shopping centers as well as Shkadarlija - the old bohemian quarter. It is intended for vacation both for business people and for those who travel for pleasure. Palace Hotel Belgrade is categorized as a 4-star hotel.
How To Get Here
By Bus
1. By Bus from Nikola Tesla Airport:
Take bus 72 from the airport and exit at the 'Brankov Most' station (about a 30-35 minute ride). From there, it's a 310-meter walk to the Palace Hotel.
2. By Minibus from Nikola Tesla Airport:
Alternatively, you can take minibus A1 from the airport and exit at the last stop, Slavija. From here, you have two options:
- Take a 15-minute walk through the city center to reach the hotel.
- Or, catch one of the following public transport options:
- Bus 31, Eco2, or trolley 29, and exit at 'Studentski Trg' station. The hotel is just a 2-minute walk from the station.
By Taxi
Alternatively, you can take a taxi from Nikola Tesla Airport. Please note that the ride should cost around €30. It’s recommended to discuss the price with the driver before you get in.
Contact
For any further information, feel free to contact us via our email!
Workshop email
Agency contact
For information about payment and invoice, please contact our agency "Impala"
+381-11-249-78-82
Adress
Toplicin Venac 23
11000 Belgrade
Sponsors & Partners
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