March 27 – April 1, 2026

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This workshop is part of a series of international collaborative events in Chile and seeks to foster fresh dialogue on metabolic research in prokaryotes and eukaryotes from systems biology and bioinformatics perspectives. It will bring together experts in genome-scale metabolic network reconstruction and mathematical analysis of such networks, alongside biologists from diverse fields with interests in single-species and community metabolism.

The Workshop comprises two activities:

1) A three-session course on Friday, March 27, on modern methods to construct genome-scale and metagenome-scale metabolic models, and on classical and non‑classical analysis approaches. Venue: John Von Neumann Seminar Room, Center for Mathematical Modeling, University of Chile, Beauchef 851, 7th Floor, North Building.

2) A Conference on March 30–April 1 by specialists in bioinformatics, systems biology, metabolic engineering, and biology, presenting diverse perspectives on the study of metabolism. Venue: Hotel Terraviña, Santa Cruz, Chile.

 Organizing Committee

• Mauricio Latorre, Universidad de O’Higgins – Chile
• Alejandro Maass, Universidad de Chile – Chile

Programs

I. Course: An introduction to genome scale metabolic reconstructions and mathematical analysis – March 27

9:00-10:00 Part I: Genome-scale metabolic analysis and reconstruction: Fundamental theory and applications. Genome-scale metabolic models are structures widely used to compute cellular phenotypes of diverse species. In this session, we will review what genome-scale metabolic models are and the theory behind Flux Balance Analysis (FBA). In addition, we will review some applications of genome-scale metabolic models ranging from internal flux distribution predictions to biological discovery. Finally, we will review the main paradigm used to build genome-scale metabolic models, as well as the different tools and databases used to build them.

10:00-10:30 Coffee Break

10:30-11:30 Part II: Discrete Metabolic Modeling: Exploring Metabolism from Species to Communities.  Metabolic models enable the simulation of cellular metabolism based on metabolic network structure and environmental conditions. One simple approach is network expansion, which assesses the reachability of metabolites starting from a set of available nutrients, referred to as seeds. In this course, the principles of network expansion as a Boolean abstraction of metabolite producibility will be introduced, along with several related discrete modelling frameworks. Through illustrative examples, participants will explore the computation of reachable metabolites in individual species, the prediction of metabolic complementarity within microbial communities, the selection of minimal communities to achieve a targeted metabolic function, and the inference of growth media requirements.

11:30-12:00 Coffee Break

12:00-13:00 Part III: Advanced uses of genome-scale metabolic models: finding minimal nutritional requirements and simulating microbial communities. In this section, we will review some advanced uses of genome-scale metabolic models. We will review the mathematical formulation of Mixed-Integer Linear Programming problems, and we will apply this to find minimal nutritional requirements and enumerate alternative media formulations with minimal cardinality. In addition, we will review the mathematical formulation to simulate microbial communities growing in steady-state community FBA (cFBA) and how to use this formulation to quantify microbial interactions.

II. Conference Metabolic Club III – March 30 to April 1

Talks Titles:

1. Marianne Buscaglia (CMM): Exploring the metabolic potential of prokaryotic communities in the Chilean coast.
2. Olivia Bulka (INRIA-Bordeaux): Metabolic modelling of non-cultivated pathogenic bacteria.
3. Francisco Cubillos (USACH): Deciphering the secrets of local beverages.
4. Clémence Frioux (INRIA-Bordeaux): Exploration of metabolism in microbial communities with computational models.
5. Mauricio Latorre (UOH): Biotechnolomics – A high-throughput, optimized platform for large-scale identification of biotechnological potential in microbial collections.
6. Alejandro Maass (CMM-CRG-UChile): Exploring the space of metabolic fluxes.
7. Sebastián Mendoza y Diego Núñez (CMM): Metabolic studies of pork cells for cultivated meat production.
8. Coralie Muller (INRIA-Bordeaux): Towards the generation of metabolomic-informed models of metabolism in complex microbial communities.
9. Valentina Parra (UChile): Pulmonary Hypertension to Cardiometabolic Disease: Systems Biology Insights into Estrogen-Driven Metabolic Network. Remodeling.
10. Lorena Pizarro (UOH): Tomato–Soil Microbiome Interactions: Linking Microbial Community Structure with Soil Biochemical Functions.
11. Pedro Saa (PUC): Convenient linear representations of the steady-state flux space for metabolic network modeling.
12. Anne Siegel (CNRS): Screening metabolic network to suggest specificities in bacterial pathway synthesis or metabolic complementarities.

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Date: Monday January 13, 2025

Continuing the series of international collaborative events held in Chile, this event aims to foster discussion on new ideas in the fields of Systems Biology and Bioinformatics. Through the development of novel questions and tools, we hope to deepen the understanding of the metabolism of microbial communities from diverse environments.

Particular emphasis will be given to methods and communities studied in the context of the project “INRIA Associated Team: SymBioDiversity: Symbolic and numerical mining and exploration of functional biodiversity” and “SYSTEMIX: Systems Biology Center for the study of the extremophile communities from mining tailings”.

Venue:

Classroom E301, Building E, Rancagua Campus, Universidad de O’Higgins, Av. Libertador Bernardo O’Higgins 611, Rancagua.

Organizing Committee

• Mauricio Latorre, Universidad de O’Higgins – Chile
• Alejandro Maass, Universidad de Chile – Chile

Program

9:00 – 9:30 Mauricio Latorre: “Structure, Interaction and Metabolism from Microbial Communities living in Heavy Metal Environments”

9:40 – 10:10 Anne Siegel: “What can we say from taxonomic affiliation : from metabolic functions to classification”

10:15 – 10:45 Coffee break

10:45-11:15 Sebastián Mendoza: “Enumerating minimal medium compositions to sustain metabolic activities from microbial communities growing at stead-state: a MILP perspective”

11:20-11:40 Clémence Frioux: “Exploring the metabolism of microbial communities with discrete models”

12:45 – 14:45 LUNCH

15:00 – 17:00 Working Groups

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Date: January 12 and 16, 2024

The aim of this workshop is to discuss on modern techniques to analyze the metabolic capacity of organisms and communities. Some topics to be included: genome scale metabolic reconstruction, flux analyses, metabolic response to environment, etc.

Venue:

Seminar Room
Department of Mathematical Engineering
University of Chile
North Building, 5th floor
Beauchef 851, Santiago

Organizing Committee

• Vicente Acuña, Universidad de Chile
• Alejandro Maass, Universidad de Chile
• Sebastián Mendoza, Universidad de Chile

Program

Friday, January  12, 2023

09:45 – 10:00 Reception

10:00 – 11:00 Anne Siegel: “Study and Comparisons of metabolic maps : adapt to the triptych of knowledge – data – scaling up”

11:00 – 11:30 Coffee break

11:30 – 12:30 Daniel Garrido: “Modeling metabolic interactions in the gut microbiome: insights into HMO utilization and butyrate production”

12:30 – 14:30 LUNCH

14:30 – 15:30 Álvaro Altamirano: “Development of computational methods for predicting metabolic interactions in microbial consortia”

15:30 – 16:00 Coffee break

16:00 – 17:00 Clémence Frioux: “Exploration of microbial ecosystems: from compositional patterns to dynamic metabolic models” (slides)

Tuesday, January 16, 2023

09:15 – 09:30 Reception

09:30 – 10:15 Yann Le Cunff: “Prior knowledge and Machine Learning : Predicting enzyme functions and analyzing patients’ microbiota”

10:30 – 11:15 Natalia Jimenez: “What’s the objective? Applications of genome-scale models: from quantitative to qualitative and everything in between”

11:30 – 12:15 Marianne Buscaglia: “Exploring the diversity and adaptations of giant viruses in cold marine environments”

12:30 – 14:30 LUNCH

14:30 – 15:15 Vicente Acuña: “Unveiling abundance-dependent metabolic phenotypes of a community”

15:30 – 16:15 Chabname Ghassemi: “Towards culturing the unculturable: logic and linear programming for seed identification in metabolic networks”

16:30 – 17:15 Sebastián Mendoza: “CF-dFBA and End-Point-Optimization: Novel methods to simulate microbial communities’ dynamics and predict cross-feeding metabolites”

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