Summer School in metabolic modeling



The course will be conducted exclusively online, providing participants the flexibility to attend remotely.


The course is tailored for PhD students, post-docs, researchers and other professionals in industry that may be interested in metabolic modeling. The audience is limited to 24 in total.



The course will introduce state-of-the-art metabolic modeling covering the full process from model reconstruction to phenotype predictions and analysis. The course will focus on metabolic model reconstruction, phenotype simulation, integration with omics data and strain optimization, including both unicellular microbes and more complex organisms, such as plants and humans, as well as microbial communities. Applications include metabolic engineering, plant sciences and human health.

The course will last 5 days (with a weekend in the middle). Each morning and afternoon will have theoretical and practical hands-on sessions. The lectures will be guided by an expert in the field that will present background information, key concepts, algorithms and computational tools. Hands-on sessions will be dedicated to extensive in silico practical work. Most days will close with a talk reflecting the different applications of metabolic modeling, both in academy and industry.

The course will focus on the use of both user-friendly software tools and python-based tools (using Jupyter Notebooks). Hence, whilst no programming skills are required, a set of introductory videos are provided before the course covering a simple introduction to python. These may be helpful for the ones less familiar with python-based tools.

The course faculty have expertise in metabolic model reconstruction, constrained based modeling, strain optimization, and omics data integration.

Learning Outcomes

The course is prepared to offer participants the opportunity to have a hands-on experience of all computational steps to reconstruct a genome-scale metabolic model – from genome to complete and validated metabolic model. Participants will also have a hands-on experience of the main methodologies for flux analysis, phenotype simulation and in silico strain optimization. In addition, this course will also offer advanced topics for combining omics data into metabolic models.

The course will offer the participants an all-around experience to the main computational tools and methods used in metabolic modeling.

Course main topics

  • Genome annotation and reconstruction of metabolic models using merlin. Check out merlin for more details.

  • Flux analysis, phenotype simulation and strain optimization using OptFlux, COBRApy and MEWpy. Check out OptFlux, COBRApy, and MEWpy for more details.

  • Analysis and integration of omics data and into genome-scale metabolic models, using Troppo. Check out Troppo for more details.

  • Novel modeling paradigms including protein allocation constraints, transcription/ translation and regulatory interactions, community modeling tools, using MEWpy. Check out MEWpy for more details.

  • (Optional) An hands-on introduction to Python and Jupyter Notebooks covering the main skills needed for the remaining of the course.


Miguel Rocha
Associate Professor with Habilitation
@DI UMinho
Senior Researcher @CEB UMinho
Isabel Rocha
Vice-Rector @Nova
Senior Researcher @CEB UMinho
Oscar Dias
Assistant Researcher @CEB UMinho
Sofia Ferreira
Postdoctoral Researcher
Lucas Carvalho
Assistant Professor
José Pedro Faria
Assistant Computational Biologist @Argonne National Laboratory on the @KBase program

Invited Speakers

Registration - Deadlines - Fees


Early Registration Regular Registration Late Registration
Student* 245€ 270€ 295€
Academia** 345€ 370€ 395€
Industry** 445€ 470€ 495€

* Student registrations will include access to all course materials and sessions. Note that, a student proof will be requested upon registration.

** Academia and industry registrations will include access to all course materials and sessions.


Early Registration: May 25th
Regular Registration: June 21st
Late Registration: June 28th



Your application can only be accepted after we have received the payment of the registration fee in our bank account. Please note that we can only accept bank transfer payments. Payment by Credit Card is not possible.

The details for the payment by bank transfer will be sent in your ‘application confirmation email’. Bank charges are the responsibility of the participant and should be paid at source. Payment must be placed right after the registration process within 15 days.

To have your bank transfer payments processed correctly, please include the full name of the person who is attending the course in the description/reason of the bank transfer. The proof of the bank transfer payment should be sent to

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