Summer School in metabolic modeling



The course will be held at the Campus of Gualtar, University of Minho, Braga (Portugal). Although we strongly suggest in person participation, online attendance will also be available.


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



The course will introduce state-of-the-art metabolic modelling 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. Applications include metabolic engineering, plant and health sciences.

The course will last 8 days (with a free day in the middle). Each day will be divided into a theoretical morning session and practical afternoon sessions, also featuring a social program. The morning lectures will be guided by an expert in the field that will present background information, key concepts, algorithms and computational tools. Afternoon 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. Participants will have some time to prepare their own projects, to be presented in the final session.

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, an optional session is included in the first day covering a simple introduction to python. This session may be needed for the ones less familiar with python-based tools.

The course faculty have expertise in metabolic model reconstruction, constrained based modelling, 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, 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.


Oscar Dias
Assistant Researcher @CEB UMinho
Miguel Rocha
Associate Professor with Habilitation @DI UMinho
Senior Researcher @CEB UMinho
Isabel Rocha
Vice-Rector @Nova
Senior Researcher @CEB UMinho

Invited Speakers

Registration - Deadlines - Fees


Early Registration Regular Registration Late Registration
Student* 250€ 300€ 350€
Academia** 350€ 400€ 450€
Industry** 450€ 500€ 550€
Early Registration Regular Registration Late Registration
Student* 200€ 250€ 300€
Academia** 300€ 350€ 400€
Industry** 400€ 450€ 500€

* Student registrations will include access to all course materials and sessions (online or on-site). If attending in person, registrations also include coffee breaks and the welcome reception. Note that, a student proof will be requested upon registration.

** Academia and industry registrations will include access to all course materials and sessions (online or on-site). If attending in person, registrations also include coffee breaks, the welcome reception and the course dinner.


Early Registration: April 30th
Regular Registration: May 31st
Late Registration: June 9th



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 10 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

Travel & Accommodation

How to reach the venue

The venue will be held at the Department of Informatics in the University of Minho - Campus of Gualtar. The Campus of Gualtar of the University of Minho is located at: Rua da Universidade, 4710 - 057 Braga, Portugal.

The Department of Informatics corresponds to the building 07 of the Campus of Gualtar. You can see the campus map here: Campus of Gualtar. The following coordinates refer to the Department of Informatics: 41.56131, -8.393804.

The sessions will be held in the room 1.10 (in the first floor) of the Department of Informatics.

How to reach the University of Minho - Campus of Gualtar

By Plane

The Airport of Porto (Sá Carneiro Airport) is the nearest airport of the venue. This airport is located in Porto (OPO), about 50 Km away from the venue. From the airport, one can take the metro line E (violet) direction Aeroporto to Estádio do Dragão. You should take the Campanhã train station exit. There are several trains to Braga that depart from this station. Alternatively, getBUS provides a direct bus service between the airport and Braga's train station.

Sá Carneiro Airport Phone: + 351 229 432 400

Porto Metro Phone: +351 225 081 000

getBUS Phone: +351 253 262 371

By Bus

Please consult one of the following public bus operators:

Transdev Phone: +351 213 581 460

Phone: +351 253 264 693

Rodonorte Phone: +351 259 340 710

By Train

Information on the available rail lines to get to Braga and train schedules may be found at The train station in Braga is a 15 minutes bus trip away from the Gualtar campus. Bus service is provided by Transportes Urbanos de Braga (TUB).

By TUB (public transports of Braga)

If you choose to travel by plane, bus or train, your destination will either be the city's coach station or the train station. To reach the Gualtar campus, you can opt to travel by bus, using the services provided by Transportes Urbanos de Braga (TUB). These buses run about every 15 minutes. Timetables and more information: Phone: +351 253 606 890


Hotel Meliá ***** Located just minutes from downtown Braga and the University of Minho. Web: Phone: +351 253 144 000 E-mail:

B&B Hotel Braga Lamaçães *** Located near the University of Minho, the Iberian Nanotechnology Centre, and a 5 minutes drive from Braga's historic center. Web: Phone: +351 253 603 680 E-mail:

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