Edition 2019

Check the course poster here.

Early bird extended until May 5th.


The course is tailored for PhD students and post-docs interested in metabolic modelling, using user-friendly tools.
No programming skills are required. Attendance is limited to 20.

Course Overview

The course will introduce state-of-the-art metabolic modelling covering the full process from model reconstruction to phenotype predictions using those models. The course will focus on user-friendly tools for metabolic model reconstruction and simulation and experimental procedures to improve those models.

The course will have a five-day duration, each day divided between morning sessions with theory and afternoon sessions with practical work. The morning lectures will be guided by an expert in the field that will present background information, key concepts, computational tools, and experimental methods. The morning lecture modules will be followed by a meet the speaker time during the coffee break or lunch. Afternoon sessions will be dedicated to extensive practical work in wet and/or dry lab.

The course faculty have expertise in metabolic model reconstruction, constrained based modelling, metabolomics and experimental procedures to improve metabolic models prediction capabilities.


The modelling component will cover reconstruction and simulation of constraint-based steady-state models. Experimental techniques will include experimental procedures for biomass composition determination and metabolomics as well as the integration of these data in metabolic models.


Learning Outcomes

The course is prepared to offer participants the opportunity to have a hands-on experience of all steps to construct a genome-scale metabolic model – from genome to a complete model and also validate the model with experimental data. The combination of computational methods with wet-lab experiments will offer the participants an all-around experience to the main tools and methods used to go from hypothesis to the lab bench and back.

Course main topics

Genome annotation and of metabolic models reconstruction with merlin.

KBase: A collaborative, open environment for systems biology of plants, microbes and their communities.

Optflux: an open-source software platform for in silico metabolic engineering.

Experimental determination of biomass composition and its inclusion in genome-scale metabolic models.

Experimental metabolomics analysis using GC-MS.

Confirmed Speakers

Oscar Dias
Invited Assistant Professor/Researcher @CEB UMinho
Invited Assistant Professor@DEB
Sophia Santos
PhD Student@CEB UMinho
Doctoral Program MIT Portugal Program | Bioengineering Systems
Miguel Rocha
Associate Professor with Habilitation @DI UMinho
Senior Researcher @CEB UMinho
Isabel Rocha
Pro-Rector @Nova
Senior Researcher @CEB UMinho
Paulo Maia
Head of development @SilicoLife
José Pedro Faria
Postdoctoral Appointee @Argonne National Laboratory on the @KBase program
Sonia Carneiro
Head of Development @SilicoLife
Rafael Carreira
Head of Development @SilicoLife

Registration Fees

(include admission, conference materials, meals and coffee breaks)
Early Registration Registration Late Registration
Academia 450€ 550€ 650€
PhD Student 350€ 450€ 550€
Industry 600€ 700€ 800€
  • Early Registration: April 30th
  • Registration: May 17th
  • Late Registration: May 24th

          Participants are expected to book and pay their own accommodation and travel expenses.


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

Payment by Bank Transfer: details 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 in the description/reason of your transfer your Full Name.

Registration form here.

Travel & Accommodation


How to reach the venue


From the Sá Carneiro Airport

The nearest airport is the Sá Carneiro Airport, located in Porto, about 50 km away.
From the airport, take the E metro line (violet): Aeroporto – Estádio do Dragão, to reach the Campanhã train station. Several trains to Braga depart from this station.
Alternatively, getBUS provides a direct bus service between the airport and the Braga coach station.


Sá Carneiro Airport
Phone: + 351 229 432 400

Porto Metro
Phone: +351 225 081 000

Phone: +351 253 262 371


By Coach

Phone: +351 213 581 460

Phone: +351 253 264 693

Phone: +351 259 340 710


By Train

Information on the available rail lines to get to Braga and train schedules may be found at www.cp.pt.
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).


Public transport in 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: www.tub.pt/
Phone: +351 253 606 890




Hotel Meliá *****
Located just minutes from downtown Braga and the University of Minho.
Web: www.melia.com/pt
Phone: +351 253 144 000
E-mail: melia.braga@meliaportugal.com

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