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News

S2M2 - Summer School in Metabolic Modeling (29 June - 3 July 2020) - 2nd Edition!!!

BioSystems group is organizing for the second time a 5-day course on metabolic modelling – Summer School in Metabolic Modeling. The course will cover the full process from model reconstruction to phenotype prediction using genome-scale metabolic models.
The focus of this course will be on user-friendly tools for genome-scale metabolic model reconstruction (merlin) and simulation (Optflux) as to introduce alternatives to improve those models with omics data integration.
See more at http://s2m2.bio.di.uminho.pt/


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A new tutorial is now available for merlin

We have implemented an extensive hands-on tutorial for merlin, which follows every step towards the reconstruction of a genome-scale metabolic model.
To access it, please click on the tutorial section on this website's upper navigation bar.


merlin version 4 will be released on 5th of November 2019

We are proud to announce that the latest version of merlin will be released on the 5th of November 2019, available for download in this website.


S2M2 - Summer School in Metabolic Modeling (3-7 June 2019)

BioSystems group is organizing a 5-day course on metabolic modelling – Summer School in Metabolic Modeling. The course will cover the full process from model reconstruction to phenotype prediction ns using genome-scale metabolic models. The focus of the course will be on user-friendly tools for metabolic model reconstruction (merlin) and simulation (Optflux) and to introduce experimental procedures to improve those models. See more at http://s2m2.bio.di.uminho.pt/
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tutorial available

A tutorial on Reconstructing high-quality large-scale metabolic models with merlin was published in:
Metabolic Network Reconstruction and Modeling: Methods and Protocols, Vol. Methods in Molecular Biology 1716, Springer, 2018. ISBN: 978-1-4939-7528-0, 1-36

merlin is now published

Dias, O., Rocha, M., Ferreira, E.C. and Rocha, I. (2015) Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Res., 10.1093/nar/gkv294.

TRIAGE is also published:

Dias, O., Gomes, D., Vilaca, P., Cardoso, J., Rocha, M., Ferreira, E., & Rocha, I. (2016). Genome-wide Semi-automated Annotation of Transporter Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics / IEEE, ACM, (1), 1–1. http://doi.org/10.1109/TCBB.2016.2527647