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News

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

BioSystem 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/

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

merlin

merlin is a simple, graphical and user-oriented solution for the reconstruction of genome-scale metabolic models.

It will guide you along the model reconstruction, providing several tools that help to improve and curate the model throughout the whole process.

Reconstruction.png

Getting started

Screenshots