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[[Image:merlin.png|center|500px|link=Home]]
 
[[Image:merlin.png|center|500px|link=Home]]
==News==
 
  
=== ''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.
 
  
<br>
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==Latest news==
===S2M2 - Summer School in Metabolic Modeling (3-7 June 2019)===
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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/ http://s2m2.bio.di.uminho.pt/]<br>
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===S2M2 - Summer School in Metabolic Modeling (29 June - 3 July 2020) - 2nd Edition!!!===
[[File:Banner.png|frameless|800px]]<br>
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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. <br>
===tutorial available===
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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. <br>
A tutorial on Reconstructing high-quality large-scale metabolic models with <i>merlin</i> was published in:<br>
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See more at [http://s2m2.bio.di.uminho.pt/ http://s2m2.bio.di.uminho.pt/]
[http://dx.doi.org/10.1007/978-1-4939-7528-0_1 Metabolic Network Reconstruction and Modeling: Methods and Protocols, Vol. Methods in Molecular Biology 1716, Springer, 2018. ISBN: 978-1-4939-7528-0, 1-36]<br>
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===''merlin'' is now published===
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[http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv294 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.]<br>
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[[File:s2m2_2020.png|frameless|800px]]
===''TRIAGE'' is also published:===
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[http://dx.doi.org/10.1109/TCBB.2016.2527647 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]
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=== A new tutorial is now available for ''merlin''===
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We have implemented an extensive hands-on tutorial for ''merlin'', which follows every step towards the reconstruction of a genome-scale metabolic model. <br>
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To access it, please click on the tutorial section on this website's upper navigation bar.
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==''merlin''==
 
==''merlin''==
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[[File:reconstruction.png|frameless|800px]]
 
[[File:reconstruction.png|frameless|800px]]
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==Ongoing work==
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We are currently working on the following features and will release a new version of '''''merlin''''' in the near future:
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* Integration of ''modelSEED'' metabolic data.
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* Integration of ''BIGG'' metabolic data.
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* Development of a plugin towards the integration of regulatory data.
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== Getting started ==
 
== Getting started ==
* [https://www.merlin-sysbio.org/index.php?title=tutorial How to use merlin]
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* [https://www.merlin-sysbio.org/tutorial.html How to use merlin]
 
* [https://www.merlin-sysbio.org/index.php?title=downloads Downloading merlin]
 
* [https://www.merlin-sysbio.org/index.php?title=downloads Downloading merlin]
 
==Screenshots==
 
 
<gallery mode="packed-overlay">
 
Image:Genes.JPG|''model genes panel''
 
Image:Proteins.JPG|''model proteins panel''
 
Image:metabolites.JPG|''model metabolites panel''
 
Image:reactions.png|''model reactions panel''
 
Image:pathway.JPG|''model pathways panel''
 
Image:enzymes.png|''enzymes annotation panel''
 
Image:transporters.JPG|''transporters annotation panel''
 
Image:compartments.JPG|''comparmtents annotation panel''
 
</gallery>
 

Latest revision as of 17:51, 21 January 2020

Merlin.png


Latest 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/


S2m2 2020.png


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

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


Ongoing work

We are currently working on the following features and will release a new version of merlin in the near future:

  • Integration of modelSEED metabolic data.
  • Integration of BIGG metabolic data.
  • Development of a plugin towards the integration of regulatory data.


Getting started