Please use this identifier to cite or link to this item: http://hdl.handle.net/1822/64082

Titlemerlin v4: an updated platform for reconstructing genome-scale metabolic models
Author(s)Lima, Diogo Batista
Lagoa, Davide Rafael Santos
Cruz, Fernando
Bastos, José
Capela, João
Ferreira, Eugénio C.
Rocha, Miguel
Dias, Oscar
Issue date2020
CitationLima, Diogo; Lagoa, D.; Cruz, Fernando; Bastos, J.; Ribeiro, João; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Oscar, merlin v4: an updated platform for reconstructing genome-scale metabolic models. BOD 2020 - IX Bioinformatics Open Days (Conference Book). Braga, Feb 19-21, 2020.
Abstract(s)The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) software is an open source user-friendly Java application developed for Windows and Unix, aimed towards the reconstruction of genome-scale metabolic models. The development of merlin follows a design philosophy of automating time-consuming steps in the reconstruction of genome-scale metabolic models, while allowing users to control the parameters of operations and manually curate the results. All major steps involved in the reconstruction of a metabolic model are implemented in merlin, including genome retrieval and its functional annotation, construction of the reactions set and associated entities, model compartmentalization and conversion to standard SBML formats. The fourth iteration of merlin includes a major overhaul of the user interface, implementation of new features, improvements to existing features, and most notably, the implementation of the object-relational mapping framework Hibernate. The graphical layout has been significantly streamlined, while supporting the latest version of AiBench, providing users with an intuitive and responsive interface. Development was also focused at new quality of life improvements, aimed mainly towards importing, exporting and duplicating merlin user projects. The development of the latest version of merlin followed a modular approach, culminating in the implementation of a plugin manager which simplifies and hastens the process of updating and debugging the various features of merlin. In addition, TranSyT, a state-of-the-art genome-wide transmembrane transport system annotation tool has been implemented to overcome the limitations of the previously available TRIAGE module. Finally, it is noteworthy to mention the implementation of BioISO, a tool aimed at evaluating a genome-scale metabolic network or biomass formulation, based on the previously available COBRA and FBA frameworks.
TypeAbstract
URIhttp://hdl.handle.net/1822/64082
Publisher versionhttp://www.bioinformaticsopendays.com/
Peer-Reviewedyes
AccessOpen access
Appears in Collections:CEB - Resumos em Livros de Atas / Abstracts in Proceedings

Files in This Item:
File Description SizeFormat 
document_53523_1.pdf514,36 kBAdobe PDFView/Open
document_53523_2.pdf427,82 kBAdobe PDFView/Open

Partilhe no FacebookPartilhe no TwitterPartilhe no DeliciousPartilhe no LinkedInPartilhe no DiggAdicionar ao Google BookmarksPartilhe no MySpacePartilhe no Orkut
Exporte no formato BibTex mendeley Exporte no formato Endnote Adicione ao seu ORCID