1) La descarga del recurso depende de la página de origen
2) Para poder descargar el recurso, es necesario ser usuario registrado en Universia


Opción 1: Descargar recurso

Opción 2: Descargar recurso

Opción 3: Descargar recurso

Detalles del recurso

Descripción

Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent model s result from "a la carte" pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction. Although very useful, introducing heterogeneous tools, that hardly interact with each other, causes loss of traceability and reproducibility in the reconstruction process. This represents a real obstacle, especially when considering less studied species whose metabolic reconstruction can greatly benefit from the comparison to good quality models of related organisms. This work proposes an adaptable workspace, AuReMe, for sustainable reconstructions or improvements of genome-scale metabolic models involving personalized pipelines. At each step, relevant information related to the modifications brought to the model by a method is stored. This ensures that the process is reproducible and documented regardless of the combination of tools used. Additionally, the workspace establishes a way to browse metabolic models and their metadata through the automatic generation of ad-hoc local wikis dedicated to monitoring and facilitating the process of reconstruction. AuReMe supports exploration and semantic query based on RDF databases. We illustrate how this workspace allowed handling, in an integrated way, the metabolic reconstructions of non-model organisms such as an extremophile bacterium or eukaryote algae. Among relevant applications, the latter reconstruction led to putative evolutionary insights of a metabolic pathway.

Pertenece a

ArchiMer, Institutional Archive of Ifremer (French Research Institute for Exploitation of the Sea)  

Autor(es)

Aite, Meaziane -  Chevallier, Marie -  Frioux, Cleamence -  Trottier, Camille -  Got, Jeanne -  Paz Cortes, Maria -  Mendoza, Sebastian N. -  Carrier, Gregory -  Dameron, Olivier -  Guillaudeux, Nicolas -  Latorre, Mauricio -  Loira, Nicolas -  Markov, Gabriel V. -  Maass, Alejandro -  Siegel, Anne - 

Id.: 71517674

Idioma: eng  - 

Versión: 1.0

Estado: Final

Tipo:  application/pdf - 

Tipo de recurso: Texto Narrativo  -  Publication  -  info:eu-repo/semantics/article  - 

Tipo de Interactividad: Expositivo

Nivel de Interactividad: muy bajo

Audiencia: Estudiante  -  Profesor  -  Autor  - 

Estructura: Atomic

Coste: no

Copyright: sí

: 2018 Aite et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Formatos:  application/pdf - 

Requerimientos técnicos:  Browser: Any - 

Relación: [IsBasedOn] Plos Computational Biology (1553-7358) (Public Library Science), 2018-05 , Vol. 14 , N. 5 , P. e1006146 (25p.)

Fecha de contribución: 07-jul-2018

Contacto:

Localización:
* DOI:10.1371/journal.pcbi.1006146

Otros recursos de la mismacolección

  1. A global perspective on the trophic geography of sharks Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the...
  2. Constraints and Priorities for Conducting Experimental Exposures of Marine Organisms to Microplastics Marine plastic pollution is a major environmental issue. Given their ubiquitous nature and small dim...
  3. Report of the Working Group on Ballast and Other Ship Vectors (WGBOSV), 5-7 March 2018 Madeira, Portugal
  4. French phytoplankton monitoring: an exploration of optimum data presentation Different ways are explored for presenting 12 years of data on phytoplankton species and toxins in s...
  5. Variation in occupancy and habitat use of Mobula alfredi at a major aggregation site Understanding variations in habitat use through time contributes to identification of habitats criti...

Aviso de cookies: Usamos cookies propias y de terceros para mejorar nuestros servicios, para análisis estadístico y para mostrarle publicidad. Si continua navegando consideramos que acepta su uso en los términos establecidos en la Política de cookies.