ORCID Profile
0000-0001-9494-3410
Current Organisations
Universidade Nova de Lisboa
,
Soluções Inovadoras de Base Biológica para Proteção de Culturas
,
Silicolife
,
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica
,
Madan Parque
,
Laboratório Colaborativo para as Biorrefinarias
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Publications
MEMOTE for standardized genome-scale metabolic model testing
Publisher: Springer Science and Business Media LLC
Date: 03-2020
Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
Publisher: Cold Spring Harbor Laboratory
Date: 21-06-2018
DOI: 10.1101/350991
Abstract: Several studies have shown that neither the formal representation nor the functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability of models across groups and software tools cannot be guaranteed. Here, we present memote ( pencobra/memote ) an open-source software containing a community-maintained, standardized set of me tabolic mo del te sts. The tests cover a range of aspects from annotations to conceptual integrity and can be extended to include experimental datasets for automatic model validation. In addition to testing a model once, memote can be configured to do so automatically, i.e., while building a GEM. A comprehensive report displays the model’s performance parameters, which supports informed model development and facilitates error detection. Memote provides a measure for model quality that is consistent across reconstruction platforms and analysis software and simplifies collaboration within the community by establishing workflows for publicly hosted and version controlled models.
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
Publisher: Springer Science and Business Media LLC
Date: 19-03-2020
DOI: 10.1038/S41587-020-0477-4
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Related Organisations
Universidade Do Minho Centro De Engenharia Biológica
Location: Portugal
Soluções Inovadoras De Base Biológica Para Proteção De Culturas
Location: Portugal
Universidade Nova De Lisboa Nova School Of Business And Economics
Location: Portugal
Universidade Nova De Lisboa Instituto De Tecnologia Química E Biológica
Location: Portugal
Laboratório Nacional De Ciência E Tecnologia Do Bioetanol
Location: Brazil
Related Funding Activities
No related grants have been discovered for Isabel Rocha.