COBREXA.jl: constraint-based reconstruction and exascale analysis

SUMMARY: COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-s...

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Autores principales: Kratochvíl, Miroslav, Heirendt, Laurent, Wilken, St Elmo, Pusa, Taneli, Arreckx, Sylvain, Noronha, Alberto, van Aalst, Marvin, Satagopam, Venkata P, Ebenhöh, Oliver, Schneider, Reinhard, Trefois, Christophe, Gu, Wei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8796381/
https://www.ncbi.nlm.nih.gov/pubmed/34791064
http://dx.doi.org/10.1093/bioinformatics/btab782
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author Kratochvíl, Miroslav
Heirendt, Laurent
Wilken, St Elmo
Pusa, Taneli
Arreckx, Sylvain
Noronha, Alberto
van Aalst, Marvin
Satagopam, Venkata P
Ebenhöh, Oliver
Schneider, Reinhard
Trefois, Christophe
Gu, Wei
author_facet Kratochvíl, Miroslav
Heirendt, Laurent
Wilken, St Elmo
Pusa, Taneli
Arreckx, Sylvain
Noronha, Alberto
van Aalst, Marvin
Satagopam, Venkata P
Ebenhöh, Oliver
Schneider, Reinhard
Trefois, Christophe
Gu, Wei
author_sort Kratochvíl, Miroslav
collection PubMed
description SUMMARY: COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report the architecture of the package, and demonstrate how the design promotes analysis scalability on several use-cases with multi-organism community models. AVAILABILITY AND IMPLEMENTATION: https://doi.org/10.17881/ZKCR-BT30. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-87963812022-01-31 COBREXA.jl: constraint-based reconstruction and exascale analysis Kratochvíl, Miroslav Heirendt, Laurent Wilken, St Elmo Pusa, Taneli Arreckx, Sylvain Noronha, Alberto van Aalst, Marvin Satagopam, Venkata P Ebenhöh, Oliver Schneider, Reinhard Trefois, Christophe Gu, Wei Bioinformatics Applications Notes SUMMARY: COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report the architecture of the package, and demonstrate how the design promotes analysis scalability on several use-cases with multi-organism community models. AVAILABILITY AND IMPLEMENTATION: https://doi.org/10.17881/ZKCR-BT30. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-11-16 /pmc/articles/PMC8796381/ /pubmed/34791064 http://dx.doi.org/10.1093/bioinformatics/btab782 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Kratochvíl, Miroslav
Heirendt, Laurent
Wilken, St Elmo
Pusa, Taneli
Arreckx, Sylvain
Noronha, Alberto
van Aalst, Marvin
Satagopam, Venkata P
Ebenhöh, Oliver
Schneider, Reinhard
Trefois, Christophe
Gu, Wei
COBREXA.jl: constraint-based reconstruction and exascale analysis
title COBREXA.jl: constraint-based reconstruction and exascale analysis
title_full COBREXA.jl: constraint-based reconstruction and exascale analysis
title_fullStr COBREXA.jl: constraint-based reconstruction and exascale analysis
title_full_unstemmed COBREXA.jl: constraint-based reconstruction and exascale analysis
title_short COBREXA.jl: constraint-based reconstruction and exascale analysis
title_sort cobrexa.jl: constraint-based reconstruction and exascale analysis
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8796381/
https://www.ncbi.nlm.nih.gov/pubmed/34791064
http://dx.doi.org/10.1093/bioinformatics/btab782
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