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cellsarts
(2026-04-30 23:00):
#paper Thiele Bioinformatics (Oxford, England)DOI:10.1093/bioinformatics/bty9412019-07-01
摘要:动机：迄今为止，基于约束的建模在功能分析宏基因组数据方面的应用一直受到限制，部分原因在于缺乏合适的工具箱。结果：为填补这一空白，我们开发了一套全面的工具箱，用于构建（i）微生物间及宿主-微生物之间的代谢互作模型，以及（ii）利用微生物基因组规模代谢重建和宏基因组数据对微生物群落进行建模。该微生物组建模工具箱扩展了基于约束的重建与分析工具箱的功能。可用性和实现：微生物组建模工具箱及相关教程请访问Bioinformatics (Oxford, England)DOI:10.1093/bioinformatics/bty9412019-07-01 Motivation: The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes. Results: To address this gap, we created a comprehensive toolbox to model (i) microbe-microbe and host-microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox. Availability and implementation: The Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.
Bioinformatics,
2019-7-1.
DOI: 10.1093/bioinformatics/bty941
Federico Baldini,
Almut Heinken,
Laurent Heirendt,
Stefania Magnusdottir,
Ronan M T Fleming,
Ines Thiele
Abstract:
Abstract
Motivation
The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.
Results
To address this gap, we created a comprehensive toolbox to model (i) microbe–microbe and host–microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox.
Availabili… >>>
Motivation
The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.
Results
To address this gap, we created a comprehensive toolbox to model (i) microbe–microbe and host–microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox.
Availabili… >>>
Abstract<br> <br> Motivation<br> The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.<br> <br> <br> Results<br> To address this gap, we created a comprehensive toolbox to model (i) microbe–microbe and host–microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox.<br> <br> <br> Availability and implementation<br> The Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.<br> <<<