Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities

Almut Heinken; Ines Thiele

doi:10.1093/bioinformatics/btac082

Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities

Almut Heinken
, Ines Thiele

Infectious Disease

Research output: Contribution to a Journal (Peer & Non Peer) › Article › peer-review

37 Citations (Scopus)

Abstract

Motivation: Constraint-Based Reconstruction and Analysis (COBRA) is a widely used approach for the interrogation and stratification of microbiome samples, yet applications to large-scale cohorts are hampered by limited scalability and efficiency of simulations. Results: We substantially improved the computation speed and scalability of a previous implementation for the construction and interrogation of personalized constraint-based microbiome models as well as implemented additional functionalities for analysis and visualization.

Original language	English
Pages (from-to)	2367-2368
Number of pages	2
Journal	Bioinformatics
Volume	38
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btac082
Publication status	Published - 15 Apr 2022

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abstract = "Motivation: Constraint-Based Reconstruction and Analysis (COBRA) is a widely used approach for the interrogation and stratification of microbiome samples, yet applications to large-scale cohorts are hampered by limited scalability and efficiency of simulations. Results: We substantially improved the computation speed and scalability of a previous implementation for the construction and interrogation of personalized constraint-based microbiome models as well as implemented additional functionalities for analysis and visualization.",

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N2 - Motivation: Constraint-Based Reconstruction and Analysis (COBRA) is a widely used approach for the interrogation and stratification of microbiome samples, yet applications to large-scale cohorts are hampered by limited scalability and efficiency of simulations. Results: We substantially improved the computation speed and scalability of a previous implementation for the construction and interrogation of personalized constraint-based microbiome models as well as implemented additional functionalities for analysis and visualization.

AB - Motivation: Constraint-Based Reconstruction and Analysis (COBRA) is a widely used approach for the interrogation and stratification of microbiome samples, yet applications to large-scale cohorts are hampered by limited scalability and efficiency of simulations. Results: We substantially improved the computation speed and scalability of a previous implementation for the construction and interrogation of personalized constraint-based microbiome models as well as implemented additional functionalities for analysis and visualization.

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Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities

Abstract

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