ArticleNature protocols2021
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS).
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers, 1 of them a synthesis that pooled it.
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Who cites it
96 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Principles for Rigorous Design and Application of Synthetic Microbial Communities.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Pooled it
- The cervicovaginal gut microbiota axis as a key determinant of systemic physiology.Gut microbes · 2026Review
- Process bigraphs and the architecture of compositional systems biology.PLoS computational biology · 2026Article
- Systems engineering of engineered live biotherapeutics: A discovery-to-translation framework for streamlining microbiome therapeutic development.Journal of controlled release : official journal of the Controlled Release Society · 2026Review
- Article
- Metabolic feedbacks drive population dynamics and can lead to oscillations among leaf bacteria.Nature communications · 2026Article
- Dynamical Systems-Constrained Metabolic Modeling Enables Forecasting of Host-Microbiome Dynamics.bioRxiv : the preprint server for biology · 2026Article
- Stochastic Forces in Microbial Community Assembly: Founding Community Size Governs Divergent Ecological Trajectories.Ecology letters · 2026Article
- Microbial biotechnology meets ecological theory: a unified framework to design industrial microbial consortia.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Review
- Predictive multispecies constraint-based metabolic modeling: case studies and best practices.Briefings in bioinformatics · 2026Review
- Interplay of Spatial Structure and Interactions in Microbial Communities.Environmental microbiology · 2026Review
- Receptor-Mitochondria Crosstalk in the Kynurenine Metabolic Pathway: Integrating Metabolomics and Clinical Mass Spectrometry.Antioxidants (Basel, Switzerland) · 2026Review
- Whole-cell modeling predicts alternative proteome allocation strategies in the archaeon Methanococcus maripaludis.Scientific reports · 2026Article
- Dynamic metabolic modelling of ATP allocation during viral infection.Journal of the Royal Society, Interface · 2026Article
- Flux sampling and context-specific genome-scale metabolic models for biotechnological applications.Trends in biotechnology · 2026Review
- Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling.Nature communications · 2026Article
- Carbon substrate type shapes spatial self-organization in a multi-species biofilm community.The ISME journal · 2026Article
- Spatial structure: shaping the ecology and evolution of microbial communities.FEMS microbiology reviews · 2026Review
- Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.Gut microbes reports · 2026Review
- Synergistic Regulation of Alzheimer's Disease and Intestinal Microbiota Metabolism Mediated by the Gut-Brain Axis: A Comprehensive Analysis from a Multidisciplinary Perspective.International journal of medical sciences · 2026Review
36 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
Abstract
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. This protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.