ArticlePloS one2020
The Community Simulator: A Python package for microbial ecology.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Cross-feeding enables robust coexistence between four bacterial species.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Eco-evolutionary dynamics lead to functionally robust and redundant communities.PLoS computational biology · 2026Article
- Physics-constrained neural ordinary differential equation models to discover and predict microbial community dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia.bioRxiv : the preprint server for biology · 2026Article
- N2SIMBA: from Network topology to SIMulation of interactions and BActerial abundance, using microbial consumer resource model.Frontiers in bioinformatics · 2026Article
- Article
- Metabolic complexity drives divergence in microbial communities.Nature ecology & evolution · 2024Article
- Phase Transition to Chaos in Complex Ecosystems with Nonreciprocal Species-Resource Interactions.Physical review letters · 2024Article
- Phase transition to chaos in complex ecosystems with non-reciprocal species-resource interactions.ArXiv · 2024Article
- Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Resource competition can explain simplicity in microbial community assembly.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Metabolic complexity drives divergence in microbial communities.bioRxiv : the preprint server for biology · 2023Article
- Controlling the human microbiome.Cell systems · 2023Review
- Enhancing plant growth promoting rhizobacterial activities through consortium exposure: A review.Frontiers in bioengineering and biotechnology · 2023Review
- Ecological landscapes guide the assembly of optimal microbial communities.PLoS computational biology · 2023Article
- Ecological modelling approaches for predicting emergent properties in microbial communities.Nature ecology & evolution · 2022Review
- Top-down and bottom-up cohesiveness in microbial community coalescence.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Emergent Diversity and Persistent Turnover in Evolving Microbial Cross-Feeding Networks.Frontiers in network physiology · 2022Article
- Diverse communities behave like typical random ecosystems.Physical review. E · 2021Article
- Engineering complex communities by directed evolution.Nature ecology & evolution · 2021Article
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Authors and funding
4 authors.
Funding
Abstract
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new open-source, freely available Python package called Community Simulator for simulating microbial population dynamics in a reproducible, transparent and scalable way. The Community Simulator includes five major elements: tools for preparing the initial states and environmental conditions for a set of samples, automatic generation of dynamical equations based on a dictionary of modeling assumptions, random parameter sampling with tunable levels of metabolic and taxonomic structure, parallel integration of the dynamical equations, and support for metacommunity dynamics with migration between samples. To significantly speed up simulations using Community Simulator, our Python package implements a new Expectation-Maximization (EM) algorithm for finding equilibrium states of community dynamics that exploits a recently discovered duality between ecological dynamics and convex optimization. We present data showing that this EM algorithm improves performance by between one and two orders compared to direct numerical integration of the corresponding ordinary differential equations. We conclude by listing several recent applications of the Community Simulator to problems in microbial ecology, and discussing possible extensions of the package for directly analyzing microbiome compositional data.
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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.