ArticlePloS one2012
BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic Literature Review of Agents Applied in Healthcare.Journal of medical systems · 2016Pooled it
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Coupling Bacterial Cell Size Regulation with Clonal Proliferation Dynamics Reveals Cell Division Based on Surface Area.bioRxiv : the preprint server for biology · 2025Article
- Article
- Disentangling the feedback loops driving spatial patterning in microbial communities.NPJ biofilms and microbiomes · 2025Review
- Competing mechanisms in bacterial invasion of human colon mucus probed with agent-based modeling.Biophysical journal · 2024Article
- Optimization of periodic treatment strategies for bacterial biofilms using an agent-basedJournal of the Royal Society, Interface · 2024Article
- Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0.PLoS computational biology · 2024Article
- Article
- Agent-Based Modeling of Microbial Communities.ACS synthetic biology · 2022Review
- Individual-Based Modeling of Spatial Dynamics of Chemotactic Microbial Populations.ACS synthetic biology · 2022Article
- Control-Based Continuation: A New Approach to Prototype Synthetic Gene Networks.ACS synthetic biology · 2022Article
- Ratiometric control of cell phenotypes in monostrain microbial consortia.Journal of the Royal Society, Interface · 2022Article
- A Self-Controlled and Self-Healing Model of Bacterial Cells.Membranes · 2022Article
- The Inclusion of the Food Microstructural Influence in Predictive Microbiology: State-of-the-Art.Foods (Basel, Switzerland) · 2021Review
- Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes.Annual review of biomedical engineering · 2021Review
- Simulating ATO Mechanism and EGFR Signaling with Fuzzy Logic and Petri Net.Journal of biomedical physics & engineering · 2021Article
- Trends in mathematical modeling of host-pathogen interactions.Cellular and molecular life sciences : CMLS · 2020Review
- Toward Engineering Biosystems With Emergent Collective Functions.Frontiers in bioengineering and biotechnology · 2020Article
- Agent-Based Models Predict Emergent Behavior of Heterogeneous Cell Populations in Dynamic Microenvironments.Frontiers in bioengineering and biotechnology · 2020Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI) recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.
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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.