BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology
| Autor: | Stephen Reid, Claire S. Grierson, Thomas E. Gorochowski, Nigel J. Savery, Thomas Todd, Kira Kowalska, Krasimira Tsaneva-Atanasova, Neeraj Oak, Antoni Matyjaszkiewicz, Mario di Bernardo |
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| Přispěvatelé: | Thomas E., Gorochowski, Antoni, Matyjaszkiewicz, Thomas, Todd, Neeraj, Oak, Kira, Kowalska, Stephen, Reid, Krasimira T., Tsaneva Atanasova, Nigel J., Savery, Claire S., Grierson, DI BERNARDO, Mario |
| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Java
Systems biology Distributed computing Population lcsh:Medicine Population Modeling Bioinformatics Microbiology Microbial Ecology 03 medical and health sciences Synthetic biology 0302 clinical medicine Documentation Synchronization (computer science) Operon BSIM MIT License education lcsh:Science Biology Computerized Simulations 030304 developmental biology computer.programming_language Physics Regulatory Networks 0303 health sciences education.field_of_study Multidisciplinary Software Tools Systems Biology Bristol BioDesign Institute lcsh:R Computational Biology Software Engineering Bacteriology Bacterial Biochemistry Computer Science lcsh:Q Synthetic Biology synthetic biology computer 030217 neurology & neurosurgery Research Article Computer Modeling |
| Zdroj: | PLoS ONE PLoS ONE, Vol 7, Iss 8, p e42790 (2012) Gorochowski, T E, Matyjaszkiewicz, A W, Todd, T, Oak, N P, Kowalska, K, Reid, S, Tsaneva-Atanasova, K T, Savery, N J, Grierson, C S & di Bernardo, M 2012, ' BSim : An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology ', PLoS ONE, vol. 7, no. 8, e42790 . https://doi.org/10.1371/journal.pone.0042790 |
| ISSN: | 1932-6203 |
| DOI: | 10.1371/journal.pone.0042790 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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