BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology
BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology
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DOI：
10.1371/journal.pone.0042790
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发表时间：
2012-08-24
期刊：
影响因子：
3.7
通讯作者：
di Bernardo, Mario
中科院分区：
文献类型：
--
作者：
Gorochowski, Thomas E.;Matyjaszkiewicz, Antoni;di Bernardo, Mario
大规模的集体行为，如同步和协调，在许多细菌种群中自发出现。随着系统生物学试图理解这些现象，合成生物学为我们自己的利益开辟了工程的可能性，人们对如何最好地模拟细菌种群越来越感兴趣。在这里，我们介绍BSim，一个高度灵活的基于代理的计算工具，用于分析单细胞动力学和群体水平的功能之间的关系。BSim包括许多细菌特性的参考实现，以便能够快速开发部分基于现有模型构建的新模型。与现有的建模工具不同，BSim充分考虑了模型的空间方面，允许描述复杂的微观结构，从而能够在更逼真的三维复杂环境中建模细菌行为。通过几个不同的例子说明了BSim打开的新机会，包括：空间多细胞计算，模拟复杂的环境，人口动态的紫胶操纵子，遗传振荡器的同步。BSim是一款开源软件，可从http://bsim-bccs.sf.net免费获取，并根据开源计划（OSI）认可的MIT许可证分发。开发人员文档和广泛的示例模拟也可以从网站上获得。BSim需要Java 1.6或更高版本。
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.