微生物生态系统时空计算（COMETS）：一个用于模拟生态系统代谢的开源协作平台
Computation Of Microbial Ecosystems in Time and Space (COMETS): An open source collaborative platform for modeling ecosystems metabolism
摘要：
代谢的基因组尺度化学计量建模已经成为用于建模细胞生理学和生长的标准系统生物学工具。这种方法的扩展也正在成为预测，理解和设计微生物群落的有价值的途径。COMETS（Computation Of Microbial Ecosystems in Time and Space）最初是作为动态通量平衡分析的扩展而开发的，它结合了细胞和分子扩散，能够模拟空间结构环境中的多种微生物物种。在这里，我们描述了如何最好地使用和应用这个平台的最新版本，COMETS 2，它结合了一个更准确的生物物理模型的微生物生物量的增长，以及几个新的生物模拟模块，包括演化动力学和胞外酶活性。COMETS 2提供了用户友好的Python和MATLAB接口，与成熟的COBRA模型和方法兼容，以及全面的文档和教程，便于代谢模拟专业知识的各级研究人员使用COMETS。该协议为安装、测试和将COMETS 2应用于不同场景提供了详细的指导方针，广泛适用于跨生物群落和规模的微生物群落。
英文摘要：
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and designing microbial communities. COMETS (Computation Of Microbial Ecosystems in Time and Space) was initially developed as an extension of dynamic flux balance analysis, which incorporates cellular and molecular diffusion, enabling simulations of multiple microbial species in spatially structured environments. Here we describe how to best use and apply the most recent version of this platform, COMETS 2, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, as well as several new biological simulation modules, including evolutionary dynamics and extracellular enzyme activity. COMETS 2 provides user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, and comprehensive documentation and tutorials, facilitating the use of COMETS for researchers at all levels of expertise with metabolic simulations. This protocol provides a detailed guideline for installing, testing and applying COMETS 2 to different scenarios, with broad applicability to microbial communities across biomes and scales.
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