Guidelines for Reproducibly Building and Simulating Systems Biology Models.
Guidelines for Reproducibly Building and Simulating Systems Biology Models.
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DOI：
10.1109/tbme.2016.2591960
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发表时间：
2016-10
期刊：
影响因子：
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通讯作者：
Karr JR
中科院分区：
文献类型：
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作者：
Medley JK;Goldberg AP;Karr JR
重复性是科学方法的基石。然而，目前许多系统生物学模型并不容易复制。本文提出了解决这一问题的方法。我们分析了最近的生殖支原体全细胞(WC)模型，以确定可重复性建模的要求。我们确定，可重复建模既需要可重复的建模，也需要可重复的模拟。需要新的标准和模拟软件工具来增强和验证建模的重复性。需要新的标准来明确地记录每个数据源和假设，并且需要新的确定性并行模拟工具来快速模拟大型、复杂的模型。我们预计，这些新的标准和软件将使研究人员能够重复构建和模拟更复杂的模型，包括WC模型。
Reproducibility is the cornerstone of the scientific method. However, currently, many systems biology models cannot easily be reproduced. This paper presents methods that address this problem. We analyzed the recent Mycoplasma genitalium whole-cell (WC) model to determine the requirements for reproducible modeling. We determined that reproducible modeling requires both repeatable model building and repeatable simulation. New standards and simulation software tools are needed to enhance and verify the reproducibility of modeling. New standards are needed to explicitly document every data source and assumption, and new deterministic parallel simulation tools are needed to quickly simulate large, complex models. We anticipate that these new standards and software will enable researchers to reproducibly build and simulate more complex models, including WC models.