Programmatic modeling for biological systems
Programmatic modeling for biological systems
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DOI：
10.1016/j.coisb.2021.05.004
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发表时间：
2021-09-01
影响因子：
3.7
通讯作者：
Lopez, Carlos F.
中科院分区：
文献类型：
--
作者：
Lubbock, Alexander L. R.;Lopez, Carlos F.
计算建模已经成为一种成熟的技术，用于编码细胞过程的数学表示，并获得驱动可测试预测的机械见解。这些模型通常使用图形用户界面或特定于领域的语言构建，并使用社区标准进行交换。模型进行稳态或动态分析，其中可以包括在单个应用程序中的模拟和校准，或在各种工具之间传输。在这里，我们描述了一种新的编程建模范式，从而建模与软件工程的最佳实践增强。我们专注于Python-一种流行的编程语言，具有大型科学包生态系统。模型可以编码为程序，增加了模块化、测试和自动文档生成器等优点，同时仍然可以扩展和导出为标准化格式，以便在需要时与外部工具一起使用。程序化建模是实现协作模型开发和增强传播性、透明度和可重复性的关键技术。
Computational modeling has become an established technique to encode mathematical representations of cellular processes and gain mechanistic insights that drive testable predictions. These models are often constructed using graphical user interfaces or domain-specific languages, with community standards used for interchange. Models undergo steady-state or dynamic analysis, which can include simulation and calibration within a single application, or transfer across various tools. Here, we describe a novel programmatic modeling paradigm, whereby modeling is augmented with software engineering best practices. We focus on Python-a popular programming language with a large scientific package ecosystem. Models can be encoded as programs, adding benefits such as modularity, testing, and automated documentation generators, while still being extensible and exportable to standardized formats for use with external tools if desired. Programmatic modeling is a key technology to enable collaborative model development and enhance dissemination, transparency, and reproducibility.