Implementation and applications of EMOD, an individual-based multi-disease modeling platform
Implementation and applications of EMOD, an individual-based multi-disease modeling platform
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DOI：
10.1093/femspd/fty059
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发表时间：
2018-07-01
影响因子：
3.3
通讯作者：
Wiswell, Christian N.
中科院分区：
文献类型：
--
作者：
Bershteyn, Anna;Gerardin, Jaline;Wiswell, Christian N.
基于个体的模型提供了在宿主内和人群层面上对传染病进行建模所必需的模块化和结构灵活性，但实施起来具有挑战性。复杂程度可能会超出大多数学术机构的学生和受训人员的能力和时间范围。在这里，我们描述了在正式软件支持下开发的多疾病框架方法的过程和优势。流行病学建模软件EMOD已经经历了十年的软件开发。它的结构使得大多数代码在疾病建模中共享，包括疟疾、艾滋病毒、结核病、登革热、脊髓灰质炎和伤寒。除了实现效率之外，共享还增加了代码使用率和测试。免费提供的代码库还包括数百个回归测试、科学功能测试和组件测试，以帮助验证功能并避免在未来开发过程中无意中更改功能。在这里，我们描述EMOD实现的细节级别、灵活的可配置性和模块化，以及软件开发原则和过程在其开发中的作用。
Individual-based models provide modularity and structural flexibility necessary for modeling of infectious diseases at the within-host and population levels, but are challenging to implement. Levels of complexity can exceed the capacity and timescales for students and trainees in most academic institutions. Here we describe the process and advantages of a multi-disease framework approach developed with formal software support. The epidemiological modeling software, EMOD, has undergone a decade of software development. It is structured so that a majority of code is shared across disease modeling including malaria, HIV, tuberculosis, dengue, polio and typhoid. In additional to implementation efficiency, the sharing increases code usage and testing. The freely available codebase also includes hundreds of regression tests, scientific feature tests and component tests to help verify functionality and avoid inadvertent changes to functionality during future development. Here we describe the levels of detail, flexible configurability and modularity enabled by EMOD and the role of software development principles and processes in its development.