A community-maintained standard library of population genetic models
A community-maintained standard library of population genetic models
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DOI：
10.7554/elife.54967
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发表时间：
2020-06-23
期刊：
影响因子：
7.7
通讯作者：
Kern, Andrew D.
中科院分区：
文献类型：
--
作者：
Adrion, Jeffrey R.;Cole, Christopher B.;Kern, Andrew D.
人口基因组数据的爆炸需要更复杂的分析模式，这些分析越来越依赖于复杂的模拟。群体遗传模拟的最新进展使模拟大型复杂模型成为可能，但为特定模拟引擎指定此类模型仍然是一项困难且容易出错的任务。计算遗传学研究人员目前独立地重新实现模拟模型，导致不一致和重复工作。这种情况给实证研究人员提供了一个主要的障碍，他们试图使用模拟来对即将进行的研究进行功效分析，或者对现有的基因组数据进行合理性检查。群体遗传学作为一个领域，也缺乏标准的基准来衡量新的推理工具。在这里，我们描述了一个新的资源，stdpopsim，试图纠正这种情况。Stdpopsim是一个社区驱动的开源项目，它提供了从一系列生物体中轻松访问不断增长的已发布模拟模型目录，并支持多个模拟引擎后端。这个资源是一个文档丰富的python库，带有一个简单的命令行界面。我们分享了一些示例，展示了如何使用stdpopsim来系统地比较人口统计推断方法，我们鼓励更广泛的开发人员社区为这一不断增长的资源做出贡献。
The explosion in population genomic data demands ever more complex modes of analysis, and increasingly, these analyses depend on sophisticated simulations. Recent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to inconsistency and duplication of effort. This situation presents a major barrier to empirical researchers seeking to use simulations for power analyses of upcoming studies or sanity checks on existing genomic data. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here, we describe a new resource, stdpopsim, that attempts to rectify this situation. Stdpopsim is a community-driven open source project, which provides easy access to a growing catalog of published simulation models from a range of organisms and supports multiple simulation engine backends. This resource is available as a well-documented python library with a simple command-line interface. We share some examples demonstrating how stdpopsim can be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource.