A community-maintained standard library of population genetic models

Jeffrey R. Adrion, Christopher B. Cole, Noah Dukler, Jared G. Galloway, Ariella L. Gladstein, Graham Gower, Christopher C. Kyriazis, Aaron P. Ragsdale, Georgia Tsambos, Franz Baumdicker, Jedidiah Carlson, Reed A. Cartwright, Arun Durvasula, Ilan Gronau, Bernard Y. Kim, Patrick McKenzie, Philipp W. Messer, Ekaterina Noskova, Diego Ortega Del Vecchyo, Fernando RacimoTravis J. Struck, Simon Gravel, Ryan N. Gutenkunst, Kirk E. Lohmueller, Peter L. Ralph, Daniel R. Schrider, Adam Siepel, Jerome Kelleher, Andrew D. Kern

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

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 com-pare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource.

Original languageEnglish (US)
Article numbere54967
Pages (from-to)1-39
Number of pages39
JournaleLife
Volume9
DOIs
StatePublished - Jun 2020

Keywords

  • Inference
  • Population genetics
  • Reproducibility
  • Simulation

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Fingerprint Dive into the research topics of 'A community-maintained standard library of population genetic models'. Together they form a unique fingerprint.

  • Cite this

    Adrion, J. R., Cole, C. B., Dukler, N., Galloway, J. G., Gladstein, A. L., Gower, G., Kyriazis, C. C., Ragsdale, A. P., Tsambos, G., Baumdicker, F., Carlson, J., Cartwright, R. A., Durvasula, A., Gronau, I., Kim, B. Y., McKenzie, P., Messer, P. W., Noskova, E., Vecchyo, D. O. D., ... Kern, A. D. (2020). A community-maintained standard library of population genetic models. eLife, 9, 1-39. [e54967]. https://doi.org/10.7554/eLife.54967