A community-maintained standard library of population genetic models

  1. Jeffrey R Adrion
  2. Christopher B Cole
  3. Noah Dukler
  4. Jared G Galloway
  5. Ariella L Gladstein
  6. Graham Gower
  7. Christopher C Kyriazis
  8. Aaron P Ragsdale
  9. Georgia Tsambos
  10. Franz Baumdicker
  11. Jedidiah Carlson
  12. Reed A Cartwright
  13. Arun Durvasula
  14. Ilan Gronau
  15. Bernard Y Kim
  16. Patrick McKenzie
  17. Philipp W Messer
  18. Ekaterina Noskova
  19. Diego Ortega Del Vecchyo
  20. Fernando Racimo
  21. Travis J Struck
  22. Simon Gravel
  23. Ryan N Gutenkunst
  24. Kirk E Lohmueller
  25. Peter L Ralph
  26. Daniel R Schrider
  27. Adam Siepel
  28. Jerome Kelleher  Is a corresponding author
  29. Andrew D Kern  Is a corresponding author
  1. University of Oregon, United States
  2. University of Oxford, United Kingdom
  3. Cold Spring Harbor Laboratory, United States
  4. University of North Carolina at Chapel Hill, United States
  5. The University of Adelaide, Australia
  6. University of California, Los Angeles, United States
  7. McGill University, Canada
  8. University of Melbourne, Australia
  9. University of Freiburg, Germany
  10. University of Washington, United States
  11. Arizona State University, United States
  12. IDC Herzliya, Israel
  13. Stanford University, United States
  14. Columbia University, United States
  15. Cornell University, United States
  16. ITMO University, Russian Federation
  17. National Autonomous University of Mexico, Mexico
  18. University of Copenhagen, Denmark
  19. University of Arizona, United States

Abstract

The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations. Re-cent 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.

Data availability

All resources are available from https://github.com/popsim-consortium/stdpopsim

Article and author information

Author details

  1. Jeffrey R Adrion

    Department of Biology, University of Oregon, Eugene, United States
    Competing interests
    No competing interests declared.
  2. Christopher B Cole

    Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6733-633X
  3. Noah Dukler

    Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8739-8052
  4. Jared G Galloway

    Department of Biology and Institute of Ecology and Evolution, University of Oregon, Eugene, United States
    Competing interests
    No competing interests declared.
  5. Ariella L Gladstein

    Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    No competing interests declared.
  6. Graham Gower

    Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6197-3872
  7. Christopher C Kyriazis

    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  8. Aaron P Ragsdale

    Human Genetics, McGill University, Montreal, Canada
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0715-3432
  9. Georgia Tsambos

    Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7001-2275
  10. Franz Baumdicker

    Department of Mathematical Stochastics, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
  11. Jedidiah Carlson

    Department of Genome Sciences, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
  12. Reed A Cartwright

    The Biodesign Institute and The School of Life Sciences, Arizona State University, Tempe, United States
    Competing interests
    No competing interests declared.
  13. Arun Durvasula

    Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0631-3238
  14. Ilan Gronau

    IDC Herzliya, Herzliya, Israel
    Competing interests
    No competing interests declared.
  15. Bernard Y Kim

    Department of Biology, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
  16. Patrick McKenzie

    Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, United States
    Competing interests
    No competing interests declared.
  17. Philipp W Messer

    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, United States
    Competing interests
    Philipp W Messer, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8453-9377
  18. Ekaterina Noskova

    Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russian Federation
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1168-0497
  19. Diego Ortega Del Vecchyo

    International Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla, Mexico
    Competing interests
    No competing interests declared.
  20. Fernando Racimo

    Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5025-2607
  21. Travis J Struck

    Molecular and Cellular Biology, University of Arizona, Tucson, United States
    Competing interests
    No competing interests declared.
  22. Simon Gravel

    Human Genetics, McGill University, Montreal, Canada
    Competing interests
    No competing interests declared.
  23. Ryan N Gutenkunst

    Molecular and Cellular Biology, University of Arizona, Tucson, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8659-0579
  24. Kirk E Lohmueller

    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3874-369X
  25. Peter L Ralph

    Institute of Ecology and Evolution, University of Oregon, Eugene, United States
    Competing interests
    No competing interests declared.
  26. Daniel R Schrider

    Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5249-4151
  27. Adam Siepel

    Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    No competing interests declared.
  28. Jerome Kelleher

    Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
    For correspondence
    jerome.kelleher@bdi.ox.ac.uk
    Competing interests
    No competing interests declared.
  29. Andrew D Kern

    Institute of Ecology and Evolution, University of Oregon, Eugene, United States
    For correspondence
    adkern@uoregon.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4381-4680

Funding

National Institute of General Medical Sciences (R35GM119856)

  • Christopher C Kyriazis
  • Kirk E Lohmueller

National Institute of General Medical Sciences (R01GM117241)

  • Jeffrey R Adrion
  • Andrew D Kern

National Institute of General Medical Sciences (R01GM127348)

  • Travis J Struck
  • Ryan N Gutenkunst

National Institute of General Medical Sciences (R00HG008696)

  • Ariella L Gladstein
  • Daniel R Schrider

National Institute of General Medical Sciences (R35GM127070)

  • Noah Dukler
  • Adam Siepel

National Human Genome Research Institute (R01HG010346)

  • Noah Dukler
  • Adam Siepel

Villum Fonden (00025300)

  • Graham Gower
  • Fernando Racimo

UC MEXUS-CONACYT

  • Diego Ortega Del Vecchyo

Robertson Foundation

  • Jerome Kelleher

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Graham Coop, University of California, Davis, United States

Version history

  1. Received: January 7, 2020
  2. Accepted: June 15, 2020
  3. Accepted Manuscript published: June 23, 2020 (version 1)
  4. Accepted Manuscript updated: June 25, 2020 (version 2)
  5. Version of Record published: August 19, 2020 (version 3)

Copyright

© 2020, Adrion et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Jeffrey R Adrion
  2. Christopher B Cole
  3. Noah Dukler
  4. Jared G Galloway
  5. Ariella L Gladstein
  6. Graham Gower
  7. Christopher C Kyriazis
  8. Aaron P Ragsdale
  9. Georgia Tsambos
  10. Franz Baumdicker
  11. Jedidiah Carlson
  12. Reed A Cartwright
  13. Arun Durvasula
  14. Ilan Gronau
  15. Bernard Y Kim
  16. Patrick McKenzie
  17. Philipp W Messer
  18. Ekaterina Noskova
  19. Diego Ortega Del Vecchyo
  20. Fernando Racimo
  21. Travis J Struck
  22. Simon Gravel
  23. Ryan N Gutenkunst
  24. Kirk E Lohmueller
  25. Peter L Ralph
  26. Daniel R Schrider
  27. Adam Siepel
  28. Jerome Kelleher
  29. Andrew D Kern
(2020)
A community-maintained standard library of population genetic models
eLife 9:e54967.
https://doi.org/10.7554/eLife.54967

Share this article

https://doi.org/10.7554/eLife.54967

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