Introduction

Note

This documentation is incomplete and under development. If you would like to help, please open an issue or pull request at GitHub.

This is the documentation for stdpopsim, the standard library for population genetic simulation models.

We designed stdpopsim to make it easier for you to run reproducible, bug-free simulations of genetic datasets from published demographic histories. Under the hood, stdpopsim relies on msprime and SLiM 3 to generate sample datasets in the tree sequence format.

First steps

  • Head to the Installation page to get stdpopsim installed on your computer.

  • Skim the Catalog to see what simulations are currently supported by stdpopsim.

  • Read the Tutorials to see some examples of stdpopsim in action.

Getting involved

Are there other features, models or organisms that you’d like to see in stdpopsim? This software is maintained by the PopSim Consortium, a global community of scientists and developers who are working together to improve standards for benchmarking and testing in population genetics. Read the Development page to find out how you can join us.

Citations

If you use stdpopsim in your work, please cite our manuscript:

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, Bernard Y. Kim, Patrick McKenzie, Philipp W. Messer, Ekaterina Noskova, Diego Ortega-Del Vecchyo, Fernando Racimo, Travis J. Struck, Simon Gravel, Ryan N. Gutenkunst, Kirk E. Lohmeuller, Peter L. Ralph, Daniel R. Schrider, Adam Siepel, Jerome Kelleher, Andrew D. Kern (2019), A community-maintained standard library of population genetic models, bioRxiv 2019.12.20.885129; doi: https://doi.org/10.1101/2019.12.20.885129

Bibtex record:

@article {Adrion2019.12.20.885129,
    author = {Adrion, Jeffrey R. and Cole, Christopher B. and Dukler, Noah
        and Galloway, Jared G. and Gladstein, Ariella L. and Gower, Graham and
        Kyriazis, Christopher C. and Ragsdale, Aaron P. and Tsambos, Georgia and
        Baumdicker, Franz and Carlson, Jedidiah and Cartwright, Reed A. and
        Durvasula, Arun and Kim, Bernard Y. and McKenzie, Patrick and Messer, Philipp W.
        and Noskova, Ekaterina and Vecchyo, Diego Ortega-Del and Racimo, Fernando
        and Struck, Travis J. and Gravel, Simon and Gutenkunst, Ryan N. and
        Lohmeuller, Kirk E. and Ralph, Peter L. and Schrider, Daniel R. and Siepel, Adam
        and Kelleher, Jerome and Kern, Andrew D.},
    title = {A community-maintained standard library of population genetic models},
    elocation-id = {2019.12.20.885129},
    year = {2019},
    doi = {10.1101/2019.12.20.885129},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2019/12/21/2019.12.20.885129},
    eprint = {https://www.biorxiv.org/content/early/2019/12/21/2019.12.20.885129.full.pdf},
    journal = {bioRxiv}
}

Licence and usage

stdpopsim is available under the GPLv3 public license. The terms of this license can be read here.