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 4 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

stdpopsim is a community effort, and we welcome YOU to join us!

Are there other features, models or organisms that you’d like to see in stdpopsim? This software is maintained by the PopSim Consortium, an open, global community of scientists and developers who are working together to improve standards for benchmarking and testing in population genetics. You can get into contact with the stdpopsim community by subscribing to our email list serve and by creating and commenting on Github issues. There is a lot of chatter through Github, and we’ve been building code there cooperatively. If you are interested in joining us please read our code of conduct. A particular goal of this project is to build a diverse and supportive community, and so we especially encourage individuals from underrepresented groups in popgen to join. A primary goal of PopSim Consortium is to be inclusive to the largest number of contributors, with the most varied and diverse backgrounds possible. As such, we are committed to providing a friendly, safe and welcoming environment for all, regardless of gender, sexual orientation, ability, ethnicity, socioeconomic status, and religion (or lack thereof). Being a member of the Consortium can provide a valuable avenue for career development, through building networks, contributing to papers and code, as well as through learning programing standards and best practices.

For further details read the Development page to find out how you can join us.

Citations

If you use stdpopsim in your work, please cite our original manuscript and/or the followup manuscript describing major additions to the catalog:

• 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 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 (2020), A community-maintained standard library of population genetic models, eLife 2020;9:e54967; doi: https://doi.org/10.7554/eLife.54967

• M. Elise Lauterbur, Mariz Izabel A. Cavassim, Ariella L. Gladstein, Graham Gower, Nathaniel S. Pope, Georgia Tsambos, Jeffrey Adrion, Saurabh Belsare, Arjun Biddanda, Victoria Caudill, Jean Cury, Ignacio Echevarria, Benjamin C. Haller, Ahmed R. Hasan, Xin Huang, Leonardo Nicola Martin Iasi, Ekaterina Noskova, Jana Obšteter, Vitor Antonio Corrêa Pavinato, Alice Pearson, David Peede, Manolo F. Perez, Murillo F. Rodrigues, Chris C. R. Smith, Jeffrey P. Spence, Anastasia Teterina, Silas Tittes, Per Unneberg, Juan Manuel Vazquez, Ryan K. Waples, Anthony Wilder Wohns, Yan Wong, Franz Baumdicker, Reed A. Cartwright, Gregor Gorjanc, Ryan N. Gutenkunst, Jerome Kelleher, Andrew D. Kern, Aaron P. Ragsdale, Peter L. Ralph, Daniel R. Schrider, Ilan Gronau (2022). Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations, bioRxiv 2022.10.29.514266; doi: https://doi.org/10.1101/2022.10.29.514266

Bibtex records:

@article {10.7554/eLife.54967,
    article_type = {journal},
    title = {A community-maintained standard library of population genetic models},
    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 Gronau, Ilan and Kim, Bernard Y and McKenzie, Patrick and
        Messer, Philipp W and Noskova, Ekaterina and Ortega-Del Vecchyo, Diego and Racimo,
        Fernando and Struck, Travis J and Gravel, Simon and Gutenkunst, Ryan N and Lohmueller,
        Kirk E and Ralph, Peter L and Schrider, Daniel R and Siepel, Adam and Kelleher, Jerome
        and Kern, Andrew D},
    editor = {Coop, Graham and Wittkopp, Patricia J and Novembre, John and Sethuraman, Arun
        and Mathieson, Sara},
    volume = 9,
    year = 2020,
    month = {jun},
    pub_date = {2020-06-23},
    pages = {e54967},
    citation = {eLife 2020;9:e54967},
    doi = {10.7554/eLife.54967},
    url = {https://doi.org/10.7554/eLife.54967},
    keywords = {simulation, reproducibility, open source},
    journal = {eLife},
    issn = {2050-084X},
    publisher = {eLife Sciences Publications, Ltd},
}

@article {Lauterbur2022.10.29.514266,
    author = {Lauterbur, M. Elise and Cavassim, Mariz Izabel A. and
        Gladstein, Ariella L. and Gower, Graham and Pope, Nathaniel S. and
        Tsambos, Georgia and Adrion, Jeffrey and Belsare, Saurabh and Biddanda,
        Arjun and Caudill, Victoria and Cury, Jean and Echevarria, Ignacio and
        Haller, Benjamin C. and Hasan, Ahmed R. and Huang, Xin and Iasi,
        Leonardo Nicola Martin and Noskova, Ekaterina and Ob{\v s}teter, Jana
        and Pavinato, Vitor Antonio Corr{\^e}a and Pearson, Alice and Peede,
        David and Perez, Manolo F. and Rodrigues, Murillo F. and Smith, Chris
        C. R. and Spence, Jeffrey P. and Teterina, Anastasia and Tittes, Silas
        and Unneberg, Per and Vazquez, Juan Manuel and Waples, Ryan K. and
        Wohns, Anthony Wilder and Wong, Yan and Baumdicker, Franz and
        Cartwright, Reed A. and Gorjanc, Gregor and Gutenkunst, Ryan N. and
        Kelleher, Jerome and Kern, Andrew D. and Ragsdale, Aaron P. and Ralph,
        Peter L. and Schrider, Daniel R. and Gronau, Ilan},
    title = {Expanding the stdpopsim species catalog, and lessons learned
        for realistic genome simulations},
    elocation-id = {2022.10.29.514266},
    year = {2022},
    doi = {10.1101/2022.10.29.514266},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2022/10/31/2022.10.29.514266},
    eprint = {https://www.biorxiv.org/content/early/2022/10/31/2022.10.29.514266.full.pdf},
    journal = {bioRxiv}
}

Licence and usage

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