@article{a1f0526b3c024a7f93363c0643185e9a,
title = "A community-maintained standard library of population genetic models",
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.",
keywords = "Inference, Population genetics, Reproducibility, Simulation",
author = "Adrion, {Jeffrey R.} and Cole, {Christopher B.} and Noah Dukler and Galloway, {Jared G.} and Gladstein, {Ariella L.} and Graham Gower and Kyriazis, {Christopher C.} and Ragsdale, {Aaron P.} and Georgia Tsambos and Franz Baumdicker and Jedidiah Carlson and Cartwright, {Reed A.} and Arun Durvasula and Ilan Gronau and Kim, {Bernard Y.} and Patrick McKenzie and Messer, {Philipp W.} and Ekaterina Noskova and Vecchyo, {Diego Ortega Del} and Fernando Racimo and Struck, {Travis J.} and Simon Gravel and Gutenkunst, {Ryan N.} and Lohmueller, {Kirk E.} and Ralph, {Peter L.} and Schrider, {Daniel R.} and Adam Siepel and Jerome Kelleher and Kern, {Andrew D.}",
note = "Funding Information: 591 TJS and RNG were funded under NIH Award R01GM127348. ALG and DRS were funded Funding Information: 595 Collaborative Grant and a DGAPA-PAPIIT grant (PAPIIT-IA200620). JK is supported Funding Information: 590 Award R35GM119856. JRA and ADK were funded under NIH Award R01GM117241. Funding Information: 594 vestigator award (project no. 00025300). DODV is funded by a UC MEXUS-CONACYT Funding Information: We thank the Probabilistic Modeling in Genomics conference organizers for making this collaboration possible, and the Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory for sponsoring the first workshop. Early on in the project we were encouraged by many people including Patrick Phillips, Richard Durbin, Dmitri Petrov, and Sohini Ramachandran. In addition we would like to thank NESCENT and Matt Hahn, Victoria Sork, and Michael Whitlock for organizing a 2014 catalysis meeting in which many of the goals of this effort were first laid out. CCK and KEL were funded under NIH Award R35GM119856. JRA and ADK were funded under NIH Award R01GM117241. TJS and RNG were funded under NIH Award R01GM127348. ALG and DRS were funded under NIH award R00HG008696. ND and AS were supported in part by NIH Awards R01HG010346 and R35GM127070. FR and GG were supported by a Villum Young Investigator award (project no. 00025300). DODV is funded by a UC MEXUS-CONACYT Collaborative Grant and a DGAPA-PAPIIT grant (PAPIIT-IA200620). JK is supported by the Robertson Foundation. Publisher Copyright: {\textcopyright} 2020, eLife Sciences Publications Ltd. All rights reserved.",
year = "2020",
month = jun,
doi = "10.7554/eLife.54967",
language = "English (US)",
volume = "9",
pages = "1--39",
journal = "eLife",
issn = "2050-084X",
publisher = "eLife Sciences Publications",
}