Dear Colleagues,
Please consider the attached manuscript entitled, "A community maintained standard library of population genetic models" for publication in eLife. This manuscript describes the first product of the PopSim Consortium, the stdpopsim library, which provides a game-changing resource to the population and statistical genetics community.
Simulation is a cornerstone tool in population and statistical genetics, wherein genomes are simulated for specific species/populations under assumed evolutionary and demographic histories. To date researchers in these fields have been forced to implement simulation models independently, leading to duplication of effort and the possibility for error. Moreover because of the bespoke nature of such simulations, rigorous benchmarking of inferential procedures against an agreed-upon, gold standard has been impossible to date. To rectify this growing issue, we have been actively creating a community to build consensus, in the hopes that population and statistical genetics might coalesce around a series of best practices and protocols that center transparency, reproducibility, and inclusiveness. The first output from this community, which we have named the PopSim Consortium, is a community-driven open source project, stdpopsim, which provides easy access to a standard catalog of published simulation models from a wide range of organisms and supports multiple population genetic simulators.
In this manuscript we outline the stdpopsim library and give examples of its utility, particularly for benchmarking software aimed at performing demographic inference. We believe that this work is a major step forward for the field generally and believe that such open-source, community-driven efforts will modernize computational genetics.
Sincerely,
Jerome Kelleher and Andrew Kern
On behalf of all authors.