sgravel / msprime-1.0-paper

Publication describing msprime 1.0

msprime-1.0-paper

This repo contains the manuscript for the publication describing the msprime 1.0 paper. As decided in issue #1, this is currently intended to be submitted to G3 as a software article.

Abstract

Coalescent simulation is a key tool in population genetics and and has been integral to coalescent theory since its earliest days. Because of the ease at which the basic model can be simulated, a large number of different simulators have been developed. However, the coalescent with recombination is far more challenging to simulate, and, until recently, it was not possible to simulate efficiently. The msprime software has revolutionised coalescent simulation, making it possible to simulate millions of whole genomes for the first time. We summarise the many features of msprime 1.0, which is built around a core model of efficiently implementing recombination via the succinct tree sequence data structure. We advocate a community oriented open-source development process as a way to reduce duplication of effort and increase the quality of simulation software.

Writing process

Like the development of msprime itself, the process of writing this article is managed through an open source development model via GitHub. Those responsible for particular features will be assigned sections of writing via issues. Those wishing to make edits should also follow these guidelines:

• For significant edits, please use the GitHub workflow described here to create a fork, feature branches and make pull requests.

• For smaller edits, using the edit file button on the paper.tex file in GitHub may be simpler than checking out the repo locally, etc.

• Please keep edits localised to a single section to make the review process simpler.

• Please insert line-breaks before 90-100 characters, ideally at semantic break points.

• For high-level/structural issues, please open an issue to discuss before making changes.