Improved Tools for Genetic Diversity Modelling

Interpreting genomic data largely relies on simulation software. One important family of software simulates population-level diversity over the course of evolution as a function of selection and demography. The ∂a∂i open-source package, developed by Ryan Gutenkunst (http://gutengroup.mcb.arizona.edu), is the leading software in the field, but is limited when handling large datasets.

This project aims to overhaul the computational engine of the ∂a∂i software by implementing a recently developed approach for solving partial differential equations. The project will use ∂a∂i's interface and code-base, but introduce a new spectrum simulation engine. Using a moment-based approach will improve performance and reduce numerical uncertainty, offering the genetics community with a general-purpose simulation tool that can address larger and more complex datasets than previously possible.

A prototype version of the computational engine is already running. The goal of this project will be to optimize the engine and embed it efficiently in the existing code-base.