JuliaCon 2022 (Times are UTC)

GeneDrive.jl: Simulate and Optimize Biological Interventions
07-29, 19:00–19:30 (UTC), Red

This talk introduces GeneDrive.jl, a package designed to study the effect of biotic and abiotic interactions on metapopulations, outlining functionalities and use cases. GeneDrive.jl is a 3-part framework for building and analyzing simulations wherein organisms are subjected to anthropogenic and environmental change. It includes: (1) Data models that exploit the power of Julia's type system. (2) Dynamic models that build on DifferentialEquations.jl. (3) Decision models that employ JuMP.jl.

Understanding and controlling biological dynamics is a concern in arenas as diverse as public health, agriculture, or conservation. Both environmental and human factors influence those dynamics, often in complex ways. Decisions about the timing, magnitude, and location where interventions are required to control the presence of harmful organisms – be they disease vectors, crop pests, or invasive species – must be made amid this ever-changing reality of biotic and abiotic interactions.

The GeneDrive.jl package facilitates replicable, scalable, and extensible computational experiments on the topic of biological dynamics and control by drawing on several pre-existing tools within the Julia ecosystem. It formalizes Julia data structures to store information and dispatch methods unique to species and genotype, enabling the straightforward incorporation of empirical knowledge. Once constructed, problems can be solved using either dynamic or optimization methods by building on the extensively developed DifferentialEquations.jl and JuMP.jl packages.

This one-time specification of the experimental data, on which both ODE and optimization solving algorithms can be called, encourages experimentation with operational levers in addition to biological ones. GeneDrive.jl employs mathematical programming for its optimization routines rather than the optimal control approaches more common in the biological sciences. This enables the inclusion of more detailed genetic and ecological information than would otherwise be tractable.

The origin of this package’s name, gene drives, are DNA sequences that spread through a population at higher frequencies than Mendelian inheritance patterns. These tools furnish a promising new approach to the mitigation of diseases carried by mosquito vectors and circumvent the problems of traditional prevention practices (e.g., growing insecticide resistance). GeneDrive.jl is applicable to biological tools beyond gene drive (see examples in the documentation), however, it is named in honor of this new technological horizon.

PhD candidate, University of California Berkeley
MS, Electrical Engineering and Computer Sciences
MS, Energy and Resources