2020-07-31 –, Purple Track
Julia is a great scientific computing language for interrogating ecological and evolutionary dynamics of intratumor heterogeneity and how it changes over time. This talk will appeal to people interested in studying Mathematical Biology and Ecology applications with Julia.
Cancer research stipulates that more heterogenous tumor cell populations ultimately drive unfavorable outcomes for patients. To study this question, we have developed software tools in Julia that harnesses evolutionary game theory methodologies like replicator-mutator dynamics and random walk model simulations through DifferentialEquations.jl and Distributions.jl along with data analysis pipelines for quantifying generalized diversity index (GDI) with DataFrames.jl and Query.jl. These tools reveal quantitative insights into how GDI changes over time under evolutionary pressures. Julia has solved our two-language problem allowing us to interrogate temporal changes in intratumor heterogeneity by simulating different tumor ecological niches over time and quantifying those changes in diversity to help fight cancer.
This talk will present this biological application and discuss how existing Julia packages make this analytical work feasible. I will also highlight some areas of biological science research where there are gaps in Julia tooling relative to other data science ecosystems such as R and Scientific Python.
Meghan Ferrall-Fairbanks received her B.S. in Mechanical Engineering with a Biomechanics minor at the University of Florida in 2012. She earned her PhD in Biomedical Engineering in 2017 from the joint Georgia Tech and Emory program under the guidance of Dr. Manu O. Platt. In her graduate dissertation work, Meghan focused on integrating wet-lab experimental and computational methods to tease apart complex enzyme-on-enzyme interactions in proteolytic networks up-regulated in tissue destructive diseases. In August 2017, she began her postdoctoral studies in the Department of Integrated Mathematical Oncology at Moffitt Cancer Center and Research Institute with Dr. Philipp M. Altrock. In her postdoctoral work, Meghan has focused on applying mathematical and computational methods to model cancer evolution in hematopoietic malignancies.