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Friday, June 23 • 2:18pm - 2:30pm
BioSimulator.jl: Stochastic Simulation in Julia

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Complex systems in biology are often difficult to treat analytically using mathematics and expensive to investigate with empirical methods. Moreover, deterministic approaches are misleading in systems that exhibit noise (e.g. rare events akin to mutation and extinction). Stochastic simulation provides investigators with the ability to simulate complex systems by integrating mathematical rigor and biological insight. However, simulations are slow, computationally expensive, and difficult to implement in software. My goal in developing BioSimulator.jl is to provide investigators with a tool that enables (1) quick and intuitive model prototyping, (2) efficient simulation, (3) visualization of simulation output, and (4) implementing new stochastic simulation algorithms. Using the Julia language allowed us to meet all four criteria with relative ease and extend to parallelized simulations. My talk will describe the theory underlying BioSimulator.jl, highlight aspects of our implementation, and present a few numerical examples.


Alfonso Landeros

University of California, Los Angeles
I am a first-year student in biomathematics. My studies are focused on stochastic processes, scientific computing, and optimization.

Friday June 23, 2017 2:18pm - 2:30pm PDT
East Pauley Pauley Ballroom, Berkeley, CA