Towards simulating large scale biological reaction networks in Julia
I will discuss our work building out DiffEqBiological and DiffEqJump, first steps towards developing a Julia package for simulating particle-based stochastic reaction-diffusion models. DiffEqBiological provides a simple DSL for specifying chemical reaction networks, which interfaces with many other Julia DiffEq packages to enable the generation and solution of corresponding ordinary differential equation (ODE) models, stochastic differential equation (SDE) models, steady-state problems and jump process models. DiffEqJump provides a library of optimized stochastic simulation algorithms (SSAs) for generating exact realizations of jump processes. These SSAs can be used directly to simulate integer-valued jump processes, such as stochastic chemical kinetics models, but can also be used as sub-components within ODE or SDE models. I’ll overview some of the optimized SSAs we’ve recently added to DiffEqJump to enable the rapid simulation of jump processes involving large numbers of jumps. Time-permitting I’ll discuss our plans to build a spatial SSA-based package from these components.
Dr. Samuel Isaacson
Department of Mathematics and Statistics
How to get here
The Kiva Conference room is on the 4th floor of the Dreyfoos Wing in the Stata Center (Building 32). Enter Building 32 at the front entrance and proceed straight ahead; there will be elevators to the right. Take the elevators to the 4th floor; exit to the left and then turn right at the end of the elevator bank. At the end of the short corridor cross the R&D Dining room. The Kiva Conference Room is to the right.
If you are visiting from outside MIT, please note that the doors lock promptly at 6pm. We will have someone by the Dreyfoos elevators to help folks find their way up.
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