papers
Publications (3)
cs.CE2015
MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME
Brian Drawert, Michael Trogdon, Salman Toor +2
Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well…
q-bio.QM2022
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu +68
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, becau…
math.NA2013
Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting
Andreas Hellander, Michael Lawson, Brian Drawert +1
The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if d…