title: MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME.
abstract: Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments.
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, CA 93106.
authors.forename: Brian
authors.initials: B
authors.lastname: Drawert
authors.affiliation: Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106.
authors.forename: Michael
authors.initials: M
authors.lastname: Trogdon
authors.affiliation: Department of Computer Science, University of Helsinki, Helsinki FI-00014, Finland, and Department of Information Technology, Division of Scientific Computing, Uppsala University, Uppsala, 75105 Sweden.
authors.forename: Salman
authors.initials: S
authors.lastname: Toor
authors.affiliation: Departments of Computer Science and Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106.
authors.forename: Linda
authors.initials: L
authors.lastname: Petzold
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, CA 93106.
authors.forename: Andreas
authors.initials: A
authors.lastname: Hellander
keywords: cloud computing; computational experiments; simulation software; spatial stochastic simulation; systems biology