title: Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist.
abstract: We present StochSS: Stochastic Simulation as a Service, an integrated development environment for modeling and simulation of both deterministic and discrete stochastic biochemical systems in up to three dimensions. An easy to use graphical user interface enables researchers to quickly develop and simulate a biological model on a desktop or laptop, which can then be expanded to incorporate increasing levels of complexity. StochSS features state-of-the-art simulation engines. As the demand for computational power increases, StochSS can seamlessly scale computing resources in the cloud. In addition, StochSS can be deployed as a multi-user software environment where collaborators share computational resources and exchange models via a public model repository. We demonstrate the capabilities and ease of use of StochSS with an example of model development and simulation at increasing levels of complexity.
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Brian
authors.identifier: 0000-0002-0543-8189
authors.initials: B
authors.lastname: Drawert
authors.affiliation: Department of Information Technology, Division of Scientific Computing, Uppsala University, Uppsala, Sweden.
authors.forename: Andreas
authors.initials: A
authors.lastname: Hellander
authors.affiliation: Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Ben
authors.initials: B
authors.lastname: Bales
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Debjani
authors.initials: D
authors.lastname: Banerjee
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bellesia
authors.affiliation: Departments of Biological Sciences and Computer Science, The University of Memphis, Memphis, Tennessee, United States of America.
authors.forename: Bernie J
authors.initials: BJ
authors.lastname: Daigle
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Douglas
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Mengyuan
authors.initials: M
authors.lastname: Gu
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Anand
authors.initials: A
authors.lastname: Gupta
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Stefan
authors.initials: S
authors.lastname: Hellander
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Chris
authors.initials: C
authors.lastname: Horuk
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Dibyendu
authors.initials: D
authors.lastname: Nath
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Aviral
authors.initials: A
authors.lastname: Takkar
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Sheng
authors.identifier: 0000-0002-1626-1729
authors.initials: S
authors.lastname: Wu
authors.affiliation: Department of Information Technology, Division of Scientific Computing, Uppsala University, Uppsala, Sweden.
authors.forename: Per
authors.initials: P
authors.lastname: Lötstedt
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Chandra
authors.identifier: 0000-0003-4972-0669
authors.initials: C
authors.lastname: Krintz
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America.|Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Linda R
authors.initials: LR
authors.lastname: Petzold
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D012984:Software; D013269:Stochastic Processes