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Title: Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

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 also demonstrate the capabilities and ease of use of StochSS with an example of model development and simulation at increasing levels of complexity.
Authors:
ORCiD logo [1] ;  [2] ;  [3] ;  [1] ;  [1] ;  [4] ;  [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [1] ; ORCiD logo [1] ;  [2] ; ORCiD logo [1] ;  [5]
  1. Univ. of California Santa Barbara, Santa Barbara, CA (United States). Dept. of Computer Science
  2. Uppsala Univ. (Sweden). Dept. of Information Technology, Division of Scientific Computing
  3. Univ. of California Santa Barbara, Santa Barbara, CA (United States). Dept. of Mechanical Engineering
  4. Univ. of Memphis, Memphis, TN (United States). Dept. of Biological Sciences and Computer Science
  5. Univ. of California Santa Barbara, Santa Barbara, CA (United States). Dept. of Computer Science and Dept. of Mechanical Engineering
Publication Date:
Grant/Contract Number:
sc0008975; R01-EB014877; R01-GM113241; W911NF-09-0001; DMS-1001012
Type:
Accepted Manuscript
Journal Name:
PLoS Computational Biology (Online)
Additional Journal Information:
Journal Name: PLoS Computational Biology (Online); Journal Volume: 12; Journal Issue: 12; Journal ID: ISSN 1553-7358
Publisher:
Public Library of Science
Research Org:
Univ. of California Santa Barbara, Santa Barbara, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division; National Institutes of Health (NIH); Institute for Collaborative Biotechnologies (ICB); US Army Research Office (ARO); National Science Foundation (NSF); eSSENCE Swedish strategic initiative on eScience
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1423939