publication . Preprint . Article . Other literature type . 2015

MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME

Andreas Hellander;
Open Access English
  • Published: 14 Aug 2015
  • Country: Algeria
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 address...
Subjects
free text keywords: cloud computing, computational experiments, simulation software, spatial stochastic simulation, systems biology, Networking and Information Technology R&D, Bioengineering, Numerical & Computational Mathematics, Applied Mathematics, Numerical and Computational Mathematics, Computation Theory and Mathematics, Computer Science - Computational Engineering, Finance, and Science, Article
Funded by
NIH| Bridging the Gap Between Molecular and Mechanical Control of Cell Morphogenesis
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM113241-03
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NSF| Collaborative Research: Next-Generation Algorithms for Stochastic Spatial Simulation of Cell Polarization
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1001012
  • Funding stream: Directorate for Mathematical & Physical Sciences | Division of Mathematical Sciences
,
NIH| Stochastic Simulation Service: A Cloud Computing Framework for Modeling and Simul
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01EB014877-01
  • Funding stream: NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING

[1] S. J. Altschuler, S. B. Angenent, Y. Wang, and L. F. Wu, On the spontaneous emergence of cell polarity, Nature, 454 (2008), pp. 886-889. [OpenAIRE]

[2] S. Andrews, N. Addy, R. Brent, and A. Arkin, Detailed simulations of cell biology with smoldyn 2.1, PLoS Comput Biol, 6 (2010), p. e1000705. [OpenAIRE]

[3] N. Barkai and S. Leibler, Circadian clocks limited by noise, Nature, 403 (2000), pp. 267-268. [OpenAIRE]

[4] F. T. Bergmann, R. Adams, S. Moodie, J. Cooper, M. Glont, M. Golebiewski, M. Hucka, C. Laibe, A. K. Miller, D. P. Nickerson, B. G. Olivier, N. Rodriguez, H. M. Sauro, M. Scharm, S. Soiland-Reyes, D. Waltemath, F. Yvon, and N. Le Novère, Combine archive and omex format: one file to share all information to reproduce a modeling project, BMC Bioinformatics, 15 (2014), p. 369.

[5] B. Drawert, S. Engblom, and A. Hellander, URDME: a modular framework for stochastic simulation of reactiontransport processes in complex geometries, BMC Systems Biology, 6 (2012), p. 76. [OpenAIRE]

[6] B. Drawert, M. Lawson, L. Petzold, and M. Khammash, The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation, J Chem Phys, 132 (2010), p. 074101. [OpenAIRE]

[7] J. Elf and M. Ehrenberg, Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases, Syst. Biol., 1 (2004), pp. 230-236. [OpenAIRE]

[8] K. Elkabany, A. Staley, and K. Park, Picloud-cloud computing for science. simplified, in SciPy 2010 Python for Scientific Computing Conference, Austin, TX (July 2010), 2010.

[9] M. Elowitz, A. Levine, E. Siggia, and P. Swain, Stochastic gene expression in a single cell, Science, 297 (2002), pp. 1183-1186. [http://www.sciencemag.org/cgi/content/abstract/297/5584/1183]. [OpenAIRE]

[10] D. Fange and J. Elf, Noise induced Min phenotypes in E. coli, PLoS Comput. Biol., 2 (2006), p. e80.

[11] T. Freisinger, B. Klünder, J. Johnson, N. Müller, G. Pichler, G. Beck, M. Costanzo, C. Boone, R. A. Cerione, E. Frey, and R. Wedlich-Söldner, Establishment of a robust single axis of cell polarity by coupling multiple positive feedback loops, Nat Commun, 4 (2013), p. 1807.

[12] C. W. Gardiner, Handbook of stochastic methods for physics, chemistry and the natural sciences, vol. 13 of Springer Series in Synergetics, Springer-Verlag, Berlin, third ed., 2004.

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 address...
Subjects
free text keywords: cloud computing, computational experiments, simulation software, spatial stochastic simulation, systems biology, Networking and Information Technology R&D, Bioengineering, Numerical & Computational Mathematics, Applied Mathematics, Numerical and Computational Mathematics, Computation Theory and Mathematics, Computer Science - Computational Engineering, Finance, and Science, Article
Funded by
NIH| Bridging the Gap Between Molecular and Mechanical Control of Cell Morphogenesis
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM113241-03
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NSF| Collaborative Research: Next-Generation Algorithms for Stochastic Spatial Simulation of Cell Polarization
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1001012
  • Funding stream: Directorate for Mathematical & Physical Sciences | Division of Mathematical Sciences
,
NIH| Stochastic Simulation Service: A Cloud Computing Framework for Modeling and Simul
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01EB014877-01
  • Funding stream: NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING

[1] S. J. Altschuler, S. B. Angenent, Y. Wang, and L. F. Wu, On the spontaneous emergence of cell polarity, Nature, 454 (2008), pp. 886-889. [OpenAIRE]

[2] S. Andrews, N. Addy, R. Brent, and A. Arkin, Detailed simulations of cell biology with smoldyn 2.1, PLoS Comput Biol, 6 (2010), p. e1000705. [OpenAIRE]

[3] N. Barkai and S. Leibler, Circadian clocks limited by noise, Nature, 403 (2000), pp. 267-268. [OpenAIRE]

[4] F. T. Bergmann, R. Adams, S. Moodie, J. Cooper, M. Glont, M. Golebiewski, M. Hucka, C. Laibe, A. K. Miller, D. P. Nickerson, B. G. Olivier, N. Rodriguez, H. M. Sauro, M. Scharm, S. Soiland-Reyes, D. Waltemath, F. Yvon, and N. Le Novère, Combine archive and omex format: one file to share all information to reproduce a modeling project, BMC Bioinformatics, 15 (2014), p. 369.

[5] B. Drawert, S. Engblom, and A. Hellander, URDME: a modular framework for stochastic simulation of reactiontransport processes in complex geometries, BMC Systems Biology, 6 (2012), p. 76. [OpenAIRE]

[6] B. Drawert, M. Lawson, L. Petzold, and M. Khammash, The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation, J Chem Phys, 132 (2010), p. 074101. [OpenAIRE]

[7] J. Elf and M. Ehrenberg, Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases, Syst. Biol., 1 (2004), pp. 230-236. [OpenAIRE]

[8] K. Elkabany, A. Staley, and K. Park, Picloud-cloud computing for science. simplified, in SciPy 2010 Python for Scientific Computing Conference, Austin, TX (July 2010), 2010.

[9] M. Elowitz, A. Levine, E. Siggia, and P. Swain, Stochastic gene expression in a single cell, Science, 297 (2002), pp. 1183-1186. [http://www.sciencemag.org/cgi/content/abstract/297/5584/1183]. [OpenAIRE]

[10] D. Fange and J. Elf, Noise induced Min phenotypes in E. coli, PLoS Comput. Biol., 2 (2006), p. e80.

[11] T. Freisinger, B. Klünder, J. Johnson, N. Müller, G. Pichler, G. Beck, M. Costanzo, C. Boone, R. A. Cerione, E. Frey, and R. Wedlich-Söldner, Establishment of a robust single axis of cell polarity by coupling multiple positive feedback loops, Nat Commun, 4 (2013), p. 1807.

[12] C. W. Gardiner, Handbook of stochastic methods for physics, chemistry and the natural sciences, vol. 13 of Springer Series in Synergetics, Springer-Verlag, Berlin, third ed., 2004.

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