Leveraging Compute Clusters for Large-Scale Parametric Screens of Reaction-Diffusion Systems

Md Shahriar Karim, Hans G. Othmer, David M. Umulis

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Reaction-diffusion (RD) models are widely used to study the spatio-temporal evolution of pattern formation during development. Nonlinear RD models are often analytically intractable, and require numerical solution methods. Interrogation of RD models for a large physiological range of parameters covers many orders of magnitude, establishing situations where solutions are stiff and solvers fail to provide accurate results to the time-dependent problem. The spatial dependence of these parameters, and the nonlinearity of the underlying dynamics, impose additional challenges. We developed an efficient approach for simulating stiff RD models of pattern formation and we used supercomputer clusters to carry out a large screen of spatially varying parameters. The proposed approach generated data for screening of RD systems within a reasonable amount of time (a few days), which scales down further if additional cluster nodes are available. The approaches outlined herein are applicable to any systems biology problem requiring numerical approximation of RD equations with spatially non-uniform properties and stiff nonlinear reactions.

Original languageEnglish (US)
Title of host publicationProceedings - 26th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2018
EditorsIgor Kotenko, Ivan Merelli, Pietro Lio
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages706-713
Number of pages8
ISBN (Electronic)9781538649756
DOIs
StatePublished - Jun 6 2018
Event26th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2018 - Cambridge, United Kingdom
Duration: Mar 21 2018Mar 23 2018

Publication series

NameProceedings - 26th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2018

Other

Other26th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2018
CountryUnited Kingdom
CityCambridge
Period3/21/183/23/18

Keywords

  • Cluster computing
  • In-silico data
  • Large-scale screens
  • Reaction-diffusion models
  • Systems biology

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