Scalable open-source reconfigurable architecture for bacterial quorum sensing simulations

Alan Ehret, Peter Jamieson, Michel A. Kinsy

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

1 Scopus citations

Abstract

Quorum sensing in cells is a generalized framework for modeling and analyzing the local density of the bacterial population in a given biological environment. It has applications in biology, medical and therapeutic domains, e.g., cancer cell research. Software-based simulations are generally slow and only provide a certain level of functional faithfulness or model fidelity. In this work we introduce a scalable open-source architecture to accelerate bacterial quorum sensing simulations called ABAQS (Agent Based Architecture for Quorum sensing Simulation). The presented architecture allows researchers to create and launch new simulations by quickly incorporating custom cell models. The architecture is highly modular and separates the functional model from control logic. It has a simple interface to enable users to readily connect their custom models to the simulation platform. To illustrate the proposed architecture, we present the implementation details and results for a small-scale model representing up to 81 cells which we have synthesized and configured on an FPGA. We also highlight some of the key features to be implemented in future versions of the proposed architecture. The open-source license of this project will allow other researchers to contribute and improve the architecture to (a) better fit their quorum sensing simulations and (b) give the community a flexible simulation acceleration tool.

Original languageEnglish (US)
Title of host publicationProceedings of the 9th International Symposium on Highly-Efficient Accelerators and Reconfigurable Technologies, HEART 2018
PublisherAssociation for Computing Machinery
ISBN (Electronic)9781450365420
DOIs
StatePublished - Jun 20 2018
Externally publishedYes
Event9th International Symposium on Highly-Efficient Accelerators and Reconfigurable Technologies, HEART 2018 - Toronto, Canada
Duration: Jun 20 2018Jun 22 2018

Publication series

NameACM International Conference Proceeding Series

Conference

Conference9th International Symposium on Highly-Efficient Accelerators and Reconfigurable Technologies, HEART 2018
Country/TerritoryCanada
CityToronto
Period6/20/186/22/18

Keywords

  • Agent Based Simulation
  • FPGA Simulation
  • Quorum Sensing

ASJC Scopus subject areas

  • Software
  • Human-Computer Interaction
  • Computer Vision and Pattern Recognition
  • Computer Networks and Communications

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