Threshold logic gene regulatory model - Prediction of dorsal-ventral patterning and hardware-based simulation of drosophila

Tejaswi Gowda, Samuel Leshner, Sarma Vrudhula, Seungchan Kim

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

1 Scopus citations

Abstract

Precise characterization of gene regulatory mechanisms is a fundamental problem in developmental biology. In this paper we present a new gene regulatory network (GRN) model which is based on threshold logic (TL). Two different set of genes are responsible for the cell patterning of the Drosophila embryo. By using the proposed threshold logic gene regulatory model (TLGRM), we derive the different gene regulatory rules for the gene products involved. We use these rules to model and explain the interaction between the genes. Very large or complex gene regulatory networks are difficult to simulate using a general purpose CPU. Specialized programmable hardware provides additional concurrency and is an alternative to a large and expensive cluster of machines. The steady state gene expression predicted by the model clearly mimics the actual wild-type gene expression along the dorsal-ventral axis in the Drosophila embryo. We thus demonstrate that for a well characterized gene regulatory system, the nature and topology of interaction is enough to model gene regulation. We also demonstrate through proof of concept that using hardware-based simulation, it is possible to achieve orders of magnitude of performance improvement over conventional CPU-based simulation.

Original languageEnglish (US)
Title of host publicationBIODEVICES 2008 - Proceedings of the 1st International Conference on Biomedical Electronics and Devices
Pages212-219
Number of pages8
StatePublished - Dec 1 2008
EventBIODEVICES 2008 - 1st International Conference on Biomedical Electronics and Devices - Funchal, Madeira, Portugal
Duration: Jan 28 2008Jan 31 2008

Publication series

NameBIODEVICES 2008 - Proceedings of the 1st International Conference on Biomedical Electronics and Devices
Volume1

Other

OtherBIODEVICES 2008 - 1st International Conference on Biomedical Electronics and Devices
CountryPortugal
CityFunchal, Madeira
Period1/28/081/31/08

Keywords

  • Drosophila embryo patterning
  • Gene regulation
  • Modeling and simulation of gene systems
  • Threshold logic

ASJC Scopus subject areas

  • Biomedical Engineering
  • Electrical and Electronic Engineering

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    Gowda, T., Leshner, S., Vrudhula, S., & Kim, S. (2008). Threshold logic gene regulatory model - Prediction of dorsal-ventral patterning and hardware-based simulation of drosophila. In BIODEVICES 2008 - Proceedings of the 1st International Conference on Biomedical Electronics and Devices (pp. 212-219). (BIODEVICES 2008 - Proceedings of the 1st International Conference on Biomedical Electronics and Devices; Vol. 1).