THRESHOLD LOGIC GENE REGULATORY MODEL - Prediction of Dorsal-ventral Patterning and Hardware-based Simulation of Drosophila

Tejaswi Gowda, Samuel Leshner, Sarma Vrudhula, Seungchan Kim

2008

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.

Paper Citation

in Harvard Style

Gowda T., Leshner S., Vrudhula S. and Kim S. (2008). THRESHOLD LOGIC GENE REGULATORY MODEL - Prediction of Dorsal-ventral Patterning and Hardware-based Simulation of Drosophila . In Proceedings of the First International Conference on Biomedical Electronics and Devices - Volume 1: BIODEVICES, (BIOSTEC 2008) ISBN 978-989-8111- 17-3, pages 212-219. DOI: 10.5220/0001054302120219

in Bibtex Style

@conference{biodevices08,
author={Tejaswi Gowda and Samuel Leshner and Sarma Vrudhula and Seungchan Kim},
title={THRESHOLD LOGIC GENE REGULATORY MODEL - Prediction of Dorsal-ventral Patterning and Hardware-based Simulation of Drosophila},
booktitle={Proceedings of the First International Conference on Biomedical Electronics and Devices - Volume 1: BIODEVICES, (BIOSTEC 2008)},
year={2008},
pages={212-219},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0001054302120219},
isbn={978-989-8111- 17-3},
}

in EndNote Style

TY - CONF
JO - Proceedings of the First International Conference on Biomedical Electronics and Devices - Volume 1: BIODEVICES, (BIOSTEC 2008)
TI - THRESHOLD LOGIC GENE REGULATORY MODEL - Prediction of Dorsal-ventral Patterning and Hardware-based Simulation of Drosophila
SN - 978-989-8111- 17-3
AU - Gowda T.
AU - Leshner S.
AU - Vrudhula S.
AU - Kim S.
PY - 2008
SP - 212
EP - 219
DO - 10.5220/0001054302120219