Authors:
Sohei Ito
1
;
Shigeki Hagihara
2
and
Naoki Yonezaki
2
Affiliations:
1
National Fisheries University, Japan
;
2
Tokyo Institute of Technology, Japan
Keyword(s):
Gene Regulatory Network, Homeostasis, Temporal Logic, Realisability.
Related
Ontology
Subjects/Areas/Topics:
Agents
;
Algorithms and Software Tools
;
Artificial Intelligence
;
Bioinformatics
;
Biomedical Engineering
;
Enterprise Information Systems
;
Information Systems Analysis and Specification
;
Methodologies and Technologies
;
Operational Research
;
Simulation
;
Systems Biology
Abstract:
Toward the system level understanding of the mechanisms contributing homeostasis in organisms, a computational
framework to model a system and analyse its properties is indispensable. The purpose of this work is to
provide a framework which enables testing and validating homeostatic properties on gene regulatory networks
in silico. Based on a qualitative analysis framework for gene networks using temporal logic, we proposed
a novel formulation of homeostasis by the notion of realisability. This formulation of homeostasis yields a
qualitative method to analyse homeostasis of gene networks. In this formulation, homeostasis is captured by
a response not for just an instantaneous stimulation such as dose-response relationships but for any input scenario
e.g. oscillating or continuous inputs, which is difficult to be captured by quantitative models. Moreover,
we can consider any number of inputs from an environment without difficulty. Such flexibility is a notable
advantage of our framewo
rk. We demonstrate the usefulness of our framework in analysing a number of small
but tricky networks.
(More)