Investigating the relation between the structure and behavior of complex
biological networks often involves posing the following two questions: Is a
hypothesized structure of a regulatory network consistent with the observed
behavior? And can a proposed structure generate a desired behavior? Answering
these questions presupposes that we are able to test the compatibility of
network structure and behavior. We cast these questions into a parameter search
problem for qualitative models of regulatory networks, in particular
piecewise-affine differential equation models. We develop a method based on
symbolic model checking that avoids enumerating all possible parametrizations,
and show that this method performs well on real biological problems, using the
IRMA synthetic network and benchmark experimental data sets. We test the
consistency between the IRMA network structure and the time-series data, and
search for parameter modifications that would improve the robustness of the
external control of the system behavior.
Description
[1005.2107] Efficient parameter search for qualitative models of regulatory networks using symbolic model checking
%0 Generic
%1 Batt2010
%A Batt, Grégory
%A Page, Michel
%A Cantone, Irene
%A Goessler, Gregor
%A Monteiro, Pedro T.
%A Jong, Hidde De
%D 2010
%K proj:0915
%T Efficient parameter search for qualitative models of regulatory networks
using symbolic model checking
%U http://arxiv.org/abs/1005.2107
%X Investigating the relation between the structure and behavior of complex
biological networks often involves posing the following two questions: Is a
hypothesized structure of a regulatory network consistent with the observed
behavior? And can a proposed structure generate a desired behavior? Answering
these questions presupposes that we are able to test the compatibility of
network structure and behavior. We cast these questions into a parameter search
problem for qualitative models of regulatory networks, in particular
piecewise-affine differential equation models. We develop a method based on
symbolic model checking that avoids enumerating all possible parametrizations,
and show that this method performs well on real biological problems, using the
IRMA synthetic network and benchmark experimental data sets. We test the
consistency between the IRMA network structure and the time-series data, and
search for parameter modifications that would improve the robustness of the
external control of the system behavior.
@misc{Batt2010,
abstract = { Investigating the relation between the structure and behavior of complex
biological networks often involves posing the following two questions: Is a
hypothesized structure of a regulatory network consistent with the observed
behavior? And can a proposed structure generate a desired behavior? Answering
these questions presupposes that we are able to test the compatibility of
network structure and behavior. We cast these questions into a parameter search
problem for qualitative models of regulatory networks, in particular
piecewise-affine differential equation models. We develop a method based on
symbolic model checking that avoids enumerating all possible parametrizations,
and show that this method performs well on real biological problems, using the
IRMA synthetic network and benchmark experimental data sets. We test the
consistency between the IRMA network structure and the time-series data, and
search for parameter modifications that would improve the robustness of the
external control of the system behavior.
},
added-at = {2010-05-13T15:01:53.000+0200},
author = {Batt, Grégory and Page, Michel and Cantone, Irene and Goessler, Gregor and Monteiro, Pedro T. and Jong, Hidde De},
biburl = {https://www.bibsonomy.org/bibtex/2accac440649d0258cddbafdc228468e4/wnpxrz},
description = {[1005.2107] Efficient parameter search for qualitative models of regulatory networks using symbolic model checking},
interhash = {60548fdffac8ba6fb3c5b49aea045a4d},
intrahash = {accac440649d0258cddbafdc228468e4},
keywords = {proj:0915},
note = {cite arxiv:1005.2107
Comment: },
timestamp = {2010-05-13T15:01:53.000+0200},
title = {Efficient parameter search for qualitative models of regulatory networks
using symbolic model checking},
url = {http://arxiv.org/abs/1005.2107},
year = 2010
}