1 research outputs found
Finding the fixed points of a Boolean network from a positive feedback vertex set
In the modeling of biological systems by Boolean networks a key problem is
finding the set of fixed points of a given network. Some constructed algorithms
consider certain structural properties of the interaction graph like those
proposed by Akutsu et al. in \cite{akutsu1998system,zhang2007algorithms} which
consider a feedback vertex set of the graph. However, these methods do not take
into account the type of action (activation, inhibition) between its
components.
In this paper we propose a new algorithm for finding the set of fixed points
of a Boolean network, based on a positive feedback vertex set of its
interaction graph and which works, by applying a sequential update schedule, in
time , where is the number of components. The
theoretical foundation of this algorithm is due a nice characterization, that
we give, of the dynamical behavior of the Boolean networks without positive
cycles and with a fixed point.
An executable file of \Afp made in Java and some examples of input files are
available at:
\href{http://www.inf.udec.cl/~lilian/FPCollector/}{\url{www.inf.udec.cl/~lilian/FPCollector/}