Analysing Gene Networks with PDP Systems. Arabidopsis thaliana, a Case Study

TitleAnalysing Gene Networks with PDP Systems. Arabidopsis thaliana, a Case Study
Publication TypeConference Contributions
Year of Publication2013
AuthorsValencia-Cabrera, L., García-Quismondo M., Pérez-Jiménez M. J., Su Y., Yu H., & Pan L.
Conference NameEleventh Brainstorming Week on Membrane Computing (11BWMC)
Volume TitleProceedings of the Eleventh Brainstorming Week on Membrane Computing (11BWMC)
ISBN Number978-84-940691-9-2
PublisherFénix Editora
Place PublishedSevilla, España
Date Published08/2013

Gene Regulatory Networks (GRNs) are a useful tool for biologists to understand
the interactions among genes in living organisms. A special kind of GRNs known
as Logic Networks (LNs) has been recently introduced. These networks consider that
the state of one or more genes can in
uence another one. In a previous work, we proposed
a Membrane Computing model which simulates the dynamics of LNs by drawing
on the improved LAPP algorithm. In this paper we provide a case study for our LN
model on a network which regulates the circadian rhythms of long{term studied plant
Arabidopsis thaliana. We outline the software tools employed and propose a methodology
for analysing LNs on our Membrane Computing model. At the end of the paper, some
conclusions and future work are included.

Keywordsbioinformatics, Gene networks, Genetics, LAPP, Logic networks, MeCoSim, Membrane computing, Modelling, Software engineering