BNS
BNS is a software tool for computing attractors in Boolean Networks with Synchronous update.
Synchronous Boolean networks [1] are used for the modeling of genetic regulatory networks.
BNS implements the algorithm presented in [2]
which is based on a SAT-based bounded model checking.
BNS uses much less space compared to BooleNet or other BDD-based approaches for computing attractors.
It can handle several orders of magnitude larger networks.
BNS reads in a Boolean network description represented in a .cnet format similar to the
Berkeley Logic Interchange Format (BLIF) format commonly used in synthesis
and verification tools and prints out the set of network's attractors.
BNS binaries are available for the following platforms:
- Linux: BNS-1.0. Tested on Red Hat Enterprise kernel 2.6.18, Ubuntu 8.04 (64 bit), and Fedora Core 8.
- Windows Cygwin: BNS-1.0. Tested on cygwin1.dll version 1.5.25.
The source code of BNS is available here. MiniSAT which availible to dowload from here is used in BNS as a SAT-solver. MiniSAT v1.14 for Linux Ubuntu 14.04 LTS is available here.
User manual for BNS.
TEST INPUT FILES
You can use the following files to test BNS:
You can also test BNS on randomly generated graphs. Statistical features of randomly generated Boolean
networks on the critical line are believed to capture the dynamics of genetic regulatory networks
of living organisms [1]. The following simple program
will generate you an n-node random Boolean network on the critical line in the .cnet format.
REFERENCES:
[1] Boolean Dynamics with Random Couplings, M. Aldana, S. Coopersmith, L. P. Kadanoff, 2002, http://arXiv.org/abs/nlin/0204062.
[2] "A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks", E. Dubrova, M. Teslenko, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 5, 2011, pp. 1393-1399.
[3] "From Genes to Flower Patterns and Evolution: Dynamic Models of Gene Regulatory Networks",
A. Chaos, M. Aldana, C. Espinosa-Soto, B. G. P. de Leon, A. G. Arroyo, E. R. Alvarez-Buylla,
Journal of Plant Growth Regulation, vol. 25, n. 4, 2006, pp. 278-289.
[4] "A Method for the Generation of Standardized Qualitative Dynamical Systems of Regulatory Networks", L. Mendoza and I. Xenarios, Journal of Theoretical Biology and Medical Modeling, 2006, vol. 3, no. 13.
[5] "A Methodology for the Structural and Functional Analysis of Signaling and Regulatory Networks", S. Klamt, J. Saez-Rodriguez, J. A. Lindquist, L. Simeoni, E. D. Gilles, JBMC Bioinformatics, 2006, vol. 7, no. 56.
[6] "Dynamical Analysis of a Generic Boolean Model for the Control of the Mammalian Cell Cycle", A. Faure, A. Naldi, C. Chaouiya, D. Thieffry, Bioinformatics, 2006, vol. 22, no. 14, pp. e124-e131.
[7] "Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast", M. I. Davidich, S. Bornholdt, PLoS ONE. 2008 Feb 27, 3(2):e1672.
[8] "The Yeast Cell-Cycle Network is Robustly Designed", Fangting Li, Tao Long, Ying Lu, Qi Ouyang, Chao Tang, PNAS April 6, 2004, vol. 101 no. 14, 4781-4786.
[9] "The Topology of the Regulatory Interactions Predicts the Expression Pattern of the Segment Polarity Genes in Drosophila Melanogaster", R. Albert and H. G. Othmer, Journal of Theoretical Biology, 2003, vol. 223, no. 1, pp. 1-18.
CONTACT PERSON:
Elena Dubrova
Department of Electronics, Computer and Software
School of Information and Communication Technology
dubrova@kth.se