CplexA
CplexA is a
software package, available for Mathematica, Python, and Matlab, to study the effects of
macromolecular assembly on cellular processes. A main challenge for
conventional computational methods to study macromolecular assembly is
tackling the exponential increase of the number of configurational
states with the number of components. CplexA uses functional
programming to efficiently compute probabilities and average properties
over such exponentially large number of states from the energetics of
the interactions. The package is particularly suited to study gene
expression at complex promoters controlled by multiple, local and
distal, DNA binding sites for transcription factors.
References
- The main reference for CplexA is Vilar, J.M.G. and Saiz, L.
(2010) CplexA:
a Mathematica package to study macromolecular-assembly
control of gene expression, Bioinformatics 26, 2060-2061.
- The biophysical background of the methods used by CplexA are
described in Saiz, L. and Vilar, J.M.G. (2006) Stochastic
dynamics of
macromolecular-assembly networks, Mol Syst Biol, 2, 2006.0024.
Availability
Online
Tutorials
Contact Information