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

  1. 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.
  2. 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

CplexA can be downloaded from http://sourceforge.net/projects/cplexa/.
Mathematica, Python, and Matlab files are available at http://sourceforge.net/projects/cplexa/files/CplexA/.


Online Tutorials



Contact Information

If you have questions and/or comments you can contact Jose Vilar or Leonor Saiz.