GESSA Software
The Graphically Extended Stochastic Simulation Algorithm (GESSA) is a hybrid model of transcriptional reprogramming due to cell signaling. To simulate this complete system, GESSA combines (1) PPBN (Pooled Probabilistic Boolean Network) graphical models of cell signaling; (2) Stochastic Simulation Algorithm (SSA) models for transcription and translation processes; (3) diffusion of external signals (ligands); and (4) active transport of specifed molecular species.
The files provided here include an open source implementation of the GESSA in Matlab (release 2008b or later). This software is copyright Michael Ochs, Elana Fertig, and Ludmila Danilova (2010) and released under the GNU General Public License version 3.
Configuration files for simulations of C. elegans vulval development are included with the software release below. Parameter selections for these simulations are described in ParameterSupplement.pdf.
Please read the Users Manual for installation and running instructions of GESSA. For any questions and citation information, please contact Ludmila Danilova, Elana Fertig, or Michael Ochs.GESSA source: GESSA-1.0.0.zip
User's manual: GESSAUsersManual.pdf
Parameter selection: ParameterSupplement.pdf
PPBN algorithm description: PPBNSupplement.pdf
