Gene Regulation Simulation Tool



       



Gene Regulation Simulation is based on the computational model described in [1] with several extensions. It consists of two programs. The first ("net2text") implements an interface for the user and the second ("model") performs the simulations and outputs their results.
All the information (general information, project aims, implementation details and user guide) is included in this report.




screenshot



graph


Download examples of inputs and outputs (the inputs are in the intermediate text format).
Download meiosisInYeast.cys.




Files:

1. net2text.jar
2. model.jar

You need to install Cytoscape. Move "model" to Cytoscape's folder and "net2text" to Cytoscape's "plugins" folder.




Refernces:

[1] “Faithful modeling of transient expression and its application to elucidating negative feedback regulation”, Amir Rubinstein, Vyacheslav Gurevich, Zohar Kasulin-Boneh, Lilach Pnueli, Yona Kassir, and Ron Y.Pinter, www.pnas.org/cgi/doi/10.1073/pnas.0611168104.