Team:Groningen/modeling files.html


Modeling Files

Single-Cell Model Files

These files where used to model the single cell interval switch:

Note: please be sure to rename all the files below after downloading, with the correct extension as indicated in the table! They are not all text files!
ModelBrickReadme.txtReadme for ModelBrick Assembler
mba.mMATLAB script file for automatic assembly of modelbricks. (Not text!)
modelbricks.zipcontains all parts used in .xml format. (Not text!)
partslibrary.matMATLAB workspace file containing all parts used in SimBiology model format. (Not text!)
Intervalswitch.sbprojThis SimBiology project file contains the complete, assembled, interval switch. The 'diagram overview' option shows the structure of the model. The 'model tasks - conserved cycles' option shows the flow of RNA polymerases and Ribosomes through the system as well as the dynamics of promoter states. (Not text!)

Please refer to the readme file for further information on usage.

The detailed "modelbrick" descriptions can be found in this appendix.

Spatial Model Files

The Matlab ".M" file implementing the spatial model can be found here. However it is renamed as a ".txt" file for Wiki-reasons. Please rename it to "spatial_model.m" before use!