Team:Groningen/modeling files.html
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<p> | <p> | ||
These files where used to model the single cell interval switch:<br></p> | These files where used to model the single cell interval switch:<br></p> | ||
- | <em>Note: please rename all | + | <em>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!</em> |
<table id="SingleCellFileTable"> | <table id="SingleCellFileTable"> | ||
<tr><td><a href="https://static.igem.org/mediawiki/igem.org/1/17/Groningen2008_ModelBrickReadme.txt">ModelBrickReadme.txt</td><td>Readme for ModelBrick Assembler</td></tr> | <tr><td><a href="https://static.igem.org/mediawiki/igem.org/1/17/Groningen2008_ModelBrickReadme.txt">ModelBrickReadme.txt</td><td>Readme for ModelBrick Assembler</td></tr> | ||
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<tr><td><a href="https://static.igem.org/mediawiki/igem.org/c/c9/Groningen2008_Partslibrary.txt">partslibrary.mat</td><td>MATLAB workspace file containing all parts used in | <tr><td><a href="https://static.igem.org/mediawiki/igem.org/c/c9/Groningen2008_Partslibrary.txt">partslibrary.mat</td><td>MATLAB workspace file containing all parts used in | ||
SimBiology model format.</td></tr> | SimBiology model format.</td></tr> | ||
+ | <tr><td><a href="https://static.igem.org/mediawiki/2008/c/c2/Groningen2008_Intervalswitch.txt">Intervalswitch.sbproj</a></td><td>This 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 | ||
+ | evolution of promoter states.</td></tr> | ||
</table> | </table> | ||
<p>Please refer to the readme file for further information on usage.</p> | <p>Please refer to the readme file for further information on usage.</p> |
Revision as of 01:06, 30 October 2008
Modeling Files
Single-Cell Model Files
These files where used to model the single cell interval switch:
ModelBrickReadme.txt | Readme for ModelBrick Assembler |
mba.m | MATLAB script file for automatic assembly of modelbricks. |
modelbricks.zip | contains all parts used in .xml format. |
partslibrary.mat | MATLAB workspace file containing all parts used in SimBiology model format. |
Intervalswitch.sbproj | This 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 evolution of promoter states. |
Please refer to the readme file for further information on usage.
The detailed "modelbrick" descriptions can be found in this appendix.
Single-Cell 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!