Team:Groningen/modeling files.html

From 2008.igem.org

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       <p>
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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>
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<em>Note: please rename all linked files below with the correct extension indicated in the table! They are not all text files!</em>
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<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>
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<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,
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interval switch. The 'diagram overview' option shows the structure of
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the model. The 'model tasks - conserved cycles' option shows the flow
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of RNA polymerases and Ribosomes through the system as well as the
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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:

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.
modelbricks.zipcontains all parts used in .xml format.
partslibrary.matMATLAB workspace file containing all parts used in SimBiology model format.
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 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!