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Team:Groningen/modeling files.html
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| - | <a href=" | + | <a href=""> Modeling </a> |
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<li class="sub"><a href="https://2008.igem.org/Team:Groningen/modeling_SingleCell.html"> Single-cell </a></li> | <li class="sub"><a href="https://2008.igem.org/Team:Groningen/modeling_SingleCell.html"> Single-cell </a></li> | ||
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<li class="sub"><a href="https://2008.igem.org/Team:Groningen/results.html#results"> Results </a></li> | <li class="sub"><a href="https://2008.igem.org/Team:Groningen/results.html#results"> Results </a></li> | ||
<li class="sub"><a href="https://2008.igem.org/Team:Groningen/results.html#conclusion"> Conclusion </a></li> | <li class="sub"><a href="https://2008.igem.org/Team:Groningen/results.html#conclusion"> Conclusion </a></li> | ||
| + | <li class="sub"><a href="https://2008.igem.org/Team:Groningen/iGEM_Criteria">iGEM Criteria</a></li> | ||
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| - | <a href=" | + | <a href="">About...</a> |
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<li class="sub"><a href="https://2008.igem.org/Team:Groningen/team.html"> The Team </a></li> | <li class="sub"><a href="https://2008.igem.org/Team:Groningen/team.html"> The Team </a></li> | ||
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| - | These files where used to model the single cell interval switch:<br> | + | 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> | ||
| - | <tr><td><a href="https://static.igem.org/mediawiki/igem.org/3/39/Groningen2008_Mba.txt">mba.m</td><td>MATLAB script file for automatic assembly of modelbricks.</td></tr> | + | <tr><td><a href="https://static.igem.org/mediawiki/igem.org/3/39/Groningen2008_Mba.txt">mba.m</td><td>MATLAB script file for automatic assembly of modelbricks. (Not text!)</td></tr> |
| - | <tr><td><a href="https://static.igem.org/mediawiki/igem.org/9/91/Groningen2008_Modelbricks.txt">modelbricks.zip</td><td>contains all parts used in .xml format.</td></tr> | + | <tr><td><a href="https://static.igem.org/mediawiki/igem.org/9/91/Groningen2008_Modelbricks.txt">modelbricks.zip</td><td>contains all parts used in .xml format. (Not text!)</td></tr> |
<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. (Not text!)</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 | ||
| + | dynamics of promoter states. (Not text!)</td></tr> | ||
</table> | </table> | ||
| - | Please refer to the readme file for further information on usage. | + | <p>Please refer to the readme file for further information on usage.</p> |
| - | + | <p>The detailed <a href="https://2008.igem.org/Team:Groningen/modeling_SingleCell.html#modelbrick">"modelbrick"</a> descriptions can be found <a href="https://static.igem.org/mediawiki/2008/f/f7/Groningen2008_Modelling_details.pdf">in this appendix.</a></p> | |
| - | </p> | + | <div class="headcontainer"><h2>Spatial Model Files</h2></div> |
| - | <div class="headcontainer"><h2> | + | |
<p> The Matlab ".M" file implementing the spatial model <a href="https://static.igem.org/mediawiki/2008/b/b2/Groningen2008_Spatial_model.txt">can be found here</a>. However it is renamed as a ".txt" file for Wiki-reasons. Please rename it to "spatial_model.m" before use!</p> | <p> The Matlab ".M" file implementing the spatial model <a href="https://static.igem.org/mediawiki/2008/b/b2/Groningen2008_Spatial_model.txt">can be found here</a>. However it is renamed as a ".txt" file for Wiki-reasons. Please rename it to "spatial_model.m" before use!</p> | ||
</div> | </div> | ||
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Latest revision as of 03:28, 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. (Not text!) |
| modelbricks.zip | contains all parts used in .xml format. (Not text!) |
| partslibrary.mat | MATLAB workspace file containing all parts used in SimBiology model format. (Not text!) |
| 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 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!
