"
Team:KULeuven/Model/Reset
From 2008.igem.org
Result:
To have a dropdown for your own team copy over all of the content below. It might be needed to adjust a thing or two. Comments have been added throughout the code what must be changed.
Inspirational websites:
- [http://javascript-array.com/scripts/simple_drop_down_menu/ Most basic dropdown menu, with no submenu's]
- [http://jquery.com/ The javascript library used to add effects and optimise the dropdown]
- [http://www.tyssendesign.com.au/articles/css/centering-a-dropdown-menu/ How to center a ul list effectively]
The dropdown has been created and developed by the KULeuven team.
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<ul>
<li>
<a href="https://2008.igem.org/Team:KULeuven">Home</a>
</li>
<li>
<a>The Team</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Team/LabsandGroups">Research Labs and Groups</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Students">Students</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Instructors">Instructors</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Advisors">Advisors</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Pictures">Pictures</a>
</div>
</li>
<li>
<a>The Project</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Project">Summary</a>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Project/Input">Input</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Evaluation">End Evaluation</a>
<a href="https://2008.igem.org/Team:KULeuven/Literature">Literature</a>
<a href="https://2008.igem.org/Team:KULeuven/Brainstorm">Brainstorm</a>
</div>
</li>
<li>
<a>Ethics</a>
<div>
</div>
</li>
<li>
<a>Submitted Parts</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Parts">Listing</a>
<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=KULeuven">Sandbox</a>
</div>
</li>
<li>
<a>Modeling</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Model/Overview">Overview</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/KineticConstants">Kinetic Constants</a>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Model/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Model/FullModel">Full Model</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Sensitivity">Sensitivity Analysis</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/MultiCell">Multi-cell Model</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Diffusion">Diffusion</a>
</div>
</li>
<li>
<a>Data Analysis</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Data/Overview">Overview</a>
<span>
<a>New Parts</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Data/GFP">GFP (LVA-tag)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/T7">T7 (UmuD-tag)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Antisense">Antisense LuxI</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/ccdB">Celldeath (ccdB)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/HybridProm">Hybrid Promotor</a>
</div>
</span>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Data/Input">Input</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Data/FullModel">Full Model</a>
</div>
</li>
<li>
<a>Software</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Software/MultiCell">Multi-cell Toolbox</a>
<a href="https://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeX">Simbiology2LaTeX Toolbox</a>
</div>
</li>
<li>
<a>Notebook</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Meeting_Calendar">Calendar</a>
<a href="https://2008.igem.org/Team:KULeuven/SummerHolidays">Summer Holidays</a>
<span>
<a>Reports</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Meeting Reports">Daily</a>
<a href="https://2008.igem.org/Team:KULeuven/Weekly Meetings">Weekly</a>
</div>
</span>
<span>
<a>Lab Data</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Freezer">Freezer</a>
<a href="https://2008.igem.org/Team:KULeuven/Primers">Primers</a>
<a href="https://2008.igem.org/Team:KULeuven/Ligation">Ligation</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Tools">Tools</a>
<a href="https://2008.igem.org/Team:KULeuven/Press">Press</a>
<a href="https://2008.igem.org/Team:KULeuven/Guestbook">Guestbook</a>
</div>
</li>
</ul>
</div>
</div>
</html>
Contents |
Pulse Generator
Position in the system
Describing the system
ODE's
Parameters
| Name | Value | Comments | Reference |
|---|---|---|---|
| Degradation rates | |||
| dRNA_cI | 0.00462 s-1 | ||
| dcI | 7.0E-4 s-1 | [http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters link] | |
| dRNA_Lac | 0.00231 s-1 | ||
| dLac | 2.888E-4 s-1 | ||
| dRNA_Ribokey:cI | 0.00231 s-1 | ||
| Dissociation constants | |||
| KRibokey:cI | 0.00212 | kass/kdiss for the Ribokey cI complex | |
| KcI | 0.00337 | binding cI on cI-Promotor | [http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters link] |
| Transcription rates | |||
| kRNA_cI | 0.025? s-1 | maximal transcription rate RNA cI (no cI repressor present) | |
| kRNA_Lac | 0.025? s-1 | ||
| Translation rates | |||
| kcI | 0.167? s-1 | ||
| kLac | 0.167 s-1 | RBS is B0032 (efficiency 0.3) | [http://partsregistry.org/Part:BBa_B0032 link] |
| Hill cooperativity | |||
| ncI | 2.0 | [http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters link] | |
Models
CellDesigner (SBML file)
Matlab
The diagram for the pulse generator system is shown below:
Following figure shows the repons of the pulse generator to a step signal of T7 polymerase.
...
Constant Lactonase Production
Position in the system
The Constant Lactonase Production-system is directly linked to the Filter.
When the filter indicates that the input is zero (there is no light), the system will (ideally) produce no lactonase. As soon as the output of the filter is one, the system starts producing lactonase and remains doing this untill the light goes off again.
Describing the system
ODE's
Parameters
| Name | Value | Comments | Reference |
|---|---|---|---|
| Degradation Constants | |||
| dlactonase | 2.888E-4 s-1 | ||
| dclosed_mRNA_lactonase | 0.0046209812 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| dopen_mRNA_lactonase | 0.0023104906 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| dopen_mRNA_lactonase_complex | 0.0023104906 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| Transcription Rates | |||
| kmRNA_lactonase | 0.03 s-1 | ||
| Translation Rates | |||
| klactonase | 0.1666667 s-1 | RBS is B0032 (efficiency of 0.3) | |
| Equilibrium constants | |||
| Keq_1 | 0.015 | closed and open mRNA | |
| Keq_2 | 0.0212 M | closed and key (binded with ribokey) complex mRNA | |
| Association/Dissociation/Reaction Rates | |||
| kass (closed mRNA lactonase + mRNA Ribokey) | 2.12 s-1 | ||
| kdiss (closed mRNA lactonase + mRNA Ribokey) | 100 s-1 | ||
| k (open mRNA lactonase) | 1.5 s-1 | ||
| k (closed mRNA lactonase) | 100 s-1 | ||
Models
CellDesigner (SBML file)
The model:
Simulation:
The number lactonase genes is held constant during the entire simulation. For the first 15.000 seconds the number of mRNA Ribokey is equal to 0.015 and the number of pT7 molecules to 0.4, then for 15000 s these numbers are set on 6 and 3 respectively (based on the results of the model of the filter) after which they are reduced back to 0.015 and 0.4.
We see that an increase in the number of mRNA Ribokey and pT7(due to an increase in light intensity) will lead to a much higher number of lactonase molecules.
