Team:LCG-UNAM-Mexico/Parameters
From 2008.igem.org
(New page: <html> <head> <title>LCG-UNAM-Mexico:Modeling</title> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <link rel="stylesheet" href="http://mx.geocities.com/apocaliptyc...) |
|||
Line 111: | Line 111: | ||
<br /> | <br /> | ||
- | <a href=" | + | <a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Modeling"><img src="https://static.igem.org/mediawiki/2008/5/5b/Model1a.jpg" border="0" /></a> <a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Parameters"><img src="https://static.igem.org/mediawiki/2008/4/43/Model2.jpg" border="0" /></a> <a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Simulation"><img src="https://static.igem.org/mediawiki/2008/7/7f/Model3.jpg" border="0" /></a><br> |
<a name="modeling"></a><img src="https://static.igem.org/mediawiki/2008/9/99/Ribbon435773498.gif" alt="ribbon" width="579" height="9" /><br /> | <a name="modeling"></a><img src="https://static.igem.org/mediawiki/2008/9/99/Ribbon435773498.gif" alt="ribbon" width="579" height="9" /><br /> | ||
</div> | </div> | ||
<table border="0" cellspacing="0" cellpadding="2" width="590"> | <table border="0" cellspacing="0" cellpadding="2" width="590"> | ||
- | <td class="pageName"><div align="center">Parameters & kinetics </div></td> | + | <td class="pageName"><div align="center"><br> |
+ | Parameters & kinetics </div></td> | ||
<tr> | <tr> | ||
<td valign="top" class="bodyText"><p align="justify"><br> | <td valign="top" class="bodyText"><p align="justify"><br> | ||
Line 449: | Line 450: | ||
<p class="style2">Defining the initial state of the system</p> | <p class="style2">Defining the initial state of the system</p> | ||
<p align="justify"> The initial concentrations of the constitutive proteins (AiiA, LuxR, CI -constitutive synthesis- and CI:CI -due to constitutive synthesis-) were estimated based on the efficiency rate of their promoters, number of promoters per cell, degradation rate of their mRNAs, translation efficiency and degradation rate of the proteins. Initial concentrations of AHL:LuxR complex, the dimer of complexes, CI and CI:CI due to complex activation were set to 0, given these are all due to the action of AHL. Number of copies of both <em>cI</em> and <em>rcnA</em> promoters are 10 based on plasmid copy number. RcnA and Unk were estimated experimentally and set consistent to the observed rate. Concentration of AHL and nickel is determined by us to obtain the desired results. </p> | <p align="justify"> The initial concentrations of the constitutive proteins (AiiA, LuxR, CI -constitutive synthesis- and CI:CI -due to constitutive synthesis-) were estimated based on the efficiency rate of their promoters, number of promoters per cell, degradation rate of their mRNAs, translation efficiency and degradation rate of the proteins. Initial concentrations of AHL:LuxR complex, the dimer of complexes, CI and CI:CI due to complex activation were set to 0, given these are all due to the action of AHL. Number of copies of both <em>cI</em> and <em>rcnA</em> promoters are 10 based on plasmid copy number. RcnA and Unk were estimated experimentally and set consistent to the observed rate. Concentration of AHL and nickel is determined by us to obtain the desired results. </p> | ||
- | <p align="justify"> <span class="style3">AHL:</span> It’s an arbitrary and adjustable value. Different outcomes can be observed <a href=" | + | <p align="justify"> <span class="style3">AHL:</span> It’s an arbitrary and adjustable value. Different outcomes can be observed <a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Simulation">manipulating this initial value</a>.<br> |
<span class="style3"><br> | <span class="style3"><br> | ||
- | Nickel (total):</span> It’s an arbitrary and adjustable value. Different outcomes can be observed <a href=" | + | Nickel (total):</span> It’s an arbitrary and adjustable value. Different outcomes can be observed <a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Simulation">manipulating this initial value</a>.<br> |
<span class="style3"><br> | <span class="style3"><br> | ||
Unk:</span> Both the Unk concentration and its rate constant are unknown. They are arbitrarily defined in such a way that the flux of the reaction 9 is consistent with experimental measurements.<br> | Unk:</span> Both the Unk concentration and its rate constant are unknown. They are arbitrarily defined in such a way that the flux of the reaction 9 is consistent with experimental measurements.<br> | ||
Line 503: | Line 504: | ||
<strong>15. </strong>Bologna Cesena Campus, iGEM 2007 WIKI. (<u><a href="http://parts.mit.edu/igem07/index.php/Bologna">http://parts.mit.edu/igem07/index.php/Bologna</a></u>) <br> | <strong>15. </strong>Bologna Cesena Campus, iGEM 2007 WIKI. (<u><a href="http://parts.mit.edu/igem07/index.php/Bologna">http://parts.mit.edu/igem07/index.php/Bologna</a></u>) <br> | ||
<strong>16. </strong>KULeuven team, iGEM 2008 WIKI. Dr. Coli, the bacterial drug delivery system. (<a href="https://2008.igem.org/Team:KULeuven/Model/CellDeath" target="_blank">https://2008.igem.org/Team:KULeuven/Model/CellDeath</a>) </p> | <strong>16. </strong>KULeuven team, iGEM 2008 WIKI. Dr. Coli, the bacterial drug delivery system. (<a href="https://2008.igem.org/Team:KULeuven/Model/CellDeath" target="_blank">https://2008.igem.org/Team:KULeuven/Model/CellDeath</a>) </p> | ||
- | <p align="justify"><a name="simulation"></a><a href="#top"><img src="https://static.igem.org/mediawiki/2008/c/cd/Boton_back.jpg" alt="Back to top" width="190" height="31" border="0"></a><a href=" | + | <p align="justify"><a name="simulation"></a><a href="#top"><img src="https://static.igem.org/mediawiki/2008/c/cd/Boton_back.jpg" alt="Back to top" width="190" height="31" border="0"></a><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Modeling"><img src="https://static.igem.org/mediawiki/2008/5/5b/Model1a.jpg" alt="Modeling the system" width="190" height="31" border="0"></a><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Simulation"><img src="https://static.igem.org/mediawiki/2008/7/7f/Model3.jpg" alt="Simulation&Analysis" width="190" height="31" border="0"></a><br> |
<img src="https://static.igem.org/mediawiki/2008/9/99/Ribbon435773498.gif" alt="ribbon" width="579" height="9" /></p> | <img src="https://static.igem.org/mediawiki/2008/9/99/Ribbon435773498.gif" alt="ribbon" width="579" height="9" /></p> | ||
<p align="justify"><br> | <p align="justify"><br> |
Revision as of 08:04, 28 October 2008
LCG-UNAM-Mexico | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
iGEM 2008 TEAM | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||