Team:KULeuven/Modeling

From 2008.igem.org

(Difference between revisions)
(HSL stuff)
(Inverter)
 
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{{:Team:KULeuven/Tools/Navigation_Bar}}
{{:Team:KULeuven/Tools/Navigation_Bar}}
-
[[Image:kulbanner.jpg|960px]]
+
= Modeling =
-
=Modeling=
+
* [https://static.igem.org/mediawiki/2008/1/19/Numbers.xls Numbers.xls]
-
 
+
-
* [[Image:Numbers.xls]]
+
* [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html Synthetic biology: Engineering Escherichia coli to see light]
* [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html Synthetic biology: Engineering Escherichia coli to see light]
-
==CellDesigner==
+
== CellDesigner ==
-
===[https://static.igem.org/mediawiki/2008/d/d9/Output_v2.zip Output] ===
+
=== [https://static.igem.org/mediawiki/2008/d/d9/Output_v2.zip Output] ===
-
[[Image:output_v2.png|400px|center|Output]]
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[[Image:output_v2.png|500px|center|Output]]
{| border="1"
{| border="1"
-
|+ Parameter values Cell Death
+
|+ Parameter values Output
! Name !! Value !! Reference
! Name !! Value !! Reference
|-
|-
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|  ||  
|  ||  
|-
|-
-
| CFP (protein) || 1.05E-4 /s || [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
+
| CFP (protein) || 1.05E-4 /s || [https://2007.igem.org/ETHZ/Parameters link]
|-
|-
| CFP (mRNA) || 0.0023 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
| CFP (mRNA) || 0.0023 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
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! Transcription Rate
! Transcription Rate
|-
|-
-
| CFP || OmpF dependend ||
+
| CFP || OmpF dependent ||
|-
|-
! Translation Rate
! Translation Rate
|-
|-
-
| CFP || 0.5 /s || Based on effenciency RBS
+
| CFP || 0.167 /s || Based on effenciency RBS
|}
|}
 +
 +
[[Image:Sim_output_1.png|500px|center|Output]]
 +
[[Image:Sim_output_2.png|500px|center|Output]]
 +
[[Image:Sim_output_3.png|500px|center|Output]]
===[https://static.igem.org/mediawiki/2008/4/47/Celldeath.zip Cell Death]===
===[https://static.igem.org/mediawiki/2008/4/47/Celldeath.zip Cell Death]===
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[[Image:celldeath.png|400px|center|Cell Death]]
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[[Image:celldeath.png|800px|center|Cell Death]]
{| border="1"
{| border="1"
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| CcdB (mRNA)|| 0.00231 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
| CcdB (mRNA)|| 0.00231 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
|-
|-
-
| HSL || 1.02E-6/s ||
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| HSL || 1.02E-6/s || [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
|-
|-
! Dissociation Rate
! Dissociation Rate
|-
|-
-
| K_a (HSL+LuxR) || 1E6 /s ||
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| k<sub>a</sub> (HSL+LuxR) || 1E6 /s || chosen to be relatively (to the other rate constants) high and such that K<sub>d</sub> equals 1E-6
|-
|-
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| K_d (HSL+LuxR) || 1 /s ||
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| k<sub>d</sub> (HSL+LuxR) || 1 /s ||
|-
|-
! Dissociation Constant
! Dissociation Constant
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[[Image:inverter_v4.png|400px|center|Inverter]]
[[Image:inverter_v4.png|400px|center|Inverter]]
 +
 +
{| border="1"
 +
|+ Parameter values Inverter
 +
! Name !! Value !! Reference
 +
|-
 +
! Degradation
 +
|  ||
 +
|-
 +
| LuxI (protein) || 0.00231 /s ||
 +
|-
 +
| LuxI (mRNA) || 0.0025 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
 +
| LuxI (complex) || 0.00125 /s ||
 +
|-
 +
| LacI (protein) || 0.00231 /s ||
 +
|-
 +
| LacI (gesloten mRNA) || 0.0046209812 /s ||
 +
|-
 +
| LacI (open mRNA) || 0.0023104906 /s ||
 +
|-
 +
| open mRNA LacI complex || 0.0023104906 /s ||
 +
|-
 +
| HSL || 1.02E-6 /s || [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
 +
|-
 +
! Dissociation Rate
 +
|-
 +
! Transcription Rate
 +
|-
 +
| LacI || 0.0011 /s ||
 +
|-
 +
| LuxI || 0.0025 /s ||
 +
|-
 +
| K_m || 1.0E-10 /s ||
 +
|-
 +
! Translation Rate
 +
|-
 +
| LuxI (RBS B0034) || 0.5 /s ||
 +
|-
 +
| LacI (RBS ?) || 0.16667 /s ||
 +
|-
 +
! Equilibrium Constant
 +
|-
 +
| closed and open mRNA LacI || 0.015 ||
 +
|-
 +
| closed and complex mRNA LacI || 0.0212 /M ||
 +
|-
 +
! Hill coëfficiënt
 +
|-
 +
| n || 2 ||
 +
|-
 +
! Others
 +
|-
 +
| LuxI --> HSL || 0.16 ||
 +
|-
 +
| LuxI (mRNA) + anti sense <-> complex LuxI || 4.22E14 ||
 +
|-
 +
|
 +
|}
===[https://static.igem.org/mediawiki/2008/0/05/Memory.zip Memory]===
===[https://static.igem.org/mediawiki/2008/0/05/Memory.zip Memory]===
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[[Image:Memory.png|400px|center|Memory]]
[[Image:Memory.png|400px|center|Memory]]
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===[https://static.igem.org/mediawiki/2008/7/72/Filter.zip Filter]===
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{| border="1"
 +
|+ Parameter values Memory
 +
! Name !! Value !! Reference
 +
|-
 +
! Degradation
 +
|-
 +
| P2ogr (protein) || 0.002265 /s ||
 +
|-
 +
| P2ogr (mRNA) || 0.002265 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
 +
| P22CII (protein) || 0.002311 /s ||
 +
|-
 +
| P22CII (mRNA)|| 0,0022651 /s || [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
 +
|-
 +
| antimRNA_luxI  || 0.0045303/s ||
 +
|-
 +
! Transcription rate
 +
|-
 +
| P2ogr || 0.0125 || 
 +
|-
 +
| P22CII || 0.0125 ||
 +
|-
 +
| AntimRNA || 0.0094 ||
 +
|-
 +
! Dissociation Constant
 +
|-
 +
| P2-ogr || 4.2156 M || [http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=P22+c2+repressor&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=258&resourcetype=HWCIT link]
 +
|-
 +
| R0053-P22CII || 0.1099 M ||
 +
|-
 +
! Hill coëfficiënt
 +
|-
 +
| n || 2 ||
 +
|-
 +
|}
 +
 
 +
===[https://static.igem.org/mediawiki/2008/8/8b/Filter_Final.zip Filter]===
[[Image:FilterCellD.png|800px|center|filter]]
[[Image:FilterCellD.png|800px|center|filter]]
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[[Image:PulseGenerator.png|400px|center|Pulse Generator]]
[[Image:PulseGenerator.png|400px|center|Pulse Generator]]
 +
 +
===Constant Lactonase production===
 +
 +
===[https://static.igem.org/mediawiki/2008/c/c0/FilterLactonaseCelldeathInverter.zip Partial Model]===
 +
 +
[[Image:Model.png|950px|center|Model]]
==Kinetic Constants==
==Kinetic Constants==
===ETHZ list of parameters===
===ETHZ list of parameters===
-
* [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters ETHZ list of parameters]
+
* [https://2007.igem.org/ETHZ/Parameters ETHZ list of parameters]
===mRNA decay===
===mRNA decay===
*[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays]
*[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays]
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*[http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i11/pdf/bi0158472.pdf Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence]
*[http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i11/pdf/bi0158472.pdf Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence]
*[http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP data T7 team Tsinghua 2007]
*[http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP data T7 team Tsinghua 2007]
 +
*[http://www.jbc.org/cgi/reprint/281/47/35677 Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase]
===LacI - LuxI===
===LacI - LuxI===
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*[http://bioinformatics.oxfordjournals.org/cgi/content/full/21/11/2722#E11 Noise-induced cooperative behavior in a multicell system]
*[http://bioinformatics.oxfordjournals.org/cgi/content/full/21/11/2722#E11 Noise-induced cooperative behavior in a multicell system]
 +
 +
*[http://www.pnas.org/content/93/18/9505 LuxI kinetics]
===HSL stuff===
===HSL stuff===
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*[http://www.pnas.org/content/96/8/4360.full HSL lactone synthesis kinetics by a LuxI-related enzyme]
*[http://www.pnas.org/content/96/8/4360.full HSL lactone synthesis kinetics by a LuxI-related enzyme]
 +
 +
*[http://www.jbc.org/cgi/content/full/279/14/13645#TBL2 Lactonase mediated HSL degradation (hydrolysis)]
===OmpR, OmpF===
===OmpR, OmpF===
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===Psid met P2ogr promotor===
===Psid met P2ogr promotor===
-
*[http://parts.mit.edu/igem07/index.php/Cambridge/Amplifier_project Cambridge amplifier project, combinatie van verschillende promotoren met verschillende activatoren, experimenteel amplification factor bepaald met GFP reporter]
+
*[https://2007.igem.org/Cambridge/Amplifier_project Cambridge amplifier project, combinatie van verschillende promotoren met verschillende activatoren, experimenteel amplification factor bepaald met GFP reporter]
 +
 
 +
*[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=178405 P<sub>sid</sub> promotor with different activators]
===Constitutive promoters===
===Constitutive promoters===
-
*Estimated transcription rate for J23105:[http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters]
+
*Estimated transcription rate for J23105:[https://2007.igem.org/title=ETHZ/Parameters]
*Scale other transcription rate with table in parts registry.
*Scale other transcription rate with table in parts registry.

Latest revision as of 15:17, 22 July 2008

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:

The dropdown has been created and developed by the KULeuven team.

<html>

<style type="text/css">
#content {z-index:4;}
#ddwrapper * {z-index:8 !important;}

div#ddwrapper {
	margin:0;
	padding:0;
	height:28px;
	width:945px;				/* change to adjust imperfections in width */
}
div#ddnav {
	margin:0 auto;				/* needed to center the dropdown */
	padding:0;
	top:5px;
	/* width: 965px */
	visibility:hidden;			/* dropdown is hidden until properly initalised by javascript */
}
div#ddtoggle {
	margin:0;
	position:fixed;
	right:2px;
	top:15px;
	height:10px;
	width:10px;
	z-index:100;
}

#ddnav ul {
	display:table-row;			/* works only for firefox, later adjusted by javascript for IE */
	margin:0 auto;
	padding:0;
}
#ddnav ul li {
	display:table-cell;			/* works only for firefox, later adjusted by javascript for IE */
	list-style:none;
	margin:0;
	padding:0 !important;
	border-right:1px solid #FFF;		/* creates illusion of spacing between tabs */
}
#ddnav ul li:last-child{border-right:none;}
#ddnav a{
	display:block;
	margin:0;
	padding:4px 14px;			/* play with dimensions for size of tabs */
	background-color:#075A90;		/* background color for tabs */
	color:#FFF !important;			/* font color for text in tabs */
	text-align:center;			/* aligning for text in tabs */
	text-decoration:none !important;
	font:bold 10pt Trebuchet MS;		/* font properties for text in tabs */
	outline:0;
}
#ddnav ul li a:hover {background-color:#99CCFF;}/* background color for tabs on mouseover */
#ddnav li a:active {outline:none;}		/* remove standard dotted border for links when clicked (IE) */
#ddnav li a:focus {-moz-outline-style:none;}	/* remove standard dotted border for links when clicked (FF) */
#ddnav div {
	display:none;
	position:absolute;
	width:9em;
	background-color:#000;			/* bug solution, do not change ! */
	border:1px solid #5970B2;		/* border color for dropdown menus */
	opacity:0.9;				/* transparancy of the dropdown menus (FF) */
	filter:alpha(opacity=90);		/* transparancy of the dropdown menus (IE) */
}
#ddnav div a {
	display:block;
	padding:5px 10px;			/* play with dimensions of block element in dropdown menus */
	position:relative;
	font:normal 8pt arial;			/* font properties for text in dropdown menus */
	text-align:left;			/* aligning of text in dropdown menus */
	cursor:pointer;
}
#ddnav div a:hover, #ddnav span a:hover {color:#000 !important;}	/* text color on mouseover */
#ddnav span div {
	position:relative;
	border:none;
	border-bottom:2px groove #5970B2;	/* separator for submenus, groove does not work in FF */
	opacity:1.0;				/* avoid stacking transparancy for submenus (FF) */
	filter:alpha(opacity=100);		/* avoid stacking transparancy for submenus (IE) */
}

/* may want to upload the following pictures to a new location */
.expand {background: url('https://static.igem.org/mediawiki/2008/e/ef/Icon-expand.png') no-repeat 95% 50%;}
.collapse {background: url('https://static.igem.org/mediawiki/2008/c/cd/Icon-collapse.png') no-repeat 95% 50%;}

.docked {background: #99ccff url("https://static.igem.org/mediawiki/2008/6/62/Ddnavundock.png") no-repeat 50% 50%;}
.undocked {background: #99ccff url("https://static.igem.org/mediawiki/2008/e/e4/Ddnavdock.png") no-repeat 50% 50%;}
</style>

<!-- IMPORTANT: save following script under a personalized webspace or download the library at www.jquery.com -->
<script type="text/javascript" src="http://student.kuleuven.be/~s0173901/wiki/js/jquery.js"></script>
<script type="text/javascript">
	function ddnav() {
		$('#ddnav ul li').hover(
			function () {
				$(this).find('div:first').css('display','block');},
			function () {
				$(this).find('div:first').css('display','none');}
		);
	}
			
	function ddnavsub() {
		$('#ddnav span > a').toggle(
			function () {
				$(this).removeClass("#ddnav expand").addClass("#ddnav collapse");
				$(this).parent().find('div:first').slideDown('fast');
				$(this).hover(
					function (){$(this).css('background-color','#99AAFF');},
					function (){$(this).css('background-color','#99AAFF');});},
			function () {
				$(this).removeClass("#ddnav collapse").addClass("#ddnav expand");
				$(this).parent().find('div:first').css('display','none');
				$(this).hover(
					function (){$(this).css('background-color','#99CCFF');},
					function (){$(this).css('background-color','#075A90');});}
		).addClass("#ddnav expand");
	}
	
	/* If you wish to omit the docking feature, remove following function ddtoggle() */	
	function ddtoggle() {
		$('#ddtoggle').toggle(
			function () {
				$(this).removeClass('undocked').addClass('docked');
				$('#ddnav').css('position','fixed');},
			function () {
				$(this).removeClass('docked').addClass('undocked');
				$('#ddnav').css('position','static');}
		);
	}

	function ddalign() {
		var _windowWidth = $(window).width();
		var _leftOffset = (_windowWidth - 965)/2;

		$('div#ddnav').css('left',_leftOffset);
	}
			
	function ddmsie() {
		$('#ddnav a').hover(
			function () {$(this).css('background-color','#99ccff');},
			function () {$(this).css('background-color','#075a90');}
		);
				
		/* toggle doesn't work yet */
		$('#ddtoggle').css('display','none');
				
		$('#ddnav ul').css('display','inline-block');
		$('#ddnav ul li').css('display','inline');
		$('#ddnav ul li').css('position','relative');
		$('#ddnav ul li>a').css('display','inline-block');
		$('#ddnav ul li>a').css('margin-right','-4px');
				
		$('#ddnav div').css('left','0');
		$('#ddnav div').css('top','100%');
		$('#ddnav span div').css('top','0');
	}
			
	function ddmozilla() {
		ddtoggle();
		$(window).bind('resize', function() {ddalign();});
	}

	$(function () {
		ddnav();
		ddnavsub();

		if(jQuery.browser.msie) ddmsie();
		if(jQuery.browser.mozilla) ddmozilla();

		$('#ddnav').css('visibility','visible');
	});
</script>

<!-- If you wish to omit the docking feature omit following line (div with id ddtoggle) -->
<div id="ddtoggle" class="undocked"></div>
<div id="ddwrapper">
<!-- Here the actual links are defined, simply replace with your own links in the appropriate sections -->
<div id="ddnav" align="center">
<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

Modeling

CellDesigner

Output

Output
Parameter values Output
Name Value Reference
Degradation
CFP (protein) 1.05E-4 /s link
CFP (mRNA) 0.0023 /s link
Transcription Rate
CFP OmpF dependent
Translation Rate
CFP 0.167 /s Based on effenciency RBS
Output
Output
Output

Cell Death

Cell Death
Parameter values Cell Death
Name Value Reference
Degradation
LuxR (protein) 0.0010 /s
LuxR (mRNA) 0.00227 /s link
CcdB (protein) 7.7E-5 /s link
CcdB (mRNA) 0.00231 /s link
HSL 1.02E-6/s link
Dissociation Rate
ka (HSL+LuxR) 1E6 /s chosen to be relatively (to the other rate constants) high and such that Kd equals 1E-6
kd (HSL+LuxR) 1 /s
Dissociation Constant
HSL-LuxR 1E-6 M/L link
Binding LuxR on LuxPromotor 1E-9 M/L link
Transcription Rate
LuxR (constitutive promotor) 0.025 mRNA/s see sections on Constitutive Promotors & E. coli transcription Rates
CcdB (LuxR repressor) k_1*K_m^n/(K_m^n + [LuxR]^n) = 0.025*1E-9/(1E-9^1+[LuxR])

Inverter

Inverter
Parameter values Inverter
Name Value Reference
Degradation
LuxI (protein) 0.00231 /s
LuxI (mRNA) 0.0025 /s link
LuxI (complex) 0.00125 /s
LacI (protein) 0.00231 /s
LacI (gesloten mRNA) 0.0046209812 /s
LacI (open mRNA) 0.0023104906 /s
open mRNA LacI complex 0.0023104906 /s
HSL 1.02E-6 /s link
Dissociation Rate
Transcription Rate
LacI 0.0011 /s
LuxI 0.0025 /s
K_m 1.0E-10 /s
Translation Rate
LuxI (RBS B0034) 0.5 /s
LacI (RBS ?) 0.16667 /s
Equilibrium Constant
closed and open mRNA LacI 0.015
closed and complex mRNA LacI 0.0212 /M
Hill coëfficiënt
n 2
Others
LuxI --> HSL 0.16
LuxI (mRNA) + anti sense <-> complex LuxI 4.22E14

Memory

Memory
Parameter values Memory
Name Value Reference
Degradation
P2ogr (protein) 0.002265 /s
P2ogr (mRNA) 0.002265 /s link
P22CII (protein) 0.002311 /s
P22CII (mRNA) 0,0022651 /s link
antimRNA_luxI 0.0045303/s
Transcription rate
P2ogr 0.0125
P22CII 0.0125
AntimRNA 0.0094
Dissociation Constant
P2-ogr 4.2156 M link
R0053-P22CII 0.1099 M
Hill coëfficiënt
n 2

Filter

filter
Parameter values Filter
Name Value Reference
Degradation
pT7_tag(protein) 0.00155/s
mRNA_RIBOKEY (RNA) 0.00462 /s link
gesloten_mRNA_T7 (RNA) 0.00462 /s link
open_mRNA_T7 (RNA) 0.00231 / slink
open_mRNA_T7_complex (RNA) 0.00231 /slink
Equilibrium Constant
closed and open mRNA 0,015
closed and key complex mRNA 0.0212 /M
Transcription Rate
mRNA_RIBOKEY Input dependent
mRNA_T7 0,0011 mRNA/s

Pulse Generator

Pulse Generator

Constant Lactonase production

Partial Model

Model

Kinetic Constants

ETHZ list of parameters

mRNA decay

T7 RNAP

LacI - LuxI

LuxI, LuxR, mRNALuxI, mRNALuxR decay

HSL stuff

OmpR, OmpF

Psid met P2ogr promotor

Constitutive promoters

  • Estimated transcription rate for J23105:[1]
  • Scale other transcription rate with table in parts registry.
  • Estimate the rate of transcription from a constitutive promotor family member.
Estimates for the rate of transcription from the constitutive promotor family members. X is the GFP fluorescence in arbitrary units according to the Registry. Y is the number of mRNA's produced per second from that promotor

E. coli transcription rates

Paper about the calculated transcription rates for every E.coli ORF
Tables with the calculated transcription rates for every E.coli ORF