Team:KULeuven/Modeling

From 2008.igem.org

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| CFP || 0.167 /s || Based on effenciency RBS
| CFP || 0.167 /s || Based on effenciency RBS
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[[Image:Sim_output_1.png|500px|center|Output]]
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[[Image:Sim_output_2.png|500px|center|Output]]
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[[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]===

Revision as of 13:10, 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:

  • [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. 

<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");
				$(this).parent().find('div:first').css('display','none');
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					function (){$(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');}
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	function ddalign() {
		var _windowWidth = $(window).width();
		var _leftOffset = (_windowWidth - 965)/2;

		$('div#ddnav').css('left',_leftOffset);
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	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');
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	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

  • [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html Synthetic biology: Engineering Escherichia coli to see light]

CellDesigner

Output

Output
Parameter values Output
Name Value Reference
Degradation
CFP (protein) 1.05E-4 /s [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
CFP (mRNA) 0.0023 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf 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 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
CcdB (protein) 7.7E-5 /s [http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]
CcdB (mRNA) 0.00231 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
HSL 1.02E-6/s [http://aem.asm.org/cgi/content/abstract/71/3/1291 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 [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]
Binding LuxR on LuxPromotor 1E-9 M/L [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 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

Memory

Memory
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

Filter

filter
Parameter values Filter
Name Value Reference
Degradation
pT7_tag(protein) 0.00155/s
mRNA_RIBOKEY (RNA) 0.00462 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
gesloten_mRNA_T7 (RNA) 0.00462 /s [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
open_mRNA_T7 (RNA) 0.00231 / s[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
open_mRNA_T7_complex (RNA) 0.00231 /s[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
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

  • [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters ETHZ list of parameters]

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]

T7 RNAP

  • [http://www.jbc.org/cgi/reprint/267/4/2640 Initiation of Transcription by T7 RNA Polymerase at Its Natural Promoters]
  • [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.jbc.org/cgi/reprint/281/47/35677 Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase]

LacI - LuxI

  • [http://www.tam.cornell.edu/tam/cms/manage/upload/Strogatz_20coupled_repressilators_PNAS.pdf Coupled repressilators]
  • [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]

LuxI, LuxR, mRNALuxI, mRNALuxR decay

  • [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

  • [http://aem.asm.org/cgi/content/abstract/71/3/1291 Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils] Fig 6: half-life 185 h ==> decay rate 1.02 * 10^-6 s^-1 ==> 0.00889 nM/h
  • [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D0X9-9&_user=877992&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000047079&_version=1&_urlVersion=0&_userid=877992&md5=36d07f326b2c2e55c4de05a1ab426e09 Kinetics of the AHL Regulatory System in a Model Biofilm System]
  • [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

  • [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=543474&blobtype=pdf A simulation model of Escherichia coli osmoregulatory switch using E-CELL system] (Relevance: High), bekijk pg.11/13
  • [http://www.jbc.org/cgi/reprint/281/25/17114 Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR] (Relevance: Medium)
  • [http://jb.oxfordjournals.org/cgi/reprint/111/6/707.pdf Transmembrane Signal Transduction and Osmoregulation in Escherichia coli: Functional Importance of the Transmembrane Regions of Membrane-Located Protein Kinase, EnvZ] (Relevance:?), geen toegang tenzij account
  • [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=209999 DNA-Binding Properties of the Transcription Activator (OmpR) for the Upstream Sequences of ompF in Escherichia coli Are Altered by envZ Mutations and Medium Osmolarity] (Relevance: Low)
  • [http://jb.asm.org/cgi/reprint/176/5/1309 A Distant Upstream Site Involved in the Negative Regulation of the Escherichia coli ompF Gene] (Relevance: ?), voor repressor regulatie van OmpF door OmpR
  • [http://jb.asm.org/cgi/reprint/176/16/5005.pdf micF Antisense RNA Has a Major Role in Osmoregulation of OmpF in Escherichia coli] (Relevance: Low), invloed 'Antisense RNA' op OmpF regulatie, hmm...

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]
  • [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=178405 Psid promotor with different activators]

Constitutive promoters

  • Estimated transcription rate for J23105:[http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters]
  • 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

[http://www.fasebj.org/cgi/content/summary/20/10/1721 Paper about the calculated transcription rates for every E.coli ORF]
[http://users.path.ox.ac.uk/~pcook/data/catalogs.html Tables with the calculated transcription rates for every E.coli ORF]

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