IGEM:Imperial/2010/Modelling - Revision history

Piotr D. Faba: Removing trash

Piotr D. Faba — Tue, 12 Oct 2010 20:58:25 GMT

Removing trash

←Older revision		Revision as of 20:58, 12 October 2010
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	{{Imperial2010/Header}}		{{Imperial2010/Header}}
-	=~~Intro~~ =	+	== Menu ==
-		+
-	~~{\| style="width:900px;background:#f5f5f5;text-align:justify;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20"~~	+
-	~~\|style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"\|Introduction to modelling~~	+
-		+
-	\|-	+
-	~~\|In the process of designing our construct two major questions arose which could be answered by computer modelling:~~	+
-		+
-	~~<ol>~~	+
-	<li><b>Output Amplification Model</b><br/>We came up with an idea of using amplification of colour output to make it show within minutes after stimulus. The question that arose concerned whether amplification will actually perform better than simple production in the cellular environment. Furthermore, we had trouble deciding whether we should design the amplification module to be consisting of 1,2 or even more amplification steps. It appeared that the problem was recognised to be difficult enough to employ modelling.</li>	+
-	<li><b>Protein Display Model</b><br/>We came up with novel idea of detecting organisms that we do not have a specific receptor for. In the particular example that we have been considering, Schistosoma's protease was meant to cleave designed by us protein displayed on bacteria's cell wall. The cleaved peptide was supposed to be recognised by the receptor which would act to activate the colour expression. That solution raised questions about the risk of false positive or whether in there are any chances for ComD receptors to get activated in the diluted environment. Modelling was recognised as suitable to answer those questions.</li>	+
-	~~</ol>~~	+
-	\|}	+
-		+
-	~~{\| style="width:900px;background:#f5f5f5;text-align:justify;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20"~~	+
-	~~\|style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"\|Quick overview of models~~	+
-		+
-	\|-	+
-	~~\|<b style="font-size:12px">Output Amplification Model</b><br/>~~	+
-		+
-	~~<b style="font-size:12px">Output Amplification Model</b><br/>~~	+
-		+
-	\|}	+
-		+
-	~~{\| style="width:900px;background:#f5f5f5;text-align:justify;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20"~~	+
-	~~\|style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"\|Results~~	+
-		+
-	\|-	+
-	\|	+
-	\|}	+
-		+
-		+
-		+
-	~~== To be changed~~ ==	+
	<html>		<html>
		+	<p>
	<head>		<head>
	<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></"></script>		<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></"></script>
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	<div class="accordionContent"><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Experiments1"><b>Experiments for the Output Amplification Model</b></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Experiments2"><b>Experiments for the Protein Display Model</b></a><br /><br /></div>		<div class="accordionContent"><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Experiments1"><b>Experiments for the Output Amplification Model</b></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Experiments2"><b>Experiments for the Protein Display Model</b></a><br /><br /></div>
	</div>		</div>
		+
	</body>		</body>
		+	</p>
	</html>		</html>

		+	<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>
	==Engineering approach to project==		==Engineering approach to project==
	[[Image:Engineering_cycle.jpg\|500px\|thumb\|center]]		[[Image:Engineering_cycle.jpg\|500px\|thumb\|center]]

Piotr D. Faba: /* Intro */ So far modelling page being made

Piotr D. Faba — Sun, 10 Oct 2010 12:39:52 GMT

Intro: So far modelling page being made

←Older revision		Revision as of 12:39, 10 October 2010
Line 1:		Line 1:
	{{Imperial2010/Header}}		{{Imperial2010/Header}}
	=Intro =		=Intro =
-	~~<html>~~
-	~~<h1>Introduction to modelling</h1>~~

-	In the process of designing our construct two major questions arose which could be answered by computer modelling:	+	{\| style="width:900px;background:#f5f5f5;text-align:justify;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20"
		+	\|style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"\|Introduction to modelling
		+
		+	\|-
		+	\|In the process of designing our construct two major questions arose which could be answered by computer modelling:

	<ol>		<ol>
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	<li><b>Protein Display Model</b><br/>We came up with novel idea of detecting organisms that we do not have a specific receptor for. In the particular example that we have been considering, Schistosoma's protease was meant to cleave designed by us protein displayed on bacteria's cell wall. The cleaved peptide was supposed to be recognised by the receptor which would act to activate the colour expression. That solution raised questions about the risk of false positive or whether in there are any chances for ComD receptors to get activated in the diluted environment. Modelling was recognised as suitable to answer those questions.</li>		<li><b>Protein Display Model</b><br/>We came up with novel idea of detecting organisms that we do not have a specific receptor for. In the particular example that we have been considering, Schistosoma's protease was meant to cleave designed by us protein displayed on bacteria's cell wall. The cleaved peptide was supposed to be recognised by the receptor which would act to activate the colour expression. That solution raised questions about the risk of false positive or whether in there are any chances for ComD receptors to get activated in the diluted environment. Modelling was recognised as suitable to answer those questions.</li>
	</ol>		</ol>
		+	\|}
		+
		+	{\| style="width:900px;background:#f5f5f5;text-align:justify;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20"
		+	\|style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"\|Quick overview of models
		+
		+	\|-
		+	\|<b style="font-size:12px">Output Amplification Model</b><br/>
		+
		+	<b style="font-size:12px">Output Amplification Model</b><br/>
		+
		+	\|}

-	~~<h1>Quick overview of models</h1>~~	+	{\| style="width:900px;background:#f5f5f5;text-align:justify;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20"
		+	\|style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"\|Results

-	~~<p style="font~~-~~size:20px">This is some text!</p>~~	+	\|-
		+	\|
		+	\|}

-	~~<h1>Results</h1>~~


-
-	~~</html>~~
	== To be changed ==		== To be changed ==
	<html>		<html>

Piotr D. Faba: /* Intro */ making the main modelling page

Piotr D. Faba — Sun, 10 Oct 2010 12:14:47 GMT

Intro: making the main modelling page

←Older revision		Revision as of 12:14, 10 October 2010
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	<ol>		<ol>
-	<li><b>Output Amplification Model</b><br/>We came up with an idea of using amplification of colour output to make it show within minutes after stimulus. The question that arose concerned deciding whether we should design the amplification module to be consisting of 1,2 or even more amplification steps. It appeared that the problem was recognised to be difficult enough to employ modelling.</li>	+	<li><b>Output Amplification Model</b><br/>We came up with an idea of using amplification of colour output to make it show within minutes after stimulus. The question that arose concerned whether amplification will actually perform better than simple production in the cellular environment. Furthermore, we had trouble deciding whether we should design the amplification module to be consisting of 1,2 or even more amplification steps. It appeared that the problem was recognised to be difficult enough to employ modelling.</li>
	<li><b>Protein Display Model</b><br/>We came up with novel idea of detecting organisms that we do not have a specific receptor for. In the particular example that we have been considering, Schistosoma's protease was meant to cleave designed by us protein displayed on bacteria's cell wall. The cleaved peptide was supposed to be recognised by the receptor which would act to activate the colour expression. That solution raised questions about the risk of false positive or whether in there are any chances for ComD receptors to get activated in the diluted environment. Modelling was recognised as suitable to answer those questions.</li>		<li><b>Protein Display Model</b><br/>We came up with novel idea of detecting organisms that we do not have a specific receptor for. In the particular example that we have been considering, Schistosoma's protease was meant to cleave designed by us protein displayed on bacteria's cell wall. The cleaved peptide was supposed to be recognised by the receptor which would act to activate the colour expression. That solution raised questions about the risk of false positive or whether in there are any chances for ComD receptors to get activated in the diluted environment. Modelling was recognised as suitable to answer those questions.</li>
	</ol>		</ol>
		+
		+	<h1>Quick overview of models</h1>
		+
		+	<p style="font-size:20px">This is some text!</p>
		+
		+	<h1>Results</h1>
		+
		+

	</html>		</html>

Piotr D. Faba at 11:55, 10 October 2010

Piotr D. Faba — Sun, 10 Oct 2010 11:55:18 GMT

←Older revision		Revision as of 11:55, 10 October 2010
Line 1:		Line 1:
	{{Imperial2010/Header}}		{{Imperial2010/Header}}
-		+	=Intro =
	<html>		<html>
	<h1>Introduction to modelling</h1>		<h1>Introduction to modelling</h1>

Piotr D. Faba: /* Introduction to modelling */

Piotr D. Faba — Sun, 10 Oct 2010 11:54:30 GMT

Introduction to modelling

←Older revision		Revision as of 11:54, 10 October 2010
Line 1:		Line 1:
	{{Imperial2010/Header}}		{{Imperial2010/Header}}

-	== Introduction to modelling ==	+	<html>
		+	<h1>Introduction to modelling</h1>
		+
		+	In the process of designing our construct two major questions arose which could be answered by computer modelling:
		+
		+	<ol>
		+	<li><b>Output Amplification Model</b><br/>We came up with an idea of using amplification of colour output to make it show within minutes after stimulus. The question that arose concerned deciding whether we should design the amplification module to be consisting of 1,2 or even more amplification steps. It appeared that the problem was recognised to be difficult enough to employ modelling.</li>
		+	<li><b>Protein Display Model</b><br/>We came up with novel idea of detecting organisms that we do not have a specific receptor for. In the particular example that we have been considering, Schistosoma's protease was meant to cleave designed by us protein displayed on bacteria's cell wall. The cleaved peptide was supposed to be recognised by the receptor which would act to activate the colour expression. That solution raised questions about the risk of false positive or whether in there are any chances for ComD receptors to get activated in the diluted environment. Modelling was recognised as suitable to answer those questions.</li>
		+	</ol>
		+
		+	</html>
		+	== To be changed ==
	<html>		<html>
	<head>		<head>
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	</body>		</body>
	</html>		</html>
-
-

	==Engineering approach to project==		==Engineering approach to project==

Piotr D. Faba: Adjusting main modelling page

Piotr D. Faba — Sun, 10 Oct 2010 11:20:52 GMT

Adjusting main modelling page

←Older revision		Revision as of 11:20, 10 October 2010
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	{{Imperial2010/Header}}		{{Imperial2010/Header}}
-	~~To Do's for Piotr:~~
-
-	~~Design experiments not only to get values of constants for model but as well to verify model and enter the debugging phase.~~

		+	== Introduction to modelling ==
	<html>		<html>
	<head>		<head>

Piotr D. Faba at 16:01, 7 October 2010

Piotr D. Faba — Thu, 07 Oct 2010 16:01:48 GMT

←Older revision		Revision as of 16:01, 7 October 2010
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	<style type="text/css">		<style type="text/css">
	#wrapper {		#wrapper {
-	width: ~~1000px~~;	+	width: 750px;
	margin-left: auto;		margin-left: auto;
	margin-right: auto;		margin-right: auto;
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	.accordionButton {		.accordionButton {
-	width: ~~1000px~~;	+	width: 750px;
	height: 20px;		height: 20px;
	float: left;		float: left;
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	display: block;		display: block;
	background: #FFCC33;		background: #FFCC33;
-	border-bottom: ~~1px~~ solid #~~FFFFFF~~;	+	border-bottom: 5px solid #FFFF99;
	cursor: pointer;		cursor: pointer;
	padding: 10px;		padding: 10px;
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	.accordionContent {		.accordionContent {
-	width: ~~1000px~~;	+	width: 750px;
	float: left;		float: left;
	text-align: center;		text-align: center;
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	</body>		</body>
	</html>		</html>
		+

Benjamin Miller at 16:15, 23 September 2010

Benjamin Miller — Thu, 23 Sep 2010 16:15:26 GMT

←Older revision		Revision as of 16:15, 23 September 2010
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		+	{{Imperial2010/Header}}
	To Do's for Piotr:		To Do's for Piotr:

Piotr D. Faba at 09:14, 17 September 2010

Piotr D. Faba — Fri, 17 Sep 2010 09:14:30 GMT

←Older revision		Revision as of 09:14, 17 September 2010
Line 1:		Line 1:
		+	To Do's for Piotr:
		+
		+	Design experiments not only to get values of constants for model but as well to verify model and enter the debugging phase.
		+
	<html>		<html>
	<head>		<head>

Piotr D. Faba: /* Engineering development */

Piotr D. Faba — Mon, 13 Sep 2010 17:13:18 GMT

Engineering development

←Older revision		Revision as of 17:13, 13 September 2010
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-	==Engineering ~~development~~==	+	==Engineering approach to project==
	[[Image:Engineering_cycle.jpg\|500px\|thumb\|center]]		[[Image:Engineering_cycle.jpg\|500px\|thumb\|center]]
	1. Influence of Specification on Design and vice versa:		1. Influence of Specification on Design and vice versa: