Calgary/project summary

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<p align="center" style="font-size:22px;"> University of Calgary 2007 Simplified Project Overview </p>
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<p align="center" style="font-size:28px;"> University of Calgary 2007 Simplified Project Overview </p>
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  E.co Lisa project descprition
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  A Step by step explanation of how E.co Lisa works
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<p style="font-size:28px;"> <em>E. co</em>Lisa Simplified Project Overview </p>
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  <p style="font-size:22px;"> <em>E. co</em>Lisa Simplified Project Overview </p>
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    <td><img width="250" height="125" src = "https://static.igem.org/mediawiki/2007/1/1c/ProjectOutline1.gif" title = "Step One of Our simplified Project Plan"></td>
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      <td width="50%"><img width="250" height="125" src = "https://static.igem.org/mediawiki/2007/1/1c/ProjectOutline1.gif" title = "Step One of Our simplified Project Plan"></td>
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    <td><p><b>( 1 ) </b></p>  
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      <td valign="top"><p><b>( 1 ) </b></p>
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      <p>Each engineered cell (blue capsule) has genes (green box with arrow) for a light sensing protein (green oval)</p></td>
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        <p>Each engineered cell (blue capsule) has genes (green box with arrow) for a light sensing protein (green oval)</p></td>
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    <td align="center"><img height="250" width="200" src = "https://static.igem.org/mediawiki/2007/7/77/ProjectOutline2.gif" title = "Step Two of Our simplified Project Plan"></td>
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      <td width="50%" align="center"><img height="250" width="200" src = "https://static.igem.org/mediawiki/2007/7/77/ProjectOutline2.gif" title = "Step Two of Our simplified Project Plan"></td>
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    <td \><p><b>( 2 ) </b></p>
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      <td ><p><b>( 2 ) </b></p>
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    <p>The light sensor is activated by passing the beam from a laser pointer over the petri plate</p></td><td width="0"></td>
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        <p>The light sensor is activated by passing the beam from a laser pointer over the petri plate</p></td>
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    <td><img width="250" height="125" src = "https://static.igem.org/mediawiki/2007/5/53/ProjectOutline3.gif" title = "Step Three of Our simplified Project Plan"></td>
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      <td width="50%"><img width="250" height="125" src = "https://static.igem.org/mediawiki/2007/5/53/ProjectOutline3.gif" title = "Step Three of Our simplified Project Plan"></td>
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    <td><p><b>( 3 ) </b></p>  
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      <td valign="top"><p><b>( 3 ) </b></p>
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      <p>The light sensor controls another gene (red box with arrow), for the protein <b> agarase</b> (red circles). Once activated by the laser pointer, the light sensor activates the agarase gene.</p></td>
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        <p>The light sensor controls another gene (red box with arrow), for the protein <b> agarase</b> (red circles). Once activated by the laser pointer, the light sensor activates the agarase gene.</p></td>
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    <td><img width="250" height="125" src = "https://static.igem.org/mediawiki/2007/5/54/ProjectOutline4.gif" title = "Step Four of Our simplified Project Plan"></td>
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      <td width="50%"><img width="250" height="125" src = "https://static.igem.org/mediawiki/2007/5/54/ProjectOutline4.gif" title = "Step Four of Our simplified Project Plan"></td>
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    <td><p><b>( 4 ) </b></p>
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      <td valign="top"><p><b>( 4 ) </b></p>
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      <p>Agarase breaks down the jello-like matrix that the cells rest on. When many cells produce agarase a depression becomes visible on the petri plate.</p></td>
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        <p>Agarase breaks down the jello-like matrix that the cells rest on. When many cells produce agarase a depression becomes visible on the petri plate.</p></td>
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  <p>The eventual goal would be to use this system to create very high resolution images "drawn" on agar plates. Beyond the simple interest of producing images on bacteria this system offers an excellent example of a very tightly controlled design for a human-bacteria interface. </p>
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  evoGEM project description
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  Step by step outline of how evoGEM is used
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<p style="font-size:22px; "> <em>evo</em>GEM Simplified Project Overview </p>
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  <p style="font-size:22px; "> <em>evo</em>GEM Simplified Project Overview </p>
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      <td><p><b>( 1 ) </b></p>
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        <p>Before the simulation is run the user will select the parametres of the program. That is they must decide what genes they would like they evolved system to express, the amount of time the simulation will be given to run and percentage chance of mutations occurring.</p></td>
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      <td><p><b>( 2 ) </b></p>
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        <p>After the user has entered the information about the desired circut (circut in this context referring to the series of parts that compose an expression system) evoGEM will begin to search through its database of registry parts and attempt to assemble a circut that meets the specifiec requirements</p></td>
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      <td><p><b>( 3 ) </b></p>
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        <p>Circuts identified by evoGEM are run through a fitness function that assesses how close the current circut is to meeting the user defined specifications</p></td>
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      <td><p><b>( 4 ) </b></p>
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        <p>evoGEM will continue to develop new circuts until it has run for the predefined length of time. At which point the system should be able to display several circuts with the capability to meet the user defined specifications.</p></td>
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  <p> evoGEM was designed using Viggo::3D, a graphics and agents management system, as such our system returns graphical visualization of the products it has produced. The images below show circuts that have been evolved by evoGEM. The large red shperes represent RNA polymerases and the small blue shperes represent the expression of the gene being transcribed. </p>
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  <div style="float:right"> <img style="padding:10px;" src="https://static.igem.org/mediawiki/2007/9/9d/EvoGemSim1.gif" alt="visual image from evoGEM" /> </div>
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  <p> Currently evoGEM is at a very naive stage of its life (it is only four months old afterall, give it a chance to get through pubertey) and the circuts evovled are very simplistic and ineffcient. The potential however is there to improve this system to the point where it will be able to reliable select effecient systems of BioBricks to suit any conceivable task. </p>
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Latest revision as of 03:56, 19 December 2007

University of Calgary 2007 Simplified Project Overview

E. coLisa Simplified Project Overview

( 1 )

Each engineered cell (blue capsule) has genes (green box with arrow) for a light sensing protein (green oval)

( 2 )

The light sensor is activated by passing the beam from a laser pointer over the petri plate

( 3 )

The light sensor controls another gene (red box with arrow), for the protein agarase (red circles). Once activated by the laser pointer, the light sensor activates the agarase gene.

( 4 )

Agarase breaks down the jello-like matrix that the cells rest on. When many cells produce agarase a depression becomes visible on the petri plate.

The eventual goal would be to use this system to create very high resolution images "drawn" on agar plates. Beyond the simple interest of producing images on bacteria this system offers an excellent example of a very tightly controlled design for a human-bacteria interface.

evoGEM Simplified Project Overview

( 1 )

Before the simulation is run the user will select the parametres of the program. That is they must decide what genes they would like they evolved system to express, the amount of time the simulation will be given to run and percentage chance of mutations occurring.

( 2 )

After the user has entered the information about the desired circut (circut in this context referring to the series of parts that compose an expression system) evoGEM will begin to search through its database of registry parts and attempt to assemble a circut that meets the specifiec requirements

( 3 )

Circuts identified by evoGEM are run through a fitness function that assesses how close the current circut is to meeting the user defined specifications

( 4 )

evoGEM will continue to develop new circuts until it has run for the predefined length of time. At which point the system should be able to display several circuts with the capability to meet the user defined specifications.

evoGEM was designed using Viggo::3D, a graphics and agents management system, as such our system returns graphical visualization of the products it has produced. The images below show circuts that have been evolved by evoGEM. The large red shperes represent RNA polymerases and the small blue shperes represent the expression of the gene being transcribed.

visual image from evoGEM

Currently evoGEM is at a very naive stage of its life (it is only four months old afterall, give it a chance to get through pubertey) and the circuts evovled are very simplistic and ineffcient. The potential however is there to improve this system to the point where it will be able to reliable select effecient systems of BioBricks to suit any conceivable task.

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