Virginia Tech/Updates/Modeling

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<center><h3><font color="#8b0000"> VT iGEM Project 2007: Modeling an Epidemic</font></h3></center>
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<p>'''Model Level 1: Gene Network Model'''<br>
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''July 11, 2007'' </p>
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<p><h3>Introduction: Modeling the Epidemic</h3>
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Our Model of infection with and spread of an epidemic has two major levels:
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<li><b>A model for the infection of one population with the virus.</b> This model uses differential equations and chemical reactions to predict what happens over time given an initial number of phage and bacteria. For our lab experiments, this model will tell us what happens in each single well of the 96 in the microtiter plate.</li>
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<li><b>A model of the spread of the virus among populations as they interact.</b> This model will predict the spread of infection between populations of E. coli grown in a 96 well plate. We will use a Automated Liquid Handling Machine to mix the wells in a variety of patterns, for example, simple diffusion and in a network based on air traffic data.</li>
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We also originally started hoping to have a third and smallest layer: a gene network model. See below for an update.</p>
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<p><h3>Updates</h3></p>
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<p>'''Model Level 1: Gene Network Model'''</p>
<p>We decided to put the work on the gene network model on hold because the model is very complex and difficult to accurately construct and its impact on the overall results is questionable.  Thus we are focusing our attention on other more vital aspects of the project for now and will hopefully return to working on this model towards the end of the summer if time permits. </p>
<p>We decided to put the work on the gene network model on hold because the model is very complex and difficult to accurately construct and its impact on the overall results is questionable.  Thus we are focusing our attention on other more vital aspects of the project for now and will hopefully return to working on this model towards the end of the summer if time permits. </p>
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<p>'''Model Level 2: Infection Model'''<br>
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<p>'''<html><a href="https://2007.igem.org/Virginia_Tech/Updates/Modeling/Infection_Model">Model Level 2: One Population Infection Model</a></html>'''</p>
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''July 11, 2007'' </p>
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<p>Here is our model:
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<p>''Reaction [rate constant]'' <br>
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Rxn_1:  B + P --> I1 [200] <br>
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Rxn_2:  I1 + P --> I2 [200] <br>
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Rxn_3:  I2 + P --> I3 [200] <br>
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Rxn_4:  I1 --> L [6.667000e-002] <br>
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Rxn_5:  I1 --> K [6.000000e-001] <br>
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Rxn_6:  I2 --> L [6.667000e-002] <br>
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Rxn_7:  I2 --> K [1.555600e-001] <br>
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Rxn_8:  I3 --> L [6.667000e-002] <br>
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Rxn_9:  I3 --> K [6.667000e-002] <br>
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Rxn_10:  K --> 100P [2.500000e-002] <br>
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Rxn_11:   B + FA --> 2B [5.000000e-002] <br>
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Rxn_12:  L + FA --> 2L [5.000000e-002] <br>
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Rxn_13:  FT --> FA [5.000000e-002] </p>
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<p>''Initial Values'' <br>
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B=10000 <br>
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P=100 <br>
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FT=1.000000e+006 </p>
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<p> B represents uninfected bacteria, P represents phage virus, I is an intermediate stage, K represents lytic, L represents lysogenic, and FT and FA are food.  The first reaction represents a phage virus infecting a bacterial cell.  When the cell becomes infected, it can either turn lytic (a mass of phage viruses are replicated inside the cell and released by bursting the cell) or lysogenic (the phage stays dormant in the cell).  This decision, to choose between lytic and lysogenic, is based on environmental factors surrounding the bacterial cell.  If there are a surfeit of phage viruses in the environment, the infecting phage has a high probability of becoming lysogenic; however, if there is a scarcity of phage viruses surrounding the bacterial cell, there is a high probability that the phage will become lytic. The intermediate I is used as a reaction to set these probabilities.  The growth of the bacteria and lysogenic cells are limited by available food.  This is done so that the cells don't grow unhindered. </p>
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<p>Observing the reactions in action:
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</p>
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<p>As the phage (P) infects the uninfected bacteria (B) the amount of uninfected cells decline and number of lysogenic (L) and lytic (K) cells increase. As the lytic cells burst and release phage into the environment, the number of lytic gradually decline and the number of phage quickly increase. </p>
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<p>'''<html><a href="https://2007.igem.org/Virginia_Tech/Updates/Modeling/PopInter_Model">Model Level 3: Spread of an Epidemic between Populations</a></html>'''</p>
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Latest revision as of 16:15, 24 July 2007

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Modeling Updates:

VT iGEM Project 2007: Engineering an Epidemic

Introduction: Modeling the Epidemic

Our Model of infection with and spread of an epidemic has two major levels:

  • A model for the infection of one population with the virus. This model uses differential equations and chemical reactions to predict what happens over time given an initial number of phage and bacteria. For our lab experiments, this model will tell us what happens in each single well of the 96 in the microtiter plate.
  • A model of the spread of the virus among populations as they interact. This model will predict the spread of infection between populations of E. coli grown in a 96 well plate. We will use a Automated Liquid Handling Machine to mix the wells in a variety of patterns, for example, simple diffusion and in a network based on air traffic data.

We also originally started hoping to have a third and smallest layer: a gene network model. See below for an update.

Updates

Model Level 1: Gene Network Model

We decided to put the work on the gene network model on hold because the model is very complex and difficult to accurately construct and its impact on the overall results is questionable. Thus we are focusing our attention on other more vital aspects of the project for now and will hopefully return to working on this model towards the end of the summer if time permits.

Model Level 2: One Population Infection Model

Model Level 3: Spread of an Epidemic between Populations


Return to Progress Updates


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