Team:Waterloo/Modeling

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You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
 
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You <strong>MUST</strong> have a team description page, a project abstract, a complete project description, and a lab notebook.  PLEASE keep all of your pages within your Team:Example namespace. 
 
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{|align="justify"
 
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|You can write a background of your team here.  Give us a background of your team, the members, etc.  Or tell us more about something of your choosing.
 
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|[[Image:Example_logo.png|200px|right|frame]]
 
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''Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)''
 
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|align="center"|[[Team:Waterloo | Team Example 2]]
 
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
!align="center"|[[Team:Waterloo|Home]]
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!align="center"|[[Team:Waterloo/Notebook|Notebook]]
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(''Or you can choose different headings.  But you must have a team page, a project page, and a notebook page.'')
 
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==Modelling Goal==
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Currently, the modelling team is considering issues that would be relevant to any industrial application of UW's 2008 project. Specifically, we are interested in determining the amount of time for which the genome of a cell should be exposed to the endonuclease to ensure, with a given percentage certainty, that the bacterial population is destroyed. In addition, we would like to know the relationship between this amount of time and the strength of the promoter used for the endonuclease.
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===Note===
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==Our Approach==
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To achieve our goal, a computer simulation of the activity of the endonuclease molecules inside a virtual cell will be used. In this simulation, endonuclease molecules will be generated randomly at a rate determined from empirical data, and their movement will be given by three-dimensional Brownian motion.  A region of space within the virtual cell will be designated as the genome, with cut sites at the appropriate locations. The computer will register "cuts" to the genome whenever one of the endonucleases comes into contact with a cut site. After a predetermined number of "cuts" have occurred, the genome will be classified as degraded (we are assuming that after this many cuts have taken place, the genome is certain to be destroyed).
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If you choose to include a '''Modeling''' page, please write about your modeling adventures here.  This is not necessary but it may be a nice list to include.
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The rate of endonuclease production in our simulation will rely on empirical data provided by the lab team. The lab team will obtain a measure of the rate of cutting of the endonuclease, by measuring the number of test-plasmids (each containing a cut site) that remain after being exposed to the endonuclease for various amounts of time. We will then adjust the endonuclease production parameter in our model, until our simulation produces comparable results to the empirical data under corresponding conditions. In this way we hope to calibrate our model to a reasonable approximation of reality.

Revision as of 02:46, 11 July 2008

Home The Team The Project Parts Submitted to the Registry Modeling Notebook

Modelling Goal

Currently, the modelling team is considering issues that would be relevant to any industrial application of UW's 2008 project. Specifically, we are interested in determining the amount of time for which the genome of a cell should be exposed to the endonuclease to ensure, with a given percentage certainty, that the bacterial population is destroyed. In addition, we would like to know the relationship between this amount of time and the strength of the promoter used for the endonuclease.

Our Approach

To achieve our goal, a computer simulation of the activity of the endonuclease molecules inside a virtual cell will be used. In this simulation, endonuclease molecules will be generated randomly at a rate determined from empirical data, and their movement will be given by three-dimensional Brownian motion. A region of space within the virtual cell will be designated as the genome, with cut sites at the appropriate locations. The computer will register "cuts" to the genome whenever one of the endonucleases comes into contact with a cut site. After a predetermined number of "cuts" have occurred, the genome will be classified as degraded (we are assuming that after this many cuts have taken place, the genome is certain to be destroyed).

The rate of endonuclease production in our simulation will rely on empirical data provided by the lab team. The lab team will obtain a measure of the rate of cutting of the endonuclease, by measuring the number of test-plasmids (each containing a cut site) that remain after being exposed to the endonuclease for various amounts of time. We will then adjust the endonuclease production parameter in our model, until our simulation produces comparable results to the empirical data under corresponding conditions. In this way we hope to calibrate our model to a reasonable approximation of reality.

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