http://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&feed=atom&action=historyTeam:Aberdeen Scotland/Modeling - Revision history2024-03-29T05:05:48ZRevision history for this page on the wikiMediaWiki 1.16.5http://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&diff=195030&oldid=prevPorter at 20:23, 27 October 20102010-10-27T20:23:34Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>In this section we describe how we used fixed point analysis to predict the equilibrium state(s) of the ayeSwitch system for different parameters. Three or more equilibrium points will give us bistability and the possibility of switching. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>In this section we describe how we used fixed point analysis to predict the equilibrium state(s) of the ayeSwitch system for different parameters. Three or more equilibrium points will give us bistability and the possibility of switching. </p></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Bifurcation"><font color="blue">Bifurcation</font></a></h3></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Bifurcation"><font color="blue">Bifurcation <ins class="diffchange diffchange-inline">and Stability</ins></font></a></h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Bifurcation analysis allows us to track the number and relative position of the equilibrium points of our system for different parameters. This section describes in detail how bifurcation analysis can help us determine the optimal range for our parameters. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Bifurcation analysis allows us to track the number and relative position of the equilibrium points of our system for different parameters. This section describes in detail how bifurcation analysis can help us determine the optimal range for our parameters. </p></div></td></tr>
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</table>Porterhttp://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&diff=193359&oldid=prevBrychan at 19:24, 27 October 20102010-10-27T19:24:25Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Stochastic_Model"><font color="blue">Stochastic Model</font></a></h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Stochastic_Model"><font color="blue">Stochastic Model</font></a></h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>There are two ways to model our system - deterministically and stochastically. Both methods have their advantages and disadvantages depending on the system in question. In our system, it was more beneficial to model the system stochastically due to the low numbers of molecules involved. This section describes in detail both methods, their advantages and disadvantages and how they are used to model our system.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>There are two ways to model our system - deterministically and stochastically. Both methods have their advantages and disadvantages depending on the system in question. In our system, it was more beneficial to model the system stochastically due to the low numbers of molecules involved. This section describes in detail both methods, their advantages and disadvantages and how they are used to model our system.</p></div></td></tr>
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</table>Brychanhttp://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&diff=138067&oldid=prevPorter at 22:07, 24 October 20102010-10-24T22:07:35Z<p></p>
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</table>Porterhttp://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&diff=138066&oldid=prevU01lmd7 at 22:07, 24 October 20102010-10-24T22:07:31Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The Hill coefficient relating to the CFP/MS2 stem loop association is assumed to be around 2 due to the number of stem loops present. This section details the method we used to calculate this value more accurately, and what the result means in terms of the parameter space analysis.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The Hill coefficient relating to the CFP/MS2 stem loop association is assumed to be around 2 due to the number of stem loops present. This section details the method we used to calculate this value more accurately, and what the result means in terms of the parameter space analysis.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Evolution"><font color="blue">Directed Evolution</font></a></h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Evolution"><font color="blue">Directed Evolution</font></a></h3></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><p>Here we describe one of the possible ways to improve our switch which we would have been able to attempt given more time. The results show an optimized version of our original system. </p></ins></div></td></tr>
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</table>U01lmd7http://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&diff=136319&oldid=prevCMcLeman at 19:09, 24 October 20102010-10-24T19:09:01Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>There are two ways to model our system - deterministically and stochastically. Both methods have their advantages and disadvantages depending on the system in question. In our system, it was more beneficial to model the system stochastically due to the low numbers of molecules involved. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>There are two ways to model our system - deterministically and stochastically. Both methods have their advantages and disadvantages depending on the system in question. In our system, it was more beneficial to model the system stochastically due to the low numbers of molecules involved<ins class="diffchange diffchange-inline">. This section describes in detail both methods, their advantages and disadvantages and how they are used to model our system</ins>.</p></div></td></tr>
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</table>CMcLemanhttp://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&diff=136045&oldid=prevCMcLeman at 18:42, 24 October 20102010-10-24T18:42:04Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Fixed_Points"><font color="blue">Nullclines and Fixed Points</font></a></h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Fixed_Points"><font color="blue">Nullclines and Fixed Points</font></a></h3></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p><del class="diffchange diffchange-inline">We </del>used fixed point analysis to predict the equilibrium state(s) of the ayeSwitch system for different parameters. Three or more equilibrium points will give us bistability and the possibility of switching. <del class="diffchange diffchange-inline"> </del></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p><ins class="diffchange diffchange-inline">In this section we describe how we </ins>used fixed point analysis to predict the equilibrium state(s) of the ayeSwitch system for different parameters. Three or more equilibrium points will give us bistability and the possibility of switching. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Bifurcation"><font color="blue">Bifurcation</font></a></h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Bifurcation"><font color="blue">Bifurcation</font></a></h3></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Bifurcation analysis allows us to track the number and relative position of the equilibrium points of our system for different parameters. <del class="diffchange diffchange-inline">Parameters below a certain value may only give us one fixed point, but increasing the value of the parameter could give us a </del>bifurcation <del class="diffchange diffchange-inline">point and then increasing the value more we </del>can <del class="diffchange diffchange-inline">get three fixed points. The further apart the fixed points are from each other, </del>the <del class="diffchange diffchange-inline">more difficult it will be to switch between them</del>.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Bifurcation analysis allows us to track the number and relative position of the equilibrium points of our system for different parameters. <ins class="diffchange diffchange-inline">This section describes in detail how </ins>bifurcation <ins class="diffchange diffchange-inline">analysis </ins>can <ins class="diffchange diffchange-inline">help us determine </ins>the <ins class="diffchange diffchange-inline">optimal range for our parameters</ins>. </p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Probability"><font color="blue">Parameter Space Analysis</font></a></h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Probability"><font color="blue">Parameter Space Analysis</font></a></h3></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><p>This section describes in detail how we analysed the parameter space for our system. The results of this will show when bistability is possible and when it is not. Using this information, we can determine the optimal parameter ranges for our system. </p></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Curve_Fitting"><font color="blue">Determination of the Hill coefficient n<sub style="font-size:10px">1</sub></font></a></h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Curve_Fitting"><font color="blue">Determination of the Hill coefficient n<sub style="font-size:10px">1</sub></font></a></h3></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><p>The Hill coefficient relating to the CFP/MS2 stem loop association is assumed to be around 2 due to the number of stem loops present. This section details the method we used to calculate this value more accurately, and what the result means in terms of the parameter space analysis.</p></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Evolution"><font color="blue">Directed Evolution</font></a></h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Evolution"><font color="blue">Directed Evolution</font></a></h3></div></td></tr>
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</table>CMcLemanhttp://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&diff=135910&oldid=prevCMcLeman at 18:30, 24 October 20102010-10-24T18:30:18Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>In this section we describe the process of developing a basic mathematical model for the ayeSwitch based on the promotion and inhibition behaviour necessary for mutual repression. We developed a set of four differential equations, one to model each of the two mRNAs and two proteins that are the active components of our system.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>In this section we describe the process of developing a basic mathematical model for the ayeSwitch based on the promotion and inhibition behaviour necessary for mutual repression. We developed a set of four differential equations, one to model each of the two mRNAs and two proteins that are the active components of our system.</p></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Fixed_Points"><font color="blue">Fixed Points</font></a></h3></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><h3><a href="https://2010.igem.org/Team:Aberdeen_Scotland/Fixed_Points"><font color="blue"><ins class="diffchange diffchange-inline">Nullclines and </ins>Fixed Points</font></a></h3></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>We used fixed point analysis to predict the equilibrium state(s) of the ayeSwitch system for different parameters. Three or more equilibrium points will give us bistability and the possibility of switching. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>We used fixed point analysis to predict the equilibrium state(s) of the ayeSwitch system for different parameters. Three or more equilibrium points will give us bistability and the possibility of switching. </p></div></td></tr>
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</table>CMcLemanhttp://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&diff=135897&oldid=prevCMcLeman at 18:29, 24 October 20102010-10-24T18:29:41Z<p></p>
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</table>CMcLemanhttp://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&diff=135485&oldid=prevCMcLeman at 17:56, 24 October 20102010-10-24T17:56:02Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Bifurcation analysis allows us to track the number and relative position of the equilibrium points of our system for different parameters. Parameters below a certain value may only give us one fixed point, but increasing the value of the parameter could give us a bifurcation point and then increasing the value more we can get three fixed points. The further apart the fixed points are from each other, the more difficult it will be to switch between them.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Bifurcation analysis allows us to track the number and relative position of the equilibrium points of our system for different parameters. Parameters below a certain value may only give us one fixed point, but increasing the value of the parameter could give us a bifurcation point and then increasing the value more we can get three fixed points. The further apart the fixed points are from each other, the more difficult it will be to switch between them.<ins class="diffchange diffchange-inline"></p></ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><p>There are two ways to model our system - deterministically and stochastically. Both methods have their advantages and disadvantages depending on the system in question. In our system, it was more beneficial to model the system stochastically due to the low numbers of molecules involved. </p></ins></div></td></tr>
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</table>CMcLemanhttp://2010.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&diff=135330&oldid=prevCMcLeman at 17:45, 24 October 20102010-10-24T17:45:31Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>We used fixed point analysis to predict the equilibrium state(s) of the ayeSwitch system for different parameters. Three or more <del class="diffchange diffchange-inline">fixed </del>points will give us bistability and the possibility of switching. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>We used fixed point analysis to predict the equilibrium state(s) of the ayeSwitch system for different parameters. Three or more <ins class="diffchange diffchange-inline">equilibrium </ins>points will give us bistability and the possibility of switching. </p></div></td></tr>
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</table>CMcLeman