http://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&feed=atom&action=historyTeam:UAB-Barcelona/Modeling - Revision history2024-03-29T05:52:36ZRevision history for this page on the wikiMediaWiki 1.16.5http://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&diff=147714&oldid=prevRubfermo: /* ASSUMPTIONS */2009-10-21T16:12:25Z<p><span class="autocomment">ASSUMPTIONS</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>- Other possible regulations are neglected. Not modeling the entire regulatory factors network.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>- Other possible regulations are neglected. Not modeling the entire regulatory factors network.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>- pH <del class="diffchange diffchange-inline">inhibition </del>is <del class="diffchange diffchange-inline">competitive and reversible</del>. <del class="diffchange diffchange-inline">No further </del>information <del class="diffchange diffchange-inline">was found in </del>the <del class="diffchange diffchange-inline">bibliography</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>- pH <ins class="diffchange diffchange-inline">dependence </ins>is <ins class="diffchange diffchange-inline">described by the following equation: (1+10^(a-pH)+10^(b*pH-c))</ins>. <ins class="diffchange diffchange-inline">For more </ins>information <ins class="diffchange diffchange-inline">see </ins>the <ins class="diffchange diffchange-inline">model equations</ins>.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>- There is no external mass transfer resistance. The overall reaction rate is slow enough to not take into account the film that surrounds the cell membrane, as well as the fact that the cell volume is much larger than the volume of the hypothetical film.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>- There is no external mass transfer resistance. The overall reaction rate is slow enough to not take into account the film that surrounds the cell membrane, as well as the fact that the cell volume is much larger than the volume of the hypothetical film.</div></td></tr>
</table>Rubfermohttp://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&diff=129818&oldid=prevJabaeza: /* Assumptions */2009-10-20T15:58:42Z<p><span class="autocomment">Assumptions</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Assumptions===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Assumptions===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Probably the most vital role that the modeler plays in modeling is in exercising his scientific judgment as to what assumptions can be validly made. Obviously an extremely rigorous model that includes every phenomenon down to microscopic detail would be so complex that it would take a long time to develop and might be impossible to solve. A modeling compromise between a rigorous description and getting an answer that is good enough is always required. This has been called “optimum sloppiness”. It involves making as many simplifying assumptions as are optimum usually corresponds to a model which is as complex as the available computing facilities will permit.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Probably the most vital role that the modeler plays in modeling is in exercising his scientific judgment as to what assumptions can be validly made. Obviously an extremely rigorous model that includes every phenomenon down to microscopic detail would be so complex that it would take a long time to develop and might be impossible to solve. A modeling compromise between a rigorous description and getting an answer that is good enough is always required. This has been called “optimum sloppiness”. It involves making as many simplifying assumptions as are optimum usually corresponds to a model which is as complex as the available computing facilities will permit.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The assumptions that are <del class="diffchange diffchange-inline">mode </del>should be carefully considered and listed. They impose limitations on the model that should always be kept in mind when evaluating its predicted results.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The assumptions that are <ins class="diffchange diffchange-inline">made </ins>should be carefully considered and listed. They impose limitations on the model that should always be kept in mind when evaluating its predicted results.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Model Assignment is not Unique===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Model Assignment is not Unique===</div></td></tr>
</table>Jabaezahttp://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&diff=107629&oldid=prevRubfermo: /* REACTIONS */2009-10-17T19:39:58Z<p><span class="autocomment">REACTIONS</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To check which reactions take place in our model and the kinetic laws assumed for all of them, please download the following file. Here you will find a table summing up all that information.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To check which reactions take place in our model and the kinetic laws assumed for all of them, please download the following file. Here you will find a table summing up all that information.</div></td></tr>
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</table>Rubfermohttp://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&diff=107626&oldid=prevRubfermo: /* SENSIBILITY ANALYSIS */2009-10-17T19:39:32Z<p><span class="autocomment">SENSIBILITY ANALYSIS</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>=== <del class="diffchange diffchange-inline">SENSIBILITY </del>ANALYSIS ===</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=== <ins class="diffchange diffchange-inline">SENSITIVITY </ins>ANALYSIS ===</div></td></tr>
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</table>Rubfermohttp://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&diff=107624&oldid=prevRubfermo: /* PARAMETERS */2009-10-17T19:39:03Z<p><span class="autocomment">PARAMETERS</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the absence of reliable experimental data, we chose some of our parameters based on expected reaction times and reactions equilibriums. Some others were taken from the bibliography cited at the end of this work. Although our simulations show that qualitative behavior of the solutions is similar for a large range of parameters. Therefore, we present here results obtained for the particular choice of parameters.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the absence of reliable experimental data, we chose some of our parameters based on expected reaction times and reactions equilibriums. Some others were taken from the bibliography cited at the end of this work. Although our simulations show that qualitative behavior of the solutions is similar for a large range of parameters. Therefore, we present here results obtained for the particular choice of parameters.</div></td></tr>
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</table>Rubfermohttp://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&diff=107623&oldid=prevRubfermo: /* PARAMETERS */2009-10-17T19:38:48Z<p><span class="autocomment">PARAMETERS</span></p>
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</table>Rubfermohttp://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&diff=107621&oldid=prevRubfermo: /* Ordinary Differential Equations (ODE's) */2009-10-17T19:38:14Z<p><span class="autocomment">Ordinary Differential Equations (ODE's)</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Ordinary Differential Equations (ODE's)=== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Ordinary Differential Equations (ODE's)=== </div></td></tr>
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</table>Rubfermohttp://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&diff=107620&oldid=prevRubfermo: /* MODELING THE DYNAMICS OF DIFFERENT INITIAL CONCENTRATIONS OF CHLOROFORM */2009-10-17T19:37:52Z<p><span class="autocomment">MODELING THE DYNAMICS OF DIFFERENT INITIAL CONCENTRATIONS OF CHLOROFORM</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== MODELING THE DYNAMICS OF DIFFERENT INITIAL CONCENTRATIONS OF CHLOROFORM ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== MODELING THE DYNAMICS OF DIFFERENT INITIAL CONCENTRATIONS OF CHLOROFORM ===</div></td></tr>
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</table>Rubfermohttp://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&diff=107617&oldid=prevRubfermo: /* PARAMETER SCAN */2009-10-17T19:36:28Z<p><span class="autocomment">PARAMETER SCAN</span></p>
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</table>Rubfermohttp://2009.igem.org/wiki/index.php?title=Team:UAB-Barcelona/Modeling&diff=107616&oldid=prevRubfermo: /* SENSIBILITY ANALYSIS */2009-10-17T19:36:15Z<p><span class="autocomment">SENSIBILITY ANALYSIS</span></p>
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