http://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&feed=atom&action=historyTeam:TUDelft/Color modeling - Revision history2024-03-29T16:02:02ZRevision history for this page on the wikiMediaWiki 1.16.5http://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&diff=104320&oldid=prevRhaghi: /* Conclusion */2008-10-30T04:02:12Z<p><span class="autocomment">Conclusion</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==The Output==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==The Output==</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In the output we use [http://www.lbl.gov/Science-Articles/Archive/assets/images/2004/Mar-24/Engineering_terpenoids.pdf mevalonate] and [<del class="diffchange diffchange-inline">http</del>://<del class="diffchange diffchange-inline">parts</del>.<del class="diffchange diffchange-inline">mit</del>.<del class="diffchange diffchange-inline">edu/igem07/index.php</del>/Image:Zeaxanthin.jpg GPP] pathways together to produce red, orange and yellow colors.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In the output we use [http://www.lbl.gov/Science-Articles/Archive/assets/images/2004/Mar-24/Engineering_terpenoids.pdf mevalonate] and [<ins class="diffchange diffchange-inline">https</ins>://<ins class="diffchange diffchange-inline">2007</ins>.<ins class="diffchange diffchange-inline">igem</ins>.<ins class="diffchange diffchange-inline">org</ins>/Image:Zeaxanthin.jpg GPP] pathways together to produce red, orange and yellow colors.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The biosynthetic model is built in '''CellDesigner&trade;'''. There are 14 substrates and 14 enzymes in total (idi counts twice as it acts on two reactions). The first substrate is Acetyl-CoA which is provided to the pathway in a constant level. The last three substrates are the color products and are consuming so we have degradation links for them. If we turn off the first switch (CrtI) then there will be no production of Lycopene and Phytoene will be degraded in time, so there is another degradation link in the model for the Phytoene . At last Lycopene, B-carotene and Zeaxanthin give red, orange and yellow colors respectively.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The biosynthetic model is built in '''CellDesigner&trade;'''. There are 14 substrates and 14 enzymes in total (idi counts twice as it acts on two reactions). The first substrate is Acetyl-CoA which is provided to the pathway in a constant level. The last three substrates are the color products and are consuming so we have degradation links for them. If we turn off the first switch (CrtI) then there will be no production of Lycopene and Phytoene will be degraded in time, so there is another degradation link in the model for the Phytoene . At last Lycopene, B-carotene and Zeaxanthin give red, orange and yellow colors respectively.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Mev_final.jpg |550px|center | <center> Color Pathway </center> | thumb]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Mev_final.jpg |550px|center | <center> Color Pathway </center> | thumb]]</div></td></tr>
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<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;"><!-- It is a test --></ins></div></td></tr>
</table>Rhaghihttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&diff=104062&oldid=prevRhaghi: /* Kinetic Equations */2008-10-30T03:55:19Z<p><span class="autocomment">Kinetic Equations</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The K coefficients for our pathway and organism were not available from databases. From the work of [http://www.molgen.mpg.de/~lieberme/data/ibsb2007_Borger_et_al.pdf Borger et al. 2007] we expected that K has a Gaussian distribution so we took the minimum and maximum possible values of K from [http://www.brenda-enzymes.info/ Brenda] and made a normal distribution of them. Now the value for K is picked randomly from this distribution. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The K coefficients for our pathway and organism were not available from databases. From the work of [http://www.molgen.mpg.de/~lieberme/data/ibsb2007_Borger_et_al.pdf Borger et al. 2007] we expected that K has a Gaussian distribution so we took the minimum and maximum possible values of K from [http://www.brenda-enzymes.info/ Brenda] and made a normal distribution of them. Now the value for K is picked randomly from this distribution. </div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>After the conversion of SBML model to the M-file, the code needed some modifications. The modified code gave the right set of differential equations which were solved by '''Matlab&reg;''' ODE solver.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>After the conversion of SBML model to the M-file, the code needed some modifications. The modified code gave the right set of differential equations which were solved by '''Matlab&reg;''' ODE solver<ins class="diffchange diffchange-inline">. The codes that used in this part are available through the [https://2008.igem.org/Team:TUDelft/Downloads Downloads] tab</ins>.</div></td></tr>
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</table>Rhaghihttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&diff=103906&oldid=prevRhaghi: /* Conclusion */2008-10-30T03:51:46Z<p><span class="autocomment">Conclusion</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The mathematical models for the production of enzymes could perfectly describe the experimental data as is obvious from the figures. The optimization algorithm finds the parameter values very well and the [http://en.wikipedia.org/wiki/Sum_of_squared_error SSE] is less than 1e-3.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The mathematical models for the production of enzymes could perfectly describe the experimental data as is obvious from the figures. The optimization algorithm finds the parameter values very well and the [http://en.wikipedia.org/wiki/Sum_of_squared_error SSE] is less than 1e-3.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>By inclusion of the inhibition terms we can see that the models show the switching behavior as expected. There are some points which are not in the switching regions like as the data point of 30&deg; C in the plot of 37&deg; C. This could be possibly due to measurement errors. Also the 42&deg; C points are not in a close neighborhood of the curves. In all of figures the experimental value for 42&deg; C is less than the one predicted by the model. The reason might be the behavior of living organisms at the extreme temperature of 42&deg; C. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>By inclusion of the inhibition terms we can see that the models show the switching behavior as expected. There are some points which are not in the switching regions like as the data point of 30&deg; C in the plot of 37&deg; C. This could be possibly due to measurement errors. Also the 42&deg; C points are not in a close neighborhood of the curves. In all of figures the experimental value for 42&deg; C is less than the one predicted by the model. The reason might be the behavior of living organisms at the extreme temperature of 42&deg; C. According to sensitivity analysis the most important parameter of the function is '''p''' which is logical due to the fact that it considerably affects the derivative. <ins class="diffchange diffchange-inline">Finally, in can be concluded that the overall view of the modeling part is satisfactory. </ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>According to sensitivity analysis the most important parameter of the function is '''p''' which is logical due to the fact that it considerably affects the derivative. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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</table>Rhaghihttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&diff=103661&oldid=prevFehtemam: /* Parameter Estimation */2008-10-30T03:42:38Z<p><span class="autocomment">Parameter Estimation</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>To find these parameters many solution like non linear set of equations has been tested. However the best results for the parameters has been concluded from the [http://en.wikipedia.org/wiki/Genetic_algorithm Genetic algorithm] search method. By this method parameters were estimated with a very good approximation. The calculations was based on the three points of the lab experiment results. The result for these method are shown in the graph below. The codes <del class="diffchange diffchange-inline">that have been used for </del>the GA <del class="diffchange diffchange-inline">can be downloaded </del>in [https://2008.igem.org/Team:TUDelft/Downloads Download] tab.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>To find these parameters many solution like non linear set of equations has been tested. However the best results for the parameters has been concluded from the [http://en.wikipedia.org/wiki/Genetic_algorithm Genetic algorithm] search method. By this method parameters were estimated with a very good approximation. The calculations was based on the three points of the lab experiment results. The result for these method are shown in the graph below. The codes <ins class="diffchange diffchange-inline">which includes </ins>the GA <ins class="diffchange diffchange-inline">optimization method is available </ins>in <ins class="diffchange diffchange-inline">the </ins>[https://2008.igem.org/Team:TUDelft/Downloads Download] tab.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Ga_wo.jpg | center | 500px | <center>The parameter estimation by GA for 37°C without inhibition</center> | thumb]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Ga_wo.jpg | center | 500px | <center>The parameter estimation by GA for 37°C without inhibition</center> | thumb]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>It is clear from the graph that the <del class="diffchange diffchange-inline">result is </del>quite good. The enzyme concentration equation based on temperature for three enzymes which should activate at 27°C, 30°C and 37°C are shown below.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>It is clear from the graph that the <ins class="diffchange diffchange-inline">results are </ins>quite good. The enzyme concentration equation based on temperature for three enzymes which should activate at 27°C, 30°C and 37°C are shown below.</div></td></tr>
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</table>Fehtemamhttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&diff=103514&oldid=prevFehtemam: /* Lab experiments for estimating parameters */2008-10-30T03:37:57Z<p><span class="autocomment">Lab experiments for estimating parameters</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For the enzymes production the hill type model was used. As a result, the temperature is the main parameter in enzyme production rate. Due to degradation, which is dependent on the enzyme concentration, after a while the enzyme concentration is in a stable situation. Moreover, with the hill type model the enzymes work as a switch which are activated on a certain temperature. The activation temperature is determined by the parameters in the hill type equation.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For the enzymes production the hill type model was used. As a result, the temperature is the main parameter in enzyme production rate. Due to degradation, which is dependent on the enzyme concentration, after a while the enzyme concentration is in a stable situation. Moreover, with the hill type model the enzymes work as a switch which are activated on a certain temperature. The activation temperature is determined by the parameters in the hill type equation.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>== Lab <del class="diffchange diffchange-inline">experiments for estimating parameters </del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>== <ins class="diffchange diffchange-inline">Experimental Data from the </ins>Lab ==</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the model, there are many parameters that were estimated arbitrarily to have an initial calculation and get a feeling about the model. However to have a good model it is necessary to have a good estimation for the parameters. To find these estimation the modeling crew decided to use the results from the lab. It means that the results from lab were used to estimate parameters that were not available exactly in databases. Two experiments have been designed for this procedure. The first one was an experiment for steady state situation which has been done by using luciferase. In this experiment the enzyme activity has been measured for a specific temperature in the steady state situation. As this experiment has been done in steady state situation it was named "static". The second experiment was designed to measure enzyme activity in a changing situation. It means that the enzyme activities were measured in a changing temperature in different time spans. As this experiment is performed in a changing situation it was named "dynamic". The results of both experiments are used to help the modeling crew to find a good estimation for parameters. An example for the lab experiment results in the steady state, which has been normalized, is shown below. These results have been used to do the calculations for the next steps.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the model, there are many parameters that were estimated arbitrarily to have an initial calculation and get a feeling about the model. However to have a good model it is necessary to have a good estimation for the parameters. To find these estimation the modeling crew decided to use the results from the lab. It means that the results from lab were used to estimate parameters that were not available exactly in databases. Two experiments have been designed for this procedure. The first one was an experiment for steady state situation which has been done by using luciferase. In this experiment the enzyme activity has been measured for a specific temperature in the steady state situation. As this experiment has been done in steady state situation it was named "static". The second experiment was designed to measure enzyme activity in a changing situation. It means that the enzyme activities were measured in a changing temperature in different time spans. As this experiment is performed in a changing situation it was named "dynamic". The results of both experiments are used to help the modeling crew to find a good estimation for parameters. An example for the lab experiment results in the steady state, which has been normalized, is shown below. These results have been used to do the calculations for the next steps.</div></td></tr>
</table>Fehtemamhttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&diff=103480&oldid=prevFehtemam: /* Effects of the temperature on enzymes */2008-10-30T03:36:40Z<p><span class="autocomment">Effects of the temperature on enzymes</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">As mentioned before for </del>the enzymes production the hill type model was used. As a result, the temperature is the main parameter in enzyme production rate. Due to degradation, which is dependent on the enzyme concentration, after a while the enzyme concentration is in a stable situation. Moreover, with the hill type model the enzymes work as a switch which are activated on a certain temperature. The activation temperature is determined by the parameters in the hill type equation.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">For </ins>the enzymes production the hill type model was used. As a result, the temperature is the main parameter in enzyme production rate. Due to degradation, which is dependent on the enzyme concentration, after a while the enzyme concentration is in a stable situation. Moreover, with the hill type model the enzymes work as a switch which are activated on a certain temperature. The activation temperature is determined by the parameters in the hill type equation.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Lab experiments for estimating parameters ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Lab experiments for estimating parameters ==</div></td></tr>
</table>Fehtemamhttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&diff=103392&oldid=prevFehtemam: /* Initial solution for ODEs */2008-10-30T03:33:47Z<p><span class="autocomment">Initial solution for ODEs</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>After the conversion of SBML model to the M-file, the code needed some modifications. The modified code gave the right set of differential equations which were solved by '''Matlab&reg;''' ODE solver.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>After the conversion of SBML model to the M-file, the code needed some modifications. The modified code gave the right set of differential equations which were solved by '''Matlab&reg;''' ODE solver.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>==<del class="diffchange diffchange-inline">Initial solution for </del>ODEs==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==<ins class="diffchange diffchange-inline">System of </ins>ODEs==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The M-file function, as mentioned before, was solved by the ode15s function of Matlab. To do this procedure some assumptions were applied. The first substrate, Acetyl-CoA, was assumed to be produced and consumed with the same rate. Also for simplification the level of enzymes was assumed to be constant. The reaction coefficients are defined the same for all reactions with some estimated numbers to give an overview about the reactions. The results for these assumptions, specific boundary condition and a time span of 200 seconds were plotted. These results show the steady state situation for the last three products after 200 seconds. The plot is:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The M-file function, as mentioned before, was solved by the ode15s function of Matlab. To do this procedure some assumptions were applied. The first substrate, Acetyl-CoA, was assumed to be produced and consumed with the same rate. Also for simplification the level of enzymes was assumed to be constant. The reaction coefficients are defined the same for all reactions with some estimated numbers to give an overview about the reactions. The results for these assumptions, specific boundary condition and a time span of 200 seconds were plotted. These results show the steady state situation for the last three products after 200 seconds. The plot is:</div></td></tr>
</table>Fehtemamhttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&diff=103374&oldid=prevFehtemam: /* Initial solution for ODEs */2008-10-30T03:33:17Z<p><span class="autocomment">Initial solution for ODEs</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Initial solution for ODEs==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Initial solution for ODEs==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The M-file function, as mentioned before, was solved by the ode15s function of Matlab. To do this procedure some assumptions were applied. The first substrate, Acetyl-CoA, was assumed to be produced and consumed with the same <del class="diffchange diffchange-inline">ratio</del>. Also for simplification the level of enzymes was assumed to be constant. The reaction coefficients are defined the same for all reactions with some <del class="diffchange diffchange-inline">non-accurate </del>numbers to give an overview about the reactions. The results for these assumptions, specific boundary condition and a time span of 200 seconds were plotted. These results show the steady state situation for the last three products after 200 seconds. The plot is:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The M-file function, as mentioned before, was solved by the ode15s function of Matlab. To do this procedure some assumptions were applied. The first substrate, Acetyl-CoA, was assumed to be produced and consumed with the same <ins class="diffchange diffchange-inline">rate</ins>. Also for simplification the level of enzymes was assumed to be constant. The reaction coefficients are defined the same for all reactions with some <ins class="diffchange diffchange-inline">estimated </ins>numbers to give an overview about the reactions. The results for these assumptions, specific boundary condition and a time span of 200 seconds were plotted. These results show the steady state situation for the last three products after 200 seconds. The plot is:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Initial_results.jpg |550px | center | <center> Initial solution for ODEs </center> | thumb]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Initial_results.jpg |550px | center | <center> Initial solution for ODEs </center> | thumb]]</div></td></tr>
</table>Fehtemamhttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&diff=103288&oldid=prevFehtemam: /* Kinetic Equations */2008-10-30T03:30:46Z<p><span class="autocomment">Kinetic Equations</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The K coefficients for our pathway and organism were not available from databases. From the work of [http://www.molgen.mpg.de/~lieberme/data/ibsb2007_Borger_et_al.pdf Borger et al. 2007] we expected that K has a Gaussian distribution so we took the minimum and maximum possible values of K from [http://www.brenda-enzymes.info/ Brenda] and made a normal distribution of them. Now the value for K is picked randomly from this distribution. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The K coefficients for our pathway and organism were not available from databases. From the work of [http://www.molgen.mpg.de/~lieberme/data/ibsb2007_Borger_et_al.pdf Borger et al. 2007] we expected that K has a Gaussian distribution so we took the minimum and maximum possible values of K from [http://www.brenda-enzymes.info/ Brenda] and made a normal distribution of them. Now the value for K is picked randomly from this distribution. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">These </del>differential equations were solved by '''Matlab&reg;''' ODE <del class="diffchange diffchange-inline">function. Due to the weaknesses in '''CellDesigner&trade;''' for defining the SBML file the converted file had many problems. To solve these problems the M-file was modified</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">After the conversion of SBML model to the M-file, the code needed some modifications. The modified code gave the right set of </ins>differential equations <ins class="diffchange diffchange-inline">which </ins>were solved by '''Matlab&reg;''' ODE <ins class="diffchange diffchange-inline">solver</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Initial solution for ODEs==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Initial solution for ODEs==</div></td></tr>
</table>Fehtemamhttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Color_modeling&diff=103143&oldid=prevFehtemam: /* Kinetic Equations */2008-10-30T03:26:10Z<p><span class="autocomment">Kinetic Equations</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The [http://www.sys-bio.org synthetic biology workbench] was used to convert the SBML model in '''CellDesigner&trade;''' into an M-file in '''Matlab&reg;'''. This M-file was the basic part of the code for modeling in '''Matlab&reg;'''. In the M-file all the related differential equations are defined as functions with the time spans and initial conditions as the inputs.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The [http://www.sys-bio.org synthetic biology workbench] was used to convert the SBML model in '''CellDesigner&trade;''' into an M-file in '''Matlab&reg;'''. This M-file was the basic part of the code for modeling in '''Matlab&reg;'''. In the M-file all the related differential equations are defined as functions with the time spans and initial conditions as the inputs.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The K coefficients for our pathway and organism were not available from databases. <del class="diffchange diffchange-inline">So </del>we took the minimum and maximum possible values of K from [http://www.brenda-enzymes.info/ Brenda] and made a normal distribution of them. Now the value for K is picked from this distribution. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The K coefficients for our pathway and organism were not available from databases. <ins class="diffchange diffchange-inline">From the work of [http://www.molgen.mpg.de/~lieberme/data/ibsb2007_Borger_et_al.pdf Borger et al. 2007] we expected that K has a Gaussian distribution so </ins>we took the minimum and maximum possible values of K from [http://www.brenda-enzymes.info/ Brenda] and made a normal distribution of them. Now the value for K is picked <ins class="diffchange diffchange-inline">randomly </ins>from this distribution. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>These differential equations were solved by '''Matlab&reg;''' ODE function. Due to the weaknesses in '''CellDesigner&trade;''' for defining the SBML file the converted file had many problems. To solve these problems the M-file was modified.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>These differential equations were solved by '''Matlab&reg;''' ODE function. Due to the weaknesses in '''CellDesigner&trade;''' for defining the SBML file the converted file had many problems. To solve these problems the M-file was modified.</div></td></tr>
</table>Fehtemam