http://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&feed=atom&action=historyTeam:Waterloo/Modeling - Revision history2024-03-29T11:23:18ZRevision history for this page on the wikiMediaWiki 1.16.5http://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&diff=162117&oldid=prevDookehster: /* Software */2009-10-22T00:46:02Z<p><span class="autocomment">Software</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It was decided early in the design stages of the mathematical simulation that representing strands of DNA as strings of nucleotides was highly inefficient. Instead, each functional block is represented as a single token, as shown in table 1.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It was decided early in the design stages of the mathematical simulation that representing strands of DNA as strings of nucleotides was highly inefficient. Instead, each functional block is represented as a single token, as shown in table 1.</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>{| class="wikitable" border="1" style="width:<del class="diffchange diffchange-inline">70</del>%;"</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>{| class="wikitable" border="1" style="width:<ins class="diffchange diffchange-inline">100</ins>%;"</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|+ Table 1: Token Mapping</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|+ Table 1: Token Mapping</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
</table>Dookehsterhttp://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&diff=137430&oldid=prevMattGingerich: /* Software */2009-10-21T03:04:06Z<p><span class="autocomment">Software</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>With this mapping of DNA sequences to characters completed, the algorithm to react two strands of DNA together is straightforward. First, the P and B tokens and their complements must be found, indicating the location of potential att sites. The validity of these att sites are then checked by ensuring that two nucleotides and a corresponding P' or B' sequence are present in the correct orientation. At this stage, each valid attP site can be reacted with any valid attB site by starting at one of the sites and iterating through the string of tokens until the other site is reached. Depending on the orientations of the two sites and whether two strands or a single molecule are involved in the reaction, the result may be an excision, an inversion, or a merge. The figure below gives a visual representation of this process.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>With this mapping of DNA sequences to characters completed, the algorithm to react two strands of DNA together is straightforward. First, the P and B tokens and their complements must be found, indicating the location of potential att sites. The validity of these att sites are then checked by ensuring that two nucleotides and a corresponding P' or B' sequence are present in the correct orientation. At this stage, each valid attP site can be reacted with any valid attB site by starting at one of the sites and iterating through the string of tokens until the other site is reached. Depending on the orientations of the two sites and whether two strands or a single molecule are involved in the reaction, the result may be an excision, an inversion, or a merge. The figure below gives a visual representation of this process.</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>[[Image:RecombinatronProcess.PNG|frame|center|The partial control flow of the simulation<del class="diffchange diffchange-inline">. Filtering </del>steps are not included.]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:RecombinatronProcess.PNG|frame|center|The partial control flow of the simulation<ins class="diffchange diffchange-inline">; filtering </ins>steps are not included.]]</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>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</div></td></tr>
</table>MattGingerichhttp://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&diff=137422&oldid=prevMattGingerich: /* Software */2009-10-21T03:03:13Z<p><span class="autocomment">Software</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>With this mapping of DNA sequences to characters completed, the algorithm to react two strands of DNA together is straightforward. First, the P and B tokens and their complements must be found, indicating the location of potential att sites. The validity of these att sites are then checked by ensuring that two nucleotides and a corresponding P' or B' sequence are present in the correct orientation. At this stage, each valid attP site can be reacted with any valid attB site by starting at one of the sites and iterating through the string of tokens until the other site is reached. Depending on the orientations of the two sites and whether two strands or a single molecule are involved in the reaction, the result may be an excision, an inversion, or a merge. The figure below gives a visual representation of this process.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>With this mapping of DNA sequences to characters completed, the algorithm to react two strands of DNA together is straightforward. First, the P and B tokens and their complements must be found, indicating the location of potential att sites. The validity of these att sites are then checked by ensuring that two nucleotides and a corresponding P' or B' sequence are present in the correct orientation. At this stage, each valid attP site can be reacted with any valid attB site by starting at one of the sites and iterating through the string of tokens until the other site is reached. Depending on the orientations of the two sites and whether two strands or a single molecule are involved in the reaction, the result may be an excision, an inversion, or a merge. The figure below gives a visual representation of this process.</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>[[Image:RecombinatronProcess.PNG|frame|center|The control flow of the simulation.]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:RecombinatronProcess.PNG|frame|center|The <ins class="diffchange diffchange-inline">partial </ins>control flow of the simulation<ins class="diffchange diffchange-inline">. Filtering steps are not included</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>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</div></td></tr>
</table>MattGingerichhttp://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&diff=136905&oldid=prevMattGingerich: /* Software */2009-10-21T02:20:18Z<p><span class="autocomment">Software</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that nucleotides are still individually represented by tokens, even though most sequences have abstract tokens. This is necessary because the behavior of the att sites is dependent on the core dinucleotide and the most useful representation of the dinucleotide is simply a pair of nucleotides.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that nucleotides are still individually represented by tokens, even though most sequences have abstract tokens. This is necessary because the behavior of the att sites is dependent on the core dinucleotide and the most useful representation of the dinucleotide is simply a pair of nucleotides.</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>With this mapping of DNA sequences to characters completed, the algorithm to react two strands of DNA together is straightforward. First, the P and B tokens and their complements must be found, indicating the location of potential att sites. The validity of these att sites are then checked by ensuring that two nucleotides and a corresponding P' or B' sequence are present in the correct orientation. At this stage, each valid attP site can be reacted with any valid attB site by starting at one of the sites and iterating through the string of tokens until the other site is reached. Depending on the orientations of the two sites and whether two strands or a single molecule are involved in the reaction, the result may be an excision, an inversion, or a merge.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>With this mapping of DNA sequences to characters completed, the algorithm to react two strands of DNA together is straightforward. First, the P and B tokens and their complements must be found, indicating the location of potential att sites. The validity of these att sites are then checked by ensuring that two nucleotides and a corresponding P' or B' sequence are present in the correct orientation. At this stage, each valid attP site can be reacted with any valid attB site by starting at one of the sites and iterating through the string of tokens until the other site is reached. Depending on the orientations of the two sites and whether two strands or a single molecule are involved in the reaction, the result may be an excision, an inversion, or a merge. <ins class="diffchange diffchange-inline">The figure below gives a visual representation of this process.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[Image:RecombinatronProcess.PNG|frame|center|The control flow of the simulation.]]</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>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</div></td></tr>
</table>MattGingerichhttp://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&diff=136740&oldid=prevApmasell: /* Software */2009-10-21T02:06:11Z<p><span class="autocomment">Software</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| A, C, G, T</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| A, C, G, T</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| <del class="diffchange diffchange-inline">Selectable Marker</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| <ins class="diffchange diffchange-inline">Selection Genes</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| <del class="diffchange diffchange-inline">Positive Selection</del>: M, N</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| <ins class="diffchange diffchange-inline">Counter Selectable Markers</ins>: M, N</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Negative Selection</del>: I, J, K, L</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Selectable Markers</ins>: I, J, K, L</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Sequence of Interest</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Sequence of Interest</div></td></tr>
</table>Apmasellhttp://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&diff=124184&oldid=prevMattGingerich: /* Software */2009-10-20T04:06:31Z<p><span class="autocomment">Software</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that nucleotides are still individually represented by tokens, even though most sequences have abstract tokens. This is necessary because the behavior of the att sites is dependent on the core dinucleotide and the most useful representation of the dinucleotide is simply a pair of nucleotides.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that nucleotides are still individually represented by tokens, even though most sequences have abstract tokens. This is necessary because the behavior of the att sites is dependent on the core dinucleotide and the most useful representation of the dinucleotide is simply a pair of nucleotides.</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>With this mapping of DNA sequences to characters completed, the algorithm to react two strands of DNA together is straightforward. First, the P and B tokens and their complements must be found, indicating the location of potential att sites. The validity of these att sites are then checked by ensuring that two nucleotides and a corresponding P' or B' sequence are present in the correct orientation. At this stage, each valid attP site can be reacted with any valid attB site by starting at one of the sites and iterating through the string of tokens until the other site is reached. Depending on the orientations of the two sites and <del class="diffchange diffchange-inline">on the number of DNA molecules (one </del>or <del class="diffchange diffchange-inline">two) </del>involved in the reaction, the result <del class="diffchange diffchange-inline">of this reaction </del>may be an excision, an inversion, or a merge.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>With this mapping of DNA sequences to characters completed, the algorithm to react two strands of DNA together is straightforward. First, the P and B tokens and their complements must be found, indicating the location of potential att sites. The validity of these att sites are then checked by ensuring that two nucleotides and a corresponding P' or B' sequence are present in the correct orientation. At this stage, each valid attP site can be reacted with any valid attB site by starting at one of the sites and iterating through the string of tokens until the other site is reached. Depending on the orientations of the two sites and <ins class="diffchange diffchange-inline">whether two strands </ins>or <ins class="diffchange diffchange-inline">a single molecule are </ins>involved in the reaction, the result may be an excision, an inversion, or a merge.</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>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</div></td></tr>
</table>MattGingerichhttp://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&diff=124176&oldid=prevMattGingerich: /* Software */2009-10-20T04:03:23Z<p><span class="autocomment">Software</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</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;"></ins></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;">Filters were set to regularly delete DNA strands that did not meet selection criteria. The frequency of the filtering was based on intuitive notions of the number of operations that could occur before stable strands were produced, where each operation consists of one reaction of a pair of att sites. These frequency values were originally set conservatively high at 30 operations for filtering based on the number of origins present on a strand and 255 operations for filtering based on selectable markers. In later testing, the frequency of filtering was drastically increased in an attempt to remove unnecessary products and improve the simulation's performance.</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>Lastly, because of the exponential behaviour of the search space, we assumed that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption was made in order to have sane parameters for termination.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Lastly, because of the exponential behaviour of the search space, we assumed that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption was made in order to have sane parameters for termination.</div></td></tr>
</table>MattGingerichhttp://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&diff=124144&oldid=prevMattGingerich: /* Software */2009-10-20T03:52:00Z<p><span class="autocomment">Software</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Nucleotides</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Nucleotides</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| A, C, G, T</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| A, C, G, T</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;">|-</ins></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;">| Selectable Marker</ins></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;">| Positive Selection: M, N</ins></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;">Negative Selection: I, J, K, L</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Sequence of Interest</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Sequence of Interest</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Complements</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Complements</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| Lowercase characters become uppercase and the <del class="diffchange diffchange-inline">reverse</del>. For origins, subtract the digit to be complemented from nine (ie. 0 and 9 are complements). For nucleotides, A/T and G/C remain complemented pairs.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| Lowercase characters become uppercase and the <ins class="diffchange diffchange-inline">vice versa</ins>. For origins, subtract the digit to be complemented from nine (ie. 0 and 9 are complements). For nucleotides, A/T and G/C remain complemented pairs.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</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 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;">Note that nucleotides are still individually represented by tokens, even though most sequences have abstract tokens. This is necessary because the behavior of the att sites is dependent on the core dinucleotide and the most useful representation of the dinucleotide is simply a pair of nucleotides.</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: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">In order </del>to <del class="diffchange diffchange-inline">run the solver</del>, <del class="diffchange diffchange-inline">we made several assumptions</del>. First, <del class="diffchange diffchange-inline">as we did not know which combinations </del>of <del class="diffchange diffchange-inline">sequences with ''</del>att<del class="diffchange diffchange-inline">'' </del>sites <del class="diffchange diffchange-inline">would be part </del>of the <del class="diffchange diffchange-inline">solution</del>, <del class="diffchange diffchange-inline">we assumed that </del>any <del class="diffchange diffchange-inline">product in our search space was a </del>valid <del class="diffchange diffchange-inline">sequence for </del>the <del class="diffchange diffchange-inline">next generation </del>of <del class="diffchange diffchange-inline">reactions</del>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">With this mapping of DNA sequences </ins>to <ins class="diffchange diffchange-inline">characters completed</ins>, <ins class="diffchange diffchange-inline">the algorithm to react two strands of DNA together is straightforward</ins>. First, <ins class="diffchange diffchange-inline">the P and B tokens and their complements must be found, indicating the location </ins>of <ins class="diffchange diffchange-inline">potential </ins>att sites<ins class="diffchange diffchange-inline">. The validity </ins>of <ins class="diffchange diffchange-inline">these att sites are then checked by ensuring that two nucleotides and a corresponding P' or B' sequence are present in </ins>the <ins class="diffchange diffchange-inline">correct orientation. At this stage</ins>, <ins class="diffchange diffchange-inline">each valid attP site can be reacted with </ins>any valid <ins class="diffchange diffchange-inline">attB site by starting at one of </ins>the <ins class="diffchange diffchange-inline">sites and iterating through the string </ins>of <ins class="diffchange diffchange-inline">tokens until the other site is reached. Depending on the orientations of the two sites and on the number of DNA molecules (one or two) involved in the reaction, the result of this reaction may be an excision, an inversion, or a merge</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: #ffa; color:black; font-size: smaller;"><div>We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. </ins>We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell.</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>Lastly, because of the exponential behaviour of the search space, we assumed that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption was made in order to have sane parameters for termination.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Lastly, because of the exponential behaviour of the search space, we assumed that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption was made in order to have sane parameters for termination.</div></td></tr>
</table>MattGingerichhttp://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&diff=124027&oldid=prevMattGingerich: /* Software */2009-10-20T03:26:18Z<p><span class="autocomment">Software</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
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<td colspan='2' style="background-color: white; color:black;">Revision as of 03:26, 20 October 2009</td>
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<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>===Software===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Software===</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;"></ins></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;">It was decided early in the design stages of the mathematical simulation that representing strands of DNA as strings of nucleotides was highly inefficient. Instead, each functional block is represented as a single token, as shown in table 1.</ins></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;"></ins></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;">{| class="wikitable" border="1" style="width:70%;"</ins></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;">|+ Table 1: Token Mapping</ins></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;">|-</ins></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;">! Sequence</ins></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;">! Corresponding Token</ins></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;">|-</ins></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;">| style="width:50%;" |P [attP site is composed of POP']</ins></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</ins></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;">|-</ins></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'</ins></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;">| Q</ins></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;">|-</ins></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;">| B [attB site is composed of BOB']</ins></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;">| B</ins></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;">|-</ins></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;">| B'</ins></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;">| D</ins></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;">|-</ins></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;">| Chromosomal Origin</ins></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;">| 0 or 9</ins></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;">|-</ins></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;">| Plasmid Origin</ins></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;">| 1 to 8</ins></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;">|-</ins></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;">| Nucleotides</ins></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;">| A, C, G, T</ins></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;">|-</ins></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;">| Sequence of Interest</ins></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;">| X, Y, Z</ins></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;">|-</ins></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;">| Complements</ins></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;">| Lowercase characters become uppercase and the reverse. For origins, subtract the digit to be complemented from nine (ie. 0 and 9 are complements). For nucleotides, A/T and G/C remain complemented pairs.</ins></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;">|}</ins></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;"></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>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. </div></td></tr>
</table>MattGingerichhttp://2009.igem.org/wiki/index.php?title=Team:Waterloo/Modeling&diff=116269&oldid=prevJlapointe: /* Software */2009-10-19T07:19:39Z<p><span class="autocomment">Software</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 07:19, 19 October 2009</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Software===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Software===</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>In order to run the solver, we <del class="diffchange diffchange-inline">make </del>several assumptions. First, as we <del class="diffchange diffchange-inline">do </del>not know which combinations of sequences with ''att'' sites <del class="diffchange diffchange-inline">are </del>part of the solution, we <del class="diffchange diffchange-inline">assume </del>that any product in our search space <del class="diffchange diffchange-inline">is </del>a valid sequence for the next generation of reactions. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to run the solver, we <ins class="diffchange diffchange-inline">made </ins>several assumptions. First, as we <ins class="diffchange diffchange-inline">did </ins>not know which combinations of sequences with ''att'' sites <ins class="diffchange diffchange-inline">would be </ins>part of the solution, we <ins class="diffchange diffchange-inline">assumed </ins>that any product in our search space <ins class="diffchange diffchange-inline">was </ins>a valid sequence for the next generation of reactions. </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>We further <del class="diffchange diffchange-inline">assume </del>that any plasmid with valid ''att'' sites and complementary operators <del class="diffchange diffchange-inline">is </del>capable of self reacting and also of reacting with any other plasmid in the history of the <del class="diffchange diffchange-inline">modelled </del>cell. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We further <ins class="diffchange diffchange-inline">assumed </ins>that any plasmid with valid ''att'' sites and complementary operators <ins class="diffchange diffchange-inline">was </ins>capable of self reacting and also of reacting with any other plasmid in the history of the <ins class="diffchange diffchange-inline">modeled </ins>cell. </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>Lastly, because of the exponential behaviour of the search space, we <del class="diffchange diffchange-inline">assume </del>that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption <del class="diffchange diffchange-inline">is </del>made in order to have sane parameters for termination.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Lastly, because of the exponential behaviour of the search space, we <ins class="diffchange diffchange-inline">assumed </ins>that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption <ins class="diffchange diffchange-inline">was </ins>made in order to have sane parameters for termination.</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>===Math===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Math===</div></td></tr>
</table>Jlapointe