http://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&feed=atom&action=historyTeam:Amsterdam/software/logbook designer/setup - Revision history2024-03-28T08:37:45ZRevision history for this page on the wikiMediaWiki 1.16.0http://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&diff=238254&oldid=prevMaartenR at 03:54, 27 September 20122012-09-27T03:54:11Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1>Logbook Designer: Setup</h1></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1>Logbook Designer: Setup</h1></div></td></tr>
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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">__TOC__</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">__NOTOC__</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have designed an online tool where a user can create their Cellular Logbook in silico by giving a backbone sequence and selecting one or more sensors manually or predefined from the parts registry database. An algorithm then computes one or more plasmids, taking into account the rules we use for our real life Cellular Logbook, and outputs the appropriate genbank files as well as the visualized version of the plasmid. The tool will also generate all possible permutations of gel bands which can be used as a read-out sheet for the gel electrophoresis results. By using this tool we are able to quickly design a plasmid with multiple sensors.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have designed an online tool where a user can create their Cellular Logbook in silico by giving a backbone sequence and selecting one or more sensors manually or predefined from the parts registry database. An algorithm then computes one or more plasmids, taking into account the rules we use for our real life Cellular Logbook, and outputs the appropriate genbank files as well as the visualized version of the plasmid. The tool will also generate all possible permutations of gel bands which can be used as a read-out sheet for the gel electrophoresis results. By using this tool we are able to quickly design a plasmid with multiple sensors.</div></td></tr>
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</table>MaartenRhttp://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&diff=232021&oldid=prevMaartenR at 02:03, 27 September 20122012-09-27T02:03:36Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Plasmid Visualization</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Plasmid Visualization</h2></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Amsterdam tool visualization1.png|left|300px|thumb|Figure 2: Graphical display of a plasmid using the Logbook Designer]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Amsterdam tool visualization1.png|left|300px|thumb|Figure 2: Graphical display of a plasmid using the Logbook Designer]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to grant the user a quick and dynamic overview of the plasmids that were just designed, a visualization of each plasmid is available with just a click on a button. Each of these visualized plasmids shows the specific features of that plasmid by color code. Hovering over each feature gives additional information, and clicking on a feature gives its DNA sequence.<<del class="diffchange diffchange-inline">br\</del>><<del class="diffchange diffchange-inline">br\><br\><br\</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to grant the user a quick and dynamic overview of the plasmids that were just designed, a visualization of each plasmid is available with just a click on a button. Each of these visualized plasmids shows the specific features of that plasmid by color code. Hovering over each feature gives additional information, and clicking on a feature gives its DNA sequence.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td></tr>
</table>MaartenRhttp://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&diff=231997&oldid=prevMaartenR at 02:03, 27 September 20122012-09-27T02:03:10Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_readout.png|right|<del class="diffchange diffchange-inline">340px</del>|thumb|Figure 3: Sensor belonging to the given band sizes]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_readout.png|right|<ins class="diffchange diffchange-inline">330px</ins>|thumb|Figure 3: Sensor belonging to the given band sizes]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.</div></td></tr>
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</table>MaartenRhttp://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&diff=231979&oldid=prevMaartenR at 02:02, 27 September 20122012-09-27T02:02:52Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_readout.png|right|<del class="diffchange diffchange-inline">320px</del>|thumb|Figure 3: Sensor belonging to the given band sizes]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_readout.png|right|<ins class="diffchange diffchange-inline">340px</ins>|thumb|Figure 3: Sensor belonging to the given band sizes]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.</div></td></tr>
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</table>MaartenRhttp://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&diff=231900&oldid=prevMaartenR at 02:01, 27 September 20122012-09-27T02:01:33Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Plasmid Visualization</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Plasmid Visualization</h2></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Amsterdam tool visualization1.png|left|300px|thumb|Figure 2: Graphical display of a plasmid using the Logbook Designer]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Amsterdam tool visualization1.png|left|300px|thumb|Figure 2: Graphical display of a plasmid using the Logbook Designer]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to grant the user a quick and dynamic overview of the plasmids that were just designed, a visualization of each plasmid is available with just a click on a button. Each of these visualized plasmids shows the specific features of that plasmid by color code. Hovering over each feature gives additional information, and clicking on a feature gives its DNA sequence.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to grant the user a quick and dynamic overview of the plasmids that were just designed, a visualization of each plasmid is available with just a click on a button. Each of these visualized plasmids shows the specific features of that plasmid by color code. Hovering over each feature gives additional information, and clicking on a feature gives its DNA sequence.<ins class="diffchange diffchange-inline"><br\><br\><br\><br\></ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td></tr>
</table>MaartenRhttp://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&diff=231874&oldid=prevMaartenR at 02:01, 27 September 20122012-09-27T02:01:07Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Genbank Output</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Genbank Output</h2></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_genbank.png|right|300px|thumb|Figure 1: Genbank output given by the Logbook Designer]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_genbank.png|right|300px|thumb|Figure 1: Genbank output given by the Logbook Designer]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Standard formats for biological data are essential to communicate and pass along biological findings. The Genbank format is the most widely used format for genome and sequence annotation. As such the Plasmid Designer is able to produce Genbank files for each plasmid with the click of a button. This way the user can use the designed construct in other biological tools such as the freeware plasmid editor ApE[http://biologylabs.utah.edu/jorgensen/wayned/ape/].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Standard formats for biological data are essential to communicate and pass along biological findings. The Genbank format is the most widely used format for genome and sequence annotation. As such the Plasmid Designer is able to produce Genbank files for each plasmid with the click of a button. This way the user can use the designed construct in other biological tools such as the freeware plasmid editor ApE[http://biologylabs.utah.edu/jorgensen/wayned/ape/].<ins class="diffchange diffchange-inline"><br\><br\><br\><br\></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><h2>Plasmid Visualization</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Plasmid Visualization</h2></div></td></tr>
</table>MaartenRhttp://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&diff=231858&oldid=prevMaartenR at 02:00, 27 September 20122012-09-27T02:00:51Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_genbank.png|right|300px|thumb|Figure 1: Genbank output given by the Logbook Designer]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_genbank.png|right|300px|thumb|Figure 1: Genbank output given by the Logbook Designer]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Standard formats for biological data are essential to communicate and pass along biological findings. The Genbank format is the most widely used format for genome and sequence annotation. As such the Plasmid Designer is able to produce Genbank files for each plasmid with the click of a button. This way the user can use the designed construct in other biological tools such as the freeware plasmid editor ApE[http://biologylabs.utah.edu/jorgensen/wayned/ape/].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Standard formats for biological data are essential to communicate and pass along biological findings. The Genbank format is the most widely used format for genome and sequence annotation. As such the Plasmid Designer is able to produce Genbank files for each plasmid with the click of a button. This way the user can use the designed construct in other biological tools such as the freeware plasmid editor ApE[http://biologylabs.utah.edu/jorgensen/wayned/ape/].</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Plasmid Visualization</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Plasmid Visualization</h2></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Amsterdam tool visualization1.png|left|300px|thumb|Figure 2: Graphical display of a plasmid using the Logbook Designer]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Amsterdam tool visualization1.png|left|300px|thumb|Figure 2: Graphical display of a plasmid using the Logbook Designer]]</div></td></tr>
</table>MaartenRhttp://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&diff=231822&oldid=prevMaartenR at 02:00, 27 September 20122012-09-27T02:00:15Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_readout.png|right|<del class="diffchange diffchange-inline">310px</del>|thumb|Figure 3: Sensor belonging to the given band sizes]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_readout.png|right|<ins class="diffchange diffchange-inline">320px</ins>|thumb|Figure 3: Sensor belonging to the given band sizes]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.</div></td></tr>
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</table>MaartenRhttp://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&diff=231810&oldid=prevMaartenR at 02:00, 27 September 20122012-09-27T02:00:03Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_readout.png|right|<del class="diffchange diffchange-inline">350px</del>|thumb|Figure 3: Sensor belonging to the given band sizes]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_readout.png|right|<ins class="diffchange diffchange-inline">310px</ins>|thumb|Figure 3: Sensor belonging to the given band sizes]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.</div></td></tr>
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</table>MaartenRhttp://2012.igem.org/wiki/index.php?title=Team:Amsterdam/software/logbook_designer/setup&diff=231792&oldid=prevMaartenR at 01:59, 27 September 20122012-09-27T01:59:45Z<p></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 01:59, 27 September 2012</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Gel Readout</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_readout.png|right|<del class="diffchange diffchange-inline">300px</del>|thumb|Figure 3: Sensor belonging to the given band sizes]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:Amsterdam_tool_readout.png|right|<ins class="diffchange diffchange-inline">350px</ins>|thumb|Figure 3: Sensor belonging to the given band sizes]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.</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>
</table>MaartenR