http://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&feed=atom&action=historyTeam:UC Berkeley Tools/Development - Revision history2024-03-28T16:01:41ZRevision history for this page on the wikiMediaWiki 1.16.5http://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&diff=87224&oldid=prevLogosandpathos: /* Helping Out In The Lab: Assembly Algorithms */2008-10-29T09:52:54Z<p><span class="autocomment">Helping Out In The Lab: Assembly Algorithms</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 09:52, 29 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 24:</td>
<td colspan="2" class="diff-lineno">Line 24:</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>==Helping Out In The Lab: Assembly Algorithms==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Helping Out In The Lab: Assembly Algorithms==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents. The [https://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley UC Berkeley wet<del class="diffchange diffchange-inline">] </del>team used these tools on a collection of 496 goal composite parts. Had no overlap been found (e.g. using naive methods), 5961 total parts would have to have been made. The program generated an assembly tree that required only 1283 total parts be built, reducing the number having to be assembled by '''4678 parts.''' This assembly took just over 4 minutes to complete using the algorithm - if this same process were attempted by hand, it would take multiple people over 3 days to complete! This saved the wet team perhaps weeks of work as well as helping them save on the cost of the reagents required for the thousands of reactions that would have been necessary.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents. The [https://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley UC Berkeley wet team<ins class="diffchange diffchange-inline">] </ins>used these tools on a collection of 496 goal composite parts. Had no overlap been found (e.g. using naive methods), 5961 total parts would have to have been made. The program generated an assembly tree that required only 1283 total parts be built, reducing the number having to be assembled by '''4678 parts.''' This assembly took just over 4 minutes to complete using the algorithm - if this same process were attempted by hand, it would take multiple people over 3 days to complete! This saved the wet team perhaps weeks of work as well as helping them save on the cost of the reagents required for the thousands of reactions that would have been necessary.</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>==PoBoL: BioBrick Data Sharing Made Easy==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==PoBoL: BioBrick Data Sharing Made Easy==</div></td></tr>
</table>Logosandpathoshttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&diff=87219&oldid=prevLogosandpathos: /* Helping Out In The Lab: Assembly Algorithms */2008-10-29T09:52:44Z<p><span class="autocomment">Helping Out In The Lab: Assembly Algorithms</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 09:52, 29 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 24:</td>
<td colspan="2" class="diff-lineno">Line 24:</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>==Helping Out In The Lab: Assembly Algorithms==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Helping Out In The Lab: Assembly Algorithms==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents. The UC Berkeley wet team used these tools on a collection of 496 goal composite parts. Had no overlap been found (e.g. using naive methods), 5961 total parts would have to have been made. The program generated an assembly tree that required only 1283 total parts be built, reducing the number having to be assembled by '''4678 parts.''' This assembly took just over 4 minutes to complete using the algorithm - if this same process were attempted by hand, it would take multiple people over 3 days to complete! This saved the wet team perhaps weeks of work as well as helping them save on the cost of the reagents required for the thousands of reactions that would have been necessary.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents. The <ins class="diffchange diffchange-inline">[https://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley </ins>UC Berkeley wet<ins class="diffchange diffchange-inline">] </ins>team used these tools on a collection of 496 goal composite parts. Had no overlap been found (e.g. using naive methods), 5961 total parts would have to have been made. The program generated an assembly tree that required only 1283 total parts be built, reducing the number having to be assembled by '''4678 parts.''' This assembly took just over 4 minutes to complete using the algorithm - if this same process were attempted by hand, it would take multiple people over 3 days to complete! This saved the wet team perhaps weeks of work as well as helping them save on the cost of the reagents required for the thousands of reactions that would have been necessary.</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>==PoBoL: BioBrick Data Sharing Made Easy==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==PoBoL: BioBrick Data Sharing Made Easy==</div></td></tr>
</table>Logosandpathoshttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&diff=87202&oldid=prevLogosandpathos: /* Helping Out In The Lab: Assembly Algorithms */2008-10-29T09:51:10Z<p><span class="autocomment">Helping Out In The Lab: Assembly Algorithms</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 09:51, 29 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 24:</td>
<td colspan="2" class="diff-lineno">Line 24:</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>==Helping Out In The Lab: Assembly Algorithms==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Helping Out In The Lab: Assembly Algorithms==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents. The UC Berkeley wet team used these tools on a collection of 496 goal composite parts. Had no overlap been found (e.g. using naive methods), 5961 total parts would have to have been made. The program generated an assembly tree that required only 1283 total parts be built<del class="diffchange diffchange-inline">. That is a savings of </del>4678 parts. This assembly took just over 4 minutes to complete using the algorithm<del class="diffchange diffchange-inline">. If </del>this same process were attempted by hand, it would take multiple people over 3 days to complete.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents. The UC Berkeley wet team used these tools on a collection of 496 goal composite parts. Had no overlap been found (e.g. using naive methods), 5961 total parts would have to have been made. The program generated an assembly tree that required only 1283 total parts be built<ins class="diffchange diffchange-inline">, reducing the number having to be assembled by '''</ins>4678 parts.<ins class="diffchange diffchange-inline">''' </ins> This assembly took just over 4 minutes to complete using the algorithm <ins class="diffchange diffchange-inline">- if </ins>this same process were attempted by hand, it would take multiple people over 3 days to complete<ins class="diffchange diffchange-inline">! This saved the wet team perhaps weeks of work as well as helping them save on the cost of the reagents required for the thousands of reactions that would have been necessary</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>==PoBoL: BioBrick Data Sharing Made Easy==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==PoBoL: BioBrick Data Sharing Made Easy==</div></td></tr>
</table>Logosandpathoshttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&diff=86527&oldid=prevDensmore: /* Increasing Collaboration Through Better Access To Database */2008-10-29T08:17:38Z<p><span class="autocomment">Increasing Collaboration Through Better Access To Database</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 08:17, 29 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 35:</td>
<td colspan="2" class="diff-lineno">Line 35:</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>==Increasing Collaboration Through Better Access To Database==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Increasing Collaboration Through Better Access To Database==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Through </del>a <del class="diffchange diffchange-inline">combination </del>of <del class="diffchange diffchange-inline">PoBoL</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">A common theme with all scientific exploration is: "How will the technology you are developing have </ins>a <ins class="diffchange diffchange-inline">positive impact on society". I think most people agree that Synthetic Biology has tremendous potential to be a force for good in the world. New drug delivery systems, smarter/cleaner energy sources, and improved food production capabilities are only the beginning. However for any of this to happen, there are going to have to be tools in place to help this to occur.</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">Clotho can aid in the human practice area of synthetic biology by providing new methods to encourage sharing and innovation. Sharing is a natural aspect of Clotho with its strong connection to databases </ins>of <ins class="diffchange diffchange-inline">parts. Innovation is encouraged by helping others to develop new designs more quickly and efficiently.</ins></div></td></tr>
</table>Densmorehttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&diff=86456&oldid=prevDensmore: /* PoBoL: BioBrick Data Sharing Made Easy */2008-10-29T08:05:45Z<p><span class="autocomment">PoBoL: BioBrick Data Sharing Made Easy</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 08:05, 29 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 31:</td>
<td colspan="2" class="diff-lineno">Line 31:</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>For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]</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;"><br clear="all"></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>==Increasing Collaboration Through Better Access To Database==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Increasing Collaboration Through Better Access To Database==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Through a combination of PoBoL</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Through a combination of PoBoL</div></td></tr>
</table>Densmorehttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&diff=86454&oldid=prevDensmore: /* PoBoL: BioBrick Data Sharing Made Easy */2008-10-29T08:04:46Z<p><span class="autocomment">PoBoL: BioBrick Data Sharing Made Easy</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 08:04, 29 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 27:</td>
<td colspan="2" class="diff-lineno">Line 27:</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>==PoBoL: BioBrick Data Sharing Made Easy==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==PoBoL: BioBrick Data Sharing Made Easy==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:PoBoLDiagram.png|thumb|left|200 px|<span style="color: <del class="diffchange diffchange-inline">blue</del>"><small>''A diagram representing the basic structural concepts behind PoBoL''</small></span>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:PoBoLDiagram.png|thumb|left|200 px|<span style="color: <ins class="diffchange diffchange-inline">white</ins>"><small>''A diagram representing the basic structural concepts behind PoBoL''</small></span>]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL <ins class="diffchange diffchange-inline">is encapsulated in the Clotho Data structure. We indicate that this is our version since it adds objects which are not part of PoBoL. These include collections of BioBricks and composite information (right and left children and order). One of the big issues current facing synthetic biology is coming up with a parts standardization. We hope that Clotho can help to raise and solve issues in this area by being a deployment vehicle for ideas. Since we have created Clotho in a highly modular way, it can be the test bed for a variety of part standardization ideas. </ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></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>For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </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>==Increasing Collaboration Through Better Access To Database==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Increasing Collaboration Through Better Access To Database==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Through a combination of PoBoL</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Through a combination of PoBoL</div></td></tr>
</table>Densmorehttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&diff=86396&oldid=prevDensmore at 07:52, 29 October 20082008-10-29T07:52:37Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 07:52, 29 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 6:</td>
<td colspan="2" class="diff-lineno">Line 6:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Clotho Beta: Future Development==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Clotho Beta: Future Development==</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 next release of Clotho after iGEM is planned for a late Spring 2009 release. This will be the official Beta release (the other releases will have been Alpha and iGEM). The main focus of the release will be to fully implement all the features currently in Clotho as well as fix bugs that are found. Clotho testing and deployment will begin with Anderson Lab at UCB and expand to Voigt Lab at UCSF. In addition to general robustness, Clotho Beta should also incorporate a few new features<del class="diffchange diffchange-inline">.</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The next release of Clotho after iGEM is planned for a late Spring 2009 release. This will be the official <ins class="diffchange diffchange-inline">''</ins>Beta<ins class="diffchange diffchange-inline">'' </ins>release (the other releases will have been Alpha and iGEM). The main focus of the release will be to fully implement all the features currently in Clotho as well as fix bugs that are found. Clotho testing and deployment will begin with Anderson Lab at UCB and expand to Voigt Lab at UCSF<ins class="diffchange diffchange-inline">. It is our goal to have Clotho be a main software component in each lab</ins>. In addition to general robustness, Clotho Beta should also incorporate a few new features <ins class="diffchange diffchange-inline">as will be described in the following sections:</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>===New Features===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===New Features===</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Biomek3000.jpg|thumb|right|150 px|<span style="color: <del class="diffchange diffchange-inline">blue</del>"><small>''A Biomek 3000, similar to the we'll be working with in the lab''</small></span>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Biomek3000.jpg|thumb|right|150 px|<span style="color: <ins class="diffchange diffchange-inline">white</ins>"><small>''A Biomek 3000, similar to the <ins class="diffchange diffchange-inline">one </ins>we'll be working with in the lab''</small></span>]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This will likely include a <del class="diffchange diffchange-inline">'</del>schematic view<del class="diffchange diffchange-inline">' </del>for assembling parts, similar to the one in [http://web.mit.edu/jagoler/www/biojade/overview.html BioJade].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This will likely include a <ins class="diffchange diffchange-inline">"</ins>schematic view<ins class="diffchange diffchange-inline">" </ins>for assembling parts, similar to the one in [http://web.mit.edu/jagoler/www/biojade/overview.html BioJade]. <ins class="diffchange diffchange-inline">We would also like </ins>to <ins class="diffchange diffchange-inline">explore a "</ins>parts <ins class="diffchange diffchange-inline">view" where </ins>the <ins class="diffchange diffchange-inline">individual parts have associated icons. A design now no longer becomes writing nucleotide sequences but rather dragging around icons which have sequence data associated with them</ins>.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">* Ability </del>to <del class="diffchange diffchange-inline">interface with devices, including robots that can be used for automated production of </del>parts <del class="diffchange diffchange-inline">designed in Clotho. (In </del>the <del class="diffchange diffchange-inline">future, this will contain a link to Anderson Lab's Biomek robot</del>.<del class="diffchange diffchange-inline">)</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; 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> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; 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">*</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; 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> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; 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> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; 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;">* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho. (In the future, this will contain a link to Anderson Lab's Biomek robot.) This aspect will be tied to the assembly algorithms already in Clotho. These algorithms will be expanded upon to deal with other assembly issues such as tracking methylated "righty" and "lefty" parts.</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 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;">*Increased support for other interchange format standards such as [http://www.sequenceontology.org/gff3.shtml GFF3]. This will allow us to begin to interface with such tools as BioStudio.</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;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 28:</td>
<td colspan="2" class="diff-lineno">Line 24:</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>==Helping Out In The Lab: Assembly Algorithms==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Helping Out In The Lab: Assembly Algorithms==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* One of the initial algorithms we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents. <ins class="diffchange diffchange-inline">The UC Berkeley wet team used these tools on a collection of 496 goal composite parts. Had no overlap been found (e.g. using naive methods), 5961 total parts would have to have been made. The program generated an assembly tree that required only 1283 total parts be built. That is a savings of 4678 parts. This assembly took just over 4 minutes to complete using the algorithm. If this same process were attempted by hand, it would take multiple people over 3 days to complete.</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">** EXPAND HERE **</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; 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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==PoBoL: BioBrick Data Sharing Made Easy==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==PoBoL: BioBrick Data Sharing Made Easy==</div></td></tr>
</table>Densmorehttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&diff=81516&oldid=prevLogosandpathos at 19:57, 28 October 20082008-10-28T19:57:53Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 19:57, 28 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 9:</td>
<td colspan="2" class="diff-lineno">Line 9:</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>===New Features===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===New Features===</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Biomek3000.jpg|thumb|right|150 px|<span style="color: blue"><small>''A Biomek 3000, similar to the we'll be working with in the lab''</small></span><del class="diffchange diffchange-inline">'</del>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Biomek3000.jpg|thumb|right|150 px|<span style="color: blue"><small>''A Biomek 3000, similar to the we'll be working with in the lab''</small></span>]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This will likely include a 'schematic view' for assembling parts, similar to the one in [http://web.mit.edu/jagoler/www/biojade/overview.html BioJade].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This will likely include a 'schematic view' for assembling parts, similar to the one in [http://web.mit.edu/jagoler/www/biojade/overview.html BioJade].</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" class="diff-lineno">Line 22:</td>
<td colspan="2" class="diff-lineno">Line 22:</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>===Improved Features:===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Improved Features:===</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* More database support <del class="diffchange diffchange-inline">(systems like </del>[http://brickit.wiki.sourceforge.net/ BrickIt!]). <del class="diffchange diffchange-inline">We plan to test this one a wide variety </del>of databases <del class="diffchange diffchange-inline">including JBEI</del>'s <del class="diffchange diffchange-inline">registry</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* More database support<ins class="diffchange diffchange-inline">: we plan to expand the number and variety of databases that Clotho can connect to, including </ins>[http://brickit.wiki.sourceforge.net/ BrickIt!]) <ins class="diffchange diffchange-inline">and the JBEI registry</ins>. <ins class="diffchange diffchange-inline"> One </ins>of <ins class="diffchange diffchange-inline">the </ins>databases <ins class="diffchange diffchange-inline">at the top of our priority list is iGEM</ins>'s <ins class="diffchange diffchange-inline">own [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]</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>* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho. This will <del class="diffchange diffchange-inline">take the form of </del>more <del class="diffchange diffchange-inline">plug in </del>extension points and more fully featured interfaces for <del class="diffchange diffchange-inline">the </del>existing <del class="diffchange diffchange-inline">ones</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho. This will <ins class="diffchange diffchange-inline">include </ins>more extension points <ins class="diffchange diffchange-inline">where plug-ins can be integrated </ins>and <ins class="diffchange diffchange-inline">a set of </ins>more fully featured interfaces for existing <ins class="diffchange diffchange-inline">extensions</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;"></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>==Helping Out In The Lab: Assembly Algorithms==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Helping Out In The Lab: Assembly Algorithms==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* <del class="diffchange diffchange-inline">Using </del>the <del class="diffchange diffchange-inline">assembly </del>algorithms<del class="diffchange diffchange-inline">, helped </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">One of </ins>the <ins class="diffchange diffchange-inline">initial </ins>algorithms <ins class="diffchange diffchange-inline">we added to Clotho was an "optimal assembly" algorithm that can take in a list of goal composite parts and return a list with the minimum number of steps required to build those parts - a particularly useful feature if the goal parts utilize many of the same basic parts as subcomponents.</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 class="diffchange diffchange-inline">** EXPAND HERE **</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>==PoBoL: BioBrick Data Sharing Made Easy==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==PoBoL: BioBrick Data Sharing Made Easy==</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;">[[Image:PoBoLDiagram.png|thumb|left|200 px|<span style="color: blue"><small>''A diagram representing the basic structural concepts behind PoBoL''</small></span>]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>PoBoL stands for "Provisional BioBrick Language", and is the name given to a technical standard for BioBrick data in synthetic biology databases. Put simply, our implementation of PoBoL</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 style="color: red; font-weight: bold; text-decoration: none;">[[Image:PoBoLDiagram.png]]</del></div></td><td colspan="2"> </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>For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For more information on the PoBoL standard, check out [http://www.pobol.org/ www.pobol.org]</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 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 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 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 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 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 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 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>==Increasing Collaboration Through Better Access To Database==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Increasing Collaboration Through Better Access To Database==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Through a combination of PoBoL</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Through a combination of PoBoL</div></td></tr>
</table>Logosandpathoshttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&diff=81221&oldid=prevLogosandpathos at 19:29, 28 October 20082008-10-28T19:29:22Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 19:29, 28 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 9:</td>
<td colspan="2" class="diff-lineno">Line 9:</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>===New Features===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===New Features===</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This <del class="diffchange diffchange-inline">most likely </del>will <del class="diffchange diffchange-inline">take an icon format </del>similar to <del class="diffchange diffchange-inline">GeneDesigner or </del>BioJade.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[Image:Biomek3000.jpg|thumb|right|150 px|<span style="color: blue"><small>''A Biomek 3000, similar to the we'll be working with in the lab''</small></span>']]</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho. <del class="diffchange diffchange-inline">This </del>will <del class="diffchange diffchange-inline">begin with </del>a link to Anderson <del class="diffchange diffchange-inline">lab</del>'s Biomek robot.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts. This will <ins class="diffchange diffchange-inline">likely include a 'schematic view' for assembling parts, </ins>similar to <ins class="diffchange diffchange-inline">the one in [http://web.mit.edu/jagoler/www/biojade/overview.html </ins>BioJade<ins class="diffchange diffchange-inline">]</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">[[Image:Biomek3000.jpg|200 px|A Biomek 3000 Pippeting Robot]]</del></div></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>* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho. <ins class="diffchange diffchange-inline">(In the future, this </ins>will <ins class="diffchange diffchange-inline">contain </ins>a link to Anderson <ins class="diffchange diffchange-inline">Lab</ins>'s Biomek robot.<ins class="diffchange diffchange-inline">)</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">*</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> </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> </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 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>===Improved Features:===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Improved Features:===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* More database support (systems like [http://brickit.wiki.sourceforge.net/ BrickIt!]). We plan to test this one a wide variety of databases including JBEI's registry.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* More database support (systems like [http://brickit.wiki.sourceforge.net/ BrickIt!]). We plan to test this one a wide variety of databases including JBEI's registry.</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;"><div>* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho. This will take the form of more plug in extension points and more fully featured interfaces for the existing ones.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho. This will take the form of more plug in extension points and more fully featured interfaces for the existing ones.</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>==Helping Out In The Lab: Assembly Algorithms==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Helping Out In The Lab: Assembly Algorithms==</div></td></tr>
</table>Logosandpathoshttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Development&diff=75521&oldid=prevDensmore: /* Clotho Beta: Future Development */2008-10-28T03:15:38Z<p><span class="autocomment">Clotho Beta: Future Development</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 03:15, 28 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 5:</td>
<td colspan="2" class="diff-lineno">Line 5:</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>==Clotho Beta: Future Development==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Clotho Beta: Future Development==</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;">The next release of Clotho after iGEM is planned for a late Spring 2009 release. This will be the official Beta release (the other releases will have been Alpha and iGEM). The main focus of the release will be to fully implement all the features currently in Clotho as well as fix bugs that are found. Clotho testing and deployment will begin with Anderson Lab at UCB and expand to Voigt Lab at UCSF. In addition to general robustness, Clotho Beta should also incorporate a few new features.</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;"><div>===New Features===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===New Features===</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* New design views to supplement the Sequence View and allow easier designing of basic and composite BioBrick parts<ins class="diffchange diffchange-inline">. This most likely will take an icon format similar to GeneDesigner or BioJade.</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Ability to interface with devices, including robots that can be used for automated production of parts designed in Clotho<ins class="diffchange diffchange-inline">. This will begin with a link to Anderson lab's Biomek robot</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Biomek3000.jpg|200 px|A Biomek 3000 Pippeting Robot]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Biomek3000.jpg|200 px|A Biomek 3000 Pippeting Robot]]</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>===Improved Features:===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Improved Features:===</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* More database support (systems like [http://brickit.wiki.sourceforge.net/ BrickIt!])</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* More database support (systems like [http://brickit.wiki.sourceforge.net/ BrickIt!])<ins class="diffchange diffchange-inline">. We plan to test this one a wide variety of databases including JBEI's registry.</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Improved Plug-in environment that allows users to add even more expanded functionality to Clotho<ins class="diffchange diffchange-inline">. This will take the form of more plug in extension points and more fully featured interfaces for the existing ones.</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></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>==Helping Out In The Lab: Assembly Algorithms==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Helping Out In The Lab: Assembly Algorithms==</div></td></tr>
</table>Densmore