http://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&feed=atom&action=historyTeam:UC Berkeley Tools/Notebook/Doug's Notebook - Revision history2024-03-29T11:37:44ZRevision history for this page on the wikiMediaWiki 1.16.5http://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&diff=57741&oldid=prevNadesri at 23:46, 17 October 20082008-10-17T23:46:56Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Doug_Professional.jpg|center|frame|Doug Densmore]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Doug_Professional.jpg|center|frame|Doug Densmore]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This is the notebook of Doug Densmore, the instructor for the team. My primary role is to develop the Clotho infrastructure that will be used to implement the various projects of the actual student team members. Clotho is meant to be a larger design environment which applies various principles of platform-based design from the electronic design automation (EDA) community within Electrical Engineering and Computer Science (EECS) to synthetic biological tools. The main aspects of PBD are its strict adherence to the separation of computation, communication and coordination. In addition, it also allows multiple views of a design (architectural and functional). Clotho is bigger than just the iGEM team and hopefully will be developed heavily into the future.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This is the notebook of Doug Densmore, the instructor for the team. My primary role is to develop the Clotho infrastructure that will be used to implement the various projects of the actual student team members. Clotho is meant to be a larger design environment which applies various principles of platform-based design from the electronic design automation (EDA) community within Electrical Engineering and Computer Science (EECS) to synthetic biological tools. The main aspects of PBD are its strict adherence to the separation of computation, communication and coordination. In addition, it also allows multiple views of a design (architectural and functional). Clotho is bigger than just the iGEM team and hopefully will be developed heavily into the future.</div></td></tr>
</table>Nadesrihttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&diff=30760&oldid=prevDensmore: /* Week of August 3rd, 2008 */2008-08-07T19:44:08Z<p><span class="autocomment">Week of August 3rd, 2008</span></p>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The next step is to integrate PoBoL based data into the Clotho environment. This will include the algorithm manager, parts navigator, and parts packager.</ins></div></td></tr>
</table>Densmorehttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&diff=30749&oldid=prevDensmore: /* Week of August 3rd, 2008 */2008-08-07T19:38:25Z<p><span class="autocomment">Week of August 3rd, 2008</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>I have been doing work on a number of other projects but it is becoming increasingly obvious that I am going to have to integrate PoBoL support into Clotho in order for it to truly be useful to the community. To that end I have created a system to create "binding files". A binding file describes the relationship between fields in a databases and both objects and fields in the PoBoL specification. This binding file now will allow Clotho to perform operations in a standardized way based on PoBoL based data and use the binding file information to understand how to query and update a database. Here are some screenshots of both how configurations and binding file.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>I have been doing work on a number of other projects but it is becoming increasingly obvious that I am going to have to integrate PoBoL support into Clotho in order for it to truly be useful to the community. To that end I have created a system to create "binding files". A binding file describes the relationship between fields in a databases and both objects and fields in the PoBoL specification. This binding file now will allow Clotho to perform operations in a standardized way based on PoBoL based data and use the binding file information to understand how to query and update a database. Here are some screenshots of both how configurations and binding file.</div></td></tr>
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</table>Densmorehttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&diff=30747&oldid=prevDensmore: /* Week of August 3rd, 2008 */2008-08-07T19:38:12Z<p><span class="autocomment">Week of August 3rd, 2008</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>I have been doing work on a number of other projects but it is becoming increasingly obvious that I am going to have to integrate PoBoL support into Clotho in order for it to truly be useful to the community. To that end I have created a system to create "binding files". A binding file describes the relationship between fields in a databases and both objects and fields in the PoBoL specification. This binding file now will allow Clotho to perform operations in a standardized way based on PoBoL based data and use the binding file information to understand how to query and update a database. Here are some screenshots of both how configurations and binding file.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>I have been doing work on a number of other projects but it is becoming increasingly obvious that I am going to have to integrate PoBoL support into Clotho in order for it to truly be useful to the community. To that end I have created a system to create "binding files". A binding file describes the relationship between fields in a databases and both objects and fields in the PoBoL specification. This binding file now will allow Clotho to perform operations in a standardized way based on PoBoL based data and use the binding file information to understand how to query and update a database. Here are some screenshots of both how configurations and binding file.</div></td></tr>
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</table>Densmorehttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&diff=30744&oldid=prevDensmore at 19:37, 7 August 20082008-08-07T19:37:18Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We are also going to begin to write up the work regarding various assembly algorithms that are in Clotho. This will be targeted toward a synthetic biology journal.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We are also going to begin to write up the work regarding various assembly algorithms that are in Clotho. This will be targeted toward a synthetic biology journal.</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;">== Week of August 3rd, 2008 ==</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;">'''They keep pulling me in!!'''</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">I have been doing work on a number of other projects but it is becoming increasingly obvious that I am going to have to integrate PoBoL support into Clotho in order for it to truly be useful to the community. To that end I have created a system to create "binding files". A binding file describes the relationship between fields in a databases and both objects and fields in the PoBoL specification. This binding file now will allow Clotho to perform operations in a standardized way based on PoBoL based data and use the binding file information to understand how to query and update a database. Here are some screenshots of both how configurations and binding file.</ins></div></td></tr>
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</table>Densmorehttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&diff=24356&oldid=prevNadesri at 05:02, 31 July 20082008-07-31T05:02:09Z<p></p>
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</table>Nadesrihttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&diff=21808&oldid=prevNadesri at 05:45, 27 July 20082008-07-27T05:45:41Z<p></p>
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</table>Nadesrihttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&diff=21807&oldid=prevNadesri at 05:45, 27 July 20082008-07-27T05:45:15Z<p></p>
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</table>Nadesrihttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&diff=17714&oldid=prevDensmore: /* Week of July 13th, 2008 */2008-07-19T03:21:01Z<p><span class="autocomment">Week of July 13th, 2008</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Week of July 13th, 2008 ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Week of July 13th, 2008 ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This week consisted primarily of two testing sessions of Clotho with the UC Berkeley wet team. Both sessions were very successful and we received a lot of good feedback. The most rewarding part is that they did not find many bugs and the ones that they did find are very easy to implement. Naturally there is a lot of work to do but we have a proof of concept feature for the majority of the various Clotho pieces. Our official alpha release is set for July 26th! We will see how things go. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This week consisted primarily of two testing sessions of Clotho with the UC Berkeley wet team. Both sessions were very successful and we received a lot of good feedback. The most rewarding part is that they did not find many bugs and the ones that they did find are very easy to implement<ins class="diffchange diffchange-inline">/fix</ins>. Naturally there is a lot of work to do but we have a proof of concept feature for the majority of the various Clotho pieces. Our official alpha release is set for July 26th! We will see how things go<ins class="diffchange diffchange-inline">. This next week will consist of chasing down bugs and cleaning up the code. After the alpha release Matt and Nade are going to continue to work on Clotho full time while I return to working on my primary research 80% of the time and working on Clotho 20% (getting it to work with Pobol)</ins>.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Clotho has changed a lot since my last post. I imagine these changes will be documented in the other member's notebook pages. The main thing that is going to happen next week (other than the Alpha release) is <del class="diffchange diffchange-inline">I am </del>going to meet with BioJADE and BioStudio developers as well as folks from JBEI about their parts registry. The goal is that Clotho Beta will interact with other tools and also migrate its internal data representation to something like Pobol for BioBricks.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Clotho has changed a lot since my last post. I imagine these changes will be documented in the other member's notebook pages. The main thing that is going to happen next week (other than the Alpha release) is <ins class="diffchange diffchange-inline">that we are </ins>going to meet with BioJADE <ins class="diffchange diffchange-inline">(Jonathan Goler) </ins>and BioStudio <ins class="diffchange diffchange-inline">(Sarah Richardson) </ins>developers as well as folks from JBEI <ins class="diffchange diffchange-inline">(Tim Ham) </ins>about their parts registry. The goal is that Clotho Beta will interact with other tools and also migrate its internal data representation to something like Pobol for BioBricks<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">We are also going to begin to write up the work regarding various assembly algorithms that are in Clotho. This will be targeted toward a synthetic biology journal</ins>.</div></td></tr>
</table>Densmorehttp://2008.igem.org/wiki/index.php?title=Team:UC_Berkeley_Tools/Notebook/Doug%27s_Notebook&diff=17713&oldid=prevDensmore at 03:15, 19 July 20082008-07-19T03:15:25Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:ClothoSequenceView2.png|thumb|center|800 px|Second pass at Clotho's sequence view]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:ClothoSequenceView2.png|thumb|center|800 px|Second pass at Clotho's sequence view]]</div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">== Week of July 13th, 2008 ==</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;">This week consisted primarily of two testing sessions of Clotho with the UC Berkeley wet team. Both sessions were very successful and we received a lot of good feedback. The most rewarding part is that they did not find many bugs and the ones that they did find are very easy to implement. Naturally there is a lot of work to do but we have a proof of concept feature for the majority of the various Clotho pieces. Our official alpha release is set for July 26th! We will see how things go. </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;">Clotho has changed a lot since my last post. I imagine these changes will be documented in the other member's notebook pages. The main thing that is going to happen next week (other than the Alpha release) is I am going to meet with BioJADE and BioStudio developers as well as folks from JBEI about their parts registry. The goal is that Clotho Beta will interact with other tools and also migrate its internal data representation to something like Pobol for BioBricks.</ins></div></td></tr>
</table>Densmore