http://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&feed=atom&action=historyTeam:UC Davis/Database - Revision history2024-03-28T22:41:05ZRevision history for this page on the wikiMediaWiki 1.16.5http://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&diff=361261&oldid=prevDHwang at 03:46, 29 October 20132013-10-29T03:46:45Z<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 03:46, 29 October 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 85:</td>
<td colspan="2" class="diff-lineno">Line 85:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table id="searchtb"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table id="searchtb"></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;"><tr></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;"><td></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;">A prototype page that shows the basic functional elements of search is shown here:</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;"></td></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;"><td id="righttd">A prototype example search is shown here:</td></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;"></tr></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></table></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></table></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2013/7/7f/New_search.jpg" class="genpic" width=650 height=200/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2013/7/7f/New_search.jpg" class="genpic" width=650 height=200/></div></td></tr>
</table>DHwanghttp://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&diff=358583&oldid=prevDHwang at 02:22, 29 October 20132013-10-29T02:22:38Z<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 02:22, 29 October 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 82:</td>
<td colspan="2" class="diff-lineno">Line 82:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Search functionality <del class="diffchange diffchange-inline">is currently geared towards location of user-specified </del>data <del class="diffchange diffchange-inline">values </del>for <del class="diffchange diffchange-inline">BioBrick parts. This demonstrates </del>a <del class="diffchange diffchange-inline">very simple, yet illustrative example of leveraging a database</del>. The results of your searches are downloadable.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Search functionality <ins class="diffchange diffchange-inline">current offers searching for part types across all experiments, or for all </ins>data for a <ins class="diffchange diffchange-inline">particular experiment</ins>. The results of your searches are <ins class="diffchange diffchange-inline">immediately </ins>downloadable<ins class="diffchange diffchange-inline">. Search functionality is to be expanded upon</ins>. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table id="searchtb"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table id="searchtb"></div></td></tr>
</table>DHwanghttp://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&diff=358504&oldid=prevDHwang at 02:20, 29 October 20132013-10-29T02:20:01Z<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 02:20, 29 October 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 75:</td>
<td colspan="2" class="diff-lineno">Line 75:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> The process is straightforward. Users register, then upload their four files that adhere to Depot <a href="https://2013.igem.org/Team:UC_Davis/Database/Standards">standards</a>, as well as other information relevant to their experiment. A prototype page that shows the basic functional elements is shown here. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> The process is straightforward. Users register, then upload their four files that adhere to Depot <a href="https://2013.igem.org/Team:UC_Davis/Database/Standards">standards</a>, as well as other information relevant to their experiment. A prototype page that shows the basic functional elements is shown here. </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p><img src="https://static.igem.org/mediawiki/2013/4/46/UCD_depot_upload.png" class="genpic"></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p><img src="https://static.igem.org/mediawiki/2013/4/46/UCD_depot_upload.png" class="genpic" <ins class="diffchange diffchange-inline">width=650</ins>></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></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 92:</td>
<td colspan="2" class="diff-lineno">Line 92:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></tr></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></tr></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></table></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></table></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2013/<del class="diffchange diffchange-inline">2</del>/<del class="diffchange diffchange-inline">2f</del>/<del class="diffchange diffchange-inline">UCD_ex_search2</del>.jpg" class="genpic" width=<del class="diffchange diffchange-inline">637 </del>height=<del class="diffchange diffchange-inline">389</del>/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2013/<ins class="diffchange diffchange-inline">7</ins>/<ins class="diffchange diffchange-inline">7f</ins>/<ins class="diffchange diffchange-inline">New_search</ins>.jpg" class="genpic" width=<ins class="diffchange diffchange-inline">650 </ins>height=<ins class="diffchange diffchange-inline">200</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><!--img src="https://static.igem.org/mediawiki/2013/4/4d/UCD_search.png"--></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--img src="https://static.igem.org/mediawiki/2013/4/4d/UCD_search.png"--></div></td></tr>
</table>DHwanghttp://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&diff=358184&oldid=prevDHwang at 02:04, 29 October 20132013-10-29T02:04:05Z<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 02:04, 29 October 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 21:</td>
<td colspan="2" class="diff-lineno">Line 21:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><body></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><body></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/7/7d/Depotbanner_UCDavis.jpg" class="banner" width=967px height=226/></a--></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/7/7d/Depotbanner_UCDavis.jpg" class="banner" width=967px height=226/></a--></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><a href="<del class="diffchange diffchange-inline">http</del>://<del class="diffchange diffchange-inline">dilbert</del>.<del class="diffchange diffchange-inline">cs</del>.<del class="diffchange diffchange-inline">ucdavis.edu</del>/<del class="diffchange diffchange-inline">Depot</del>/"><img src="https://static.igem.org/mediawiki/2013/3/30/Depotbanner_UCDavis_mod.jpg" class="banner" width=967px height=226/></a></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><a href="<ins class="diffchange diffchange-inline">https</ins>://<ins class="diffchange diffchange-inline">2013</ins>.<ins class="diffchange diffchange-inline">igem</ins>.<ins class="diffchange diffchange-inline">org</ins>/<ins class="diffchange diffchange-inline">Team:UC_Davis</ins>/<ins class="diffchange diffchange-inline">Database</ins>"><img src="https://static.igem.org/mediawiki/2013/3/30/Depotbanner_UCDavis_mod.jpg" class="banner" width=967px height=226/></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div class="floatboxwide"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div class="floatboxwide"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Sharing is what makes us human, but as synthetic biologists, how can we improve the ways we share with each other? Originally proposed as a way for our team to share the multivariate characterization data for our RiboTALs, The Depot was expanded to promote sharing in iGEM for any BioBrick type. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Sharing is what makes us human, but as synthetic biologists, how can we improve the ways we share with each other? Originally proposed as a way for our team to share the multivariate characterization data for our RiboTALs, The Depot was expanded to promote sharing in iGEM for any BioBrick type. </div></td></tr>
</table>DHwanghttp://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&diff=357988&oldid=prevDHwang at 01:57, 29 October 20132013-10-29T01:57:54Z<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 01:57, 29 October 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 63:</td>
<td colspan="2" class="diff-lineno">Line 63:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>An online database needs its standards; unfortunately, Biobrick-raw-data (BRD), standardization has been and still is a difficult problem to address because it requires answering many interconnected questions of comparability and enforceability<a href="#external_links"><sup><del class="diffchange diffchange-inline">5</del></sup></a>. Additionally, BRD standardization is even harder to address because the needs of the community, in both and wet and dry lab, are not strictly defined in an young, changing field like synthetic biology.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>An online database needs its standards; unfortunately, Biobrick-raw-data (BRD), standardization has been and still is a difficult problem to address because it requires answering many interconnected questions of comparability and enforceability<a href="#external_links"><sup><ins class="diffchange diffchange-inline">1</ins></sup></a>. Additionally, BRD standardization is even harder to address because the needs of the community, in both and wet and dry lab, are not strictly defined in an young, changing field like synthetic biology.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Our approach, The Depot, is not an attempt to answer all BRD standardization questions at once. We instead focused two matters, data <b>format</b> standards and openness of raw data, while keeping the aforementioned issues of comparability and enforceability in mind.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Our approach, The Depot, is not an attempt to answer all BRD standardization questions at once. We instead focused two matters, data <b>format</b> standards and openness of raw data, while keeping the aforementioned issues of comparability and enforceability in mind.</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 150:</td>
<td colspan="2" class="diff-lineno">Line 150:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a id="external_links"><h3>External Links</h3></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a id="external_links"><h3>External Links</h3></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><sup>1 <del class="diffchange diffchange-inline"></sup><a href="https://2011.igem.org/Jamborees">https://2011.igem.org/Jamborees</a><br></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><sup>1 </sup><a href="http://openwetware.org/wiki/Parts_characterization#Discussion_Topics">http://openwetware.org/wiki/Parts_characterization#Discussion_Topics</a><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><sup>2 </sup><a href="https://2012.igem.org/Jamborees">https://2012.igem.org/Jamborees</a><br></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><del class="diffchange diffchange-inline"><sup>3 </sup><a href="http://www.ncbi.nlm.nih.gov/genbank">http://www.ncbi.nlm.nih.gov/genbank</a><br></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><del class="diffchange diffchange-inline"><sup>4 </sup><a href="http://www.pdb.org/pdb/home/home.do">http://www.pdb.org/pdb/home/home.do</a><br></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><del class="diffchange diffchange-inline"><sup>5 </del></sup><a href="http://openwetware.org/wiki/Parts_characterization#Discussion_Topics">http://openwetware.org/wiki/Parts_characterization#Discussion_Topics</a><br<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><del class="diffchange diffchange-inline"><sup>6 </sup><a href="http://www.jbioleng.org/content/3/1/4">http://www.jbioleng.org/content/3/1/4</a</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></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
</table>DHwanghttp://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&diff=357916&oldid=prevDHwang at 01:55, 29 October 20132013-10-29T01:55:52Z<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 01:55, 29 October 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 49:</td>
<td colspan="2" class="diff-lineno">Line 49:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">From the registry, to the wikis, iGEM is founded upon the idea of sharing. Having an open culture allows scientific communities to validate successes and understand failures, while supporting future researchers downstream. To participate in this open culture, our </del>team wanted to share our <del class="diffchange diffchange-inline">RiboTALs' multivariate characterization data </del>in the most useful way possible. <del class="diffchange diffchange-inline">While </del>the <del class="diffchange diffchange-inline">current use </del>of registry pages <del class="diffchange diffchange-inline">serve many part types and iGEM teams well</del>, <del class="diffchange diffchange-inline">the complexity </del>and <del class="diffchange diffchange-inline">volume of data </del>we <del class="diffchange diffchange-inline">collected made this method of sharing feel less appropriate, and less accessible</del>. <del class="diffchange diffchange-inline">We also noticed in </del>our <del class="diffchange diffchange-inline">research of sharing data that teams focused on sharing conclusions and calculations of their </del>data, <del class="diffchange diffchange-inline">but rarely found the time </del>to <del class="diffchange diffchange-inline">share their raw numbers</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Our </ins>team wanted to share our <ins class="diffchange diffchange-inline">work </ins>in the <ins class="diffchange diffchange-inline">clearest and </ins>most useful way possible<ins class="diffchange diffchange-inline">, given the multivariance of RiboTals</ins>. <ins class="diffchange diffchange-inline">We did so in </ins>the <ins class="diffchange diffchange-inline">prescribed way </ins>of <ins class="diffchange diffchange-inline">sharing part characterizations through the iGEM </ins>registry<ins class="diffchange diffchange-inline">'s experience </ins>pages, <ins class="diffchange diffchange-inline">but excel charts </ins>and <ins class="diffchange diffchange-inline">text summaries left us feeling like </ins>we <ins class="diffchange diffchange-inline">could do more to communicate our work</ins>. <ins class="diffchange diffchange-inline">An imminent solution was to upload </ins>our <ins class="diffchange diffchange-inline">raw, RiboTal </ins>data <ins class="diffchange diffchange-inline">in an intuitive</ins>, <ins class="diffchange diffchange-inline">easy-</ins>to<ins class="diffchange diffchange-inline">-follow form; we implemented such a solution in what we call The Depot, which we expanded to include characterization data for all part types</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">With continued research</del>, <del class="diffchange diffchange-inline">it was clear that our dilemma with RiboTALs was not unique</del>. <del class="diffchange diffchange-inline">Sharing </del>data <del class="diffchange diffchange-inline">for </del><<del class="diffchange diffchange-inline">b</del>><del class="diffchange diffchange-inline">any</del><<del class="diffchange diffchange-inline">/b</del>> <del class="diffchange diffchange-inline">part type in a way that </del>is <del class="diffchange diffchange-inline">useful </del>to <del class="diffchange diffchange-inline">everyone is an extremely difficult objective</del>, <del class="diffchange diffchange-inline">but we wanted </del>to <del class="diffchange diffchange-inline">take a step towards making it easier. Now we </del>are <del class="diffchange diffchange-inline">pleased </del>to <del class="diffchange diffchange-inline">introduce our step towards that solution, </del>The Depot<del class="diffchange diffchange-inline">, </del>an <del class="diffchange diffchange-inline">open BioBrick characterization database </del>to <del class="diffchange diffchange-inline">further promote sharing in </del>iGEM.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">In addition to being a useful way for iGEM-ers to share their data</ins>, <ins class="diffchange diffchange-inline">The Depot can be a platform for iGEM-ers to think about the human elements of synthetic biology</ins>. <ins class="diffchange diffchange-inline">In participating in The Depot, iGEM-ers would encounter issues of sharing raw </ins>data <ins class="diffchange diffchange-inline">such as, </ins><<ins class="diffchange diffchange-inline">br</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">-How would others want to use my work? </ins><<ins class="diffchange diffchange-inline">br</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">-Who </ins>is <ins class="diffchange diffchange-inline">my work relevant </ins>to, <ins class="diffchange diffchange-inline">and how should I account for that? <br></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">-What can be standardized </ins>to <ins class="diffchange diffchange-inline">make shared data comparable, and therefore more useful for everyone? <br><br></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">We </ins>are <ins class="diffchange diffchange-inline">very excited </ins>to <ins class="diffchange diffchange-inline">present </ins>The Depot <ins class="diffchange diffchange-inline">as </ins>an <ins class="diffchange diffchange-inline">intuitive way to share data, as well as a platform </ins>to iGEM<ins class="diffchange diffchange-inline">-ers to think about the human elements of sharing their work</ins>. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></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><a id="approaches"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a id="approaches"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><h1 class="title">Approaches to Data Standardization: <del class="diffchange diffchange-inline">The Past and The Depot</del></h1></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><h1 class="title">Approaches to Data Standardization: </h1></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Past approaches to designing </del>a <del class="diffchange diffchange-inline">BioBrick characterization database dealt with </del>difficult questions<a href="#external_links"><sup>5</sup></a><del class="diffchange diffchange-inline">, which entailed two main topics: what are reasonable standards that a database can enforce, and how to make characterizations across labs or experiments comparable</del>. <del class="diffchange diffchange-inline">To answer these questions</del>, <del class="diffchange diffchange-inline">one would have </del>to <del class="diffchange diffchange-inline">make many, many decisions. Decisions like choosing between </del>the <del class="diffchange diffchange-inline">use </del>of <del class="diffchange diffchange-inline">different characterization protocols, lab equipment, machine settings, data format</del>, and <del class="diffchange diffchange-inline">the list goes on </del>and <del class="diffchange diffchange-inline">on for each part type. Additionally</del>, <del class="diffchange diffchange-inline">these decisions </del>are <del class="diffchange diffchange-inline">posed for a global scale</del>, <del class="diffchange diffchange-inline">where accessibility and timetables are major concerns. Moreover, since synthetic biology is a relatively young </del>field<del class="diffchange diffchange-inline">, many facets of part characterizations are likely to change over time. The complexity of decisions and </del>synthetic biology<del class="diffchange diffchange-inline">'s youth make shelving the idea of a completely standardized database very appealing</del>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">An online database needs its standards; unfortunately, Biobrick-raw-data (BRD), standardization has been and still is </ins>a difficult <ins class="diffchange diffchange-inline">problem to address because it requires answering many interconnected </ins>questions <ins class="diffchange diffchange-inline">of comparability and enforceability</ins><a href="#external_links"><sup>5</sup></a>. <ins class="diffchange diffchange-inline">Additionally</ins>, <ins class="diffchange diffchange-inline">BRD standardization is even harder </ins>to <ins class="diffchange diffchange-inline">address because </ins>the <ins class="diffchange diffchange-inline">needs </ins>of <ins class="diffchange diffchange-inline">the community</ins>, <ins class="diffchange diffchange-inline">in both </ins>and <ins class="diffchange diffchange-inline">wet </ins>and <ins class="diffchange diffchange-inline">dry lab</ins>, are <ins class="diffchange diffchange-inline">not strictly defined in an young</ins>, <ins class="diffchange diffchange-inline">changing </ins>field <ins class="diffchange diffchange-inline">like </ins>synthetic biology.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">We agreed</del>, <del class="diffchange diffchange-inline">at least in some senses. An enforced</del>, <del class="diffchange diffchange-inline">strictly standardized database for all part types </del>is not <del class="diffchange diffchange-inline">the approach we took for the Depot</del>. <del class="diffchange diffchange-inline">In our approach</del>, <del class="diffchange diffchange-inline">we instead created a flexible </del>data <del class="diffchange diffchange-inline">format standard that many different characterizations could easily conform to. Additionally, we standardized sections of the protocol to promoters, a part type with a history</del><<del class="diffchange diffchange-inline">a href="#external_links"</del>><del class="diffchange diffchange-inline"><sup>6</del></<del class="diffchange diffchange-inline">sup></a</del>> of data <del class="diffchange diffchange-inline">standardization</del>, <del class="diffchange diffchange-inline">more comparable across experiments</del>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Our approach</ins>, <ins class="diffchange diffchange-inline">The Depot</ins>, is not <ins class="diffchange diffchange-inline">an attempt to answer all BRD standardization questions at once</ins>. <ins class="diffchange diffchange-inline">We instead focused two matters</ins>, data <<ins class="diffchange diffchange-inline">b</ins>><ins class="diffchange diffchange-inline">format</ins></<ins class="diffchange diffchange-inline">b</ins>> <ins class="diffchange diffchange-inline">standards and openness </ins>of <ins class="diffchange diffchange-inline">raw </ins>data, <ins class="diffchange diffchange-inline">while keeping the aforementioned issues of comparability and enforceability in mind</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
</table>DHwanghttp://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&diff=321453&oldid=prevAsoon at 23:24, 18 October 20132013-10-18T23:24:27Z<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 23:24, 18 October 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 66:</td>
<td colspan="2" class="diff-lineno">Line 66:</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><div class="floatbox"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div class="floatbox"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><a id="upload"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><a id="upload"<ins class="diffchange diffchange-inline">></a</ins>></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><h1 class="title">Uploading to the Depot<<del class="diffchange diffchange-inline">/h1</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><h1 class="title">Uploading to the Depot<<ins class="diffchange diffchange-inline">a href="#top" class="to_top"</ins>><ins class="diffchange diffchange-inline">^back to top</ins></a<ins class="diffchange diffchange-inline">></h1</ins>></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div></a></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;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> The process is straightforward. Users register, then upload their four files that adhere to Depot <a href="https://2013.igem.org/Team:UC_Davis/Database/Standards">standards</a>, as well as other information relevant to their experiment. A prototype page that shows the basic functional elements is shown here. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> The process is straightforward. Users register, then upload their four files that adhere to Depot <a href="https://2013.igem.org/Team:UC_Davis/Database/Standards">standards</a>, as well as other information relevant to their experiment. A prototype page that shows the basic functional elements is shown here. </div></td></tr>
</table>Asoonhttp://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&diff=318254&oldid=prevAsoon at 22:21, 11 October 20132013-10-11T22:21:31Z<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 22:21, 11 October 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 20:</td>
<td colspan="2" class="diff-lineno">Line 20:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></head></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></head></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><body></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><body></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/7/7d/Depotbanner_UCDavis.jpg" class="banner" width=967px height=226/></a></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><<ins class="diffchange diffchange-inline">!--</ins>a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/7/7d/Depotbanner_UCDavis<ins class="diffchange diffchange-inline">.jpg" class="banner" width=967px height=226/></a--></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"><a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/3/30/Depotbanner_UCDavis_mod</ins>.jpg" class="banner" width=967px height=226/></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div class="floatboxwide"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div class="floatboxwide"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Sharing is what makes us human, but as synthetic biologists, how can we improve the ways we share with each other? Originally proposed as a way for our team to share the multivariate characterization data for our RiboTALs, The Depot was expanded to promote sharing in iGEM for any BioBrick type. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Sharing is what makes us human, but as synthetic biologists, how can we improve the ways we share with each other? Originally proposed as a way for our team to share the multivariate characterization data for our RiboTALs, The Depot was expanded to promote sharing in iGEM for any BioBrick type. </div></td></tr>
</table>Asoonhttp://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&diff=237813&oldid=prevDHwang at 02:54, 28 September 20132013-09-28T02:54:42Z<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 02:54, 28 September 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 102:</td>
<td colspan="2" class="diff-lineno">Line 102:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <tr></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <tr></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <td></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/4/4e/<del class="diffchange diffchange-inline">Depotbutton_UCDavis</del>.jpg" class="blur"></a></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/4/4e/<ins class="diffchange diffchange-inline">Visitdepot_UCDavis</ins>.jpg" class="blur"></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <a href="http://dilbert.cs.ucdavis.edu/Depot/"><h3>Visit the Depot</h3></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <a href="http://dilbert.cs.ucdavis.edu/Depot/"><h3>Visit the Depot</h3></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </td></div></td></tr>
</table>DHwanghttp://2013.igem.org/wiki/index.php?title=Team:UC_Davis/Database&diff=237115&oldid=prevDHwang at 02:44, 28 September 20132013-09-28T02:44:01Z<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 02:44, 28 September 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 54:</td>
<td colspan="2" class="diff-lineno">Line 54:</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><a id="approaches"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a id="approaches"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><h1 class="title">Approaches to Standardization: The Past and The Depot</h1></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><h1 class="title">Approaches to <ins class="diffchange diffchange-inline">Data </ins>Standardization: The Past and The Depot</h1></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p></div></td></tr>
</table>DHwang