Team:UC Davis/Database/Standards

From 2013.igem.org

(Difference between revisions)
 
(11 intermediate revisions not shown)
Line 5: Line 5:
.black td{vertical-align:top;
.black td{vertical-align:top;
               text-align:justify;}
               text-align:justify;}
 +
#randcss5{clear:both;}
</style>
</style>
</head>
</head>
Line 10: Line 11:
<div>
<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>
+
<a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/3/30/Depotbanner_UCDavis_mod.jpg" class="banner" width=967px height=226/></a>
</div>
</div>
Line 18: Line 19:
     <tr>
     <tr>
       <td>
       <td>
-
         <a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/4/4e/Depotbutton_UCDavis.jpg" class="blur"></a>
+
         <a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/4/4e/Visitdepot_UCDavis.jpg" class="blur"></a>
-
        <a href="http://dilbert.cs.ucdavis.edu/Depot/"><h1 id="randcss5">Visit <br> the <br>    Depot</h1></a>
+
       </td>
       </td>
     </tr>
     </tr>
Line 29: Line 29:
<p>
<p>
Although there have been differing methods of characterizing Biobricks, the vast majority of characterizations use the measurement of fluorescence and cell density in a microplate reader. The standards can accommodate some other types of characterizations, but are best suited to report data as described.
Although there have been differing methods of characterizing Biobricks, the vast majority of characterizations use the measurement of fluorescence and cell density in a microplate reader. The standards can accommodate some other types of characterizations, but are best suited to report data as described.
-
<br>
+
<br><br>
Additionally, The Depot defines an uploadable experiment as: empirical measurements of a response from a single part type in the same construct that are affected by the same set of user-controlled variables.  
Additionally, The Depot defines an uploadable experiment as: empirical measurements of a response from a single part type in the same construct that are affected by the same set of user-controlled variables.  
</p>
</p>
 +
<br>
-
<h3>All Part Types</h3>
 
<p>
<p>
<table class="black">
<table class="black">
-
Characterization for all part types require four files:
+
Uploading to The Depot requires the following:
<tr>
<tr>
<td><img src="https://static.igem.org/mediawiki/2013/6/66/UCDavis_exTecanraw.jpg" width=389 height=300 /></td>
<td><img src="https://static.igem.org/mediawiki/2013/6/66/UCDavis_exTecanraw.jpg" width=389 height=300 /></td>
Line 44: Line 44:
<tr>
<tr>
<td><img src="https://static.igem.org/mediawiki/2013/c/cf/UCD_database_plate_layout.png" width=400px height=300px></td>
<td><img src="https://static.igem.org/mediawiki/2013/c/cf/UCD_database_plate_layout.png" width=400px height=300px></td>
-
<td>2. Standardized data file (csv) that reports your plate layout in the <a href="docs.google.com/spreadsheet/ccc?key=0AuZVn6NXAPHhdHk1MmVKd2tab3ZNd3dWY2ExQ25kbEE#gid=0">linked tabular format</a> that is partly shown here.</td>
+
<td>2. Standardized data file (csv) that reports your plate layout with information on how each well varies within the experiment. The <a href="http://docs.google.com/spreadsheet/ccc?key=0AuZVn6NXAPHhdHk1MmVKd2tab3ZNd3dWY2ExQ25kbEE#gid=0">linked tabular format</a> that is partly shown here. Sheet two in the link contains a hypothetical example filled in.</td>
</tr>
</tr>
<tr>
<tr>
Line 50: Line 50:
<img src="https://static.igem.org/mediawiki/2013/6/6e/UCD_fluo_celldensity.png" width=257px height=300px></td>
<img src="https://static.igem.org/mediawiki/2013/6/6e/UCD_fluo_celldensity.png" width=257px height=300px></td>
<td>
<td>
-
3. Standardized data file (csv), that reports your fluorescence and cell density measurements in the <a href="docs.google.com/spreadsheet/ccc?key=0AuZVn6NXAPHhdE9nMjlRZEJnTFFHM1lpVWltWW9nbXc#gid=0">linked tabular format</a> that is partly shown here.</td>
+
3. Standardized data file (csv), that reports your measurements over time (ex: fluorescence, cell density, temperature) in the <a href="http://docs.google.com/spreadsheet/ccc?key=0AuZVn6NXAPHhdE9nMjlRZEJnTFFHM1lpVWltWW9nbXc#gid=0">linked tabular format</a> that is partly shown here. Sheet two in the link contains a hypothetical example filled in. </td>
</tr>
</tr>
<tr>
<tr>
<td><img src="https://static.igem.org/mediawiki/2013/4/44/UCD_metadata_template.png"></td>
<td><img src="https://static.igem.org/mediawiki/2013/4/44/UCD_metadata_template.png"></td>
-
<td>4. The metadata file (csv) that reports information on your experiment's conditions and settings in the <a href="docs.google.com/spreadsheet/ccc?key=0AuZVn6NXAPHhdEE2VFBSdkJ6RzNZXzhiQU9BZnRsSHc#gid=0">linked tabular format</a> that is fully shown here.</td>
+
<td>4. The metadata file (csv) that reports information on your experiment's conditions and settings in the <a href="http://docs.google.com/spreadsheet/ccc?key=0AuZVn6NXAPHhdEE2VFBSdkJ6RzNZXzhiQU9BZnRsSHc#gid=0">linked tabular format</a> that is fully shown here. Sheet two in the link contains a hypothetical example filled in.</td>
</tr>
</tr>
<tr>
<tr>
Line 62: Line 62:
</table>
</table>
<p><br />
<p><br />
-
The following standards for specific part types inherit the requirements above in addition to their further requirements.
 
</p>
</p>
-
<br>
 
-
<h3>Constitutive Promoters</h3>
 
-
<p>
 
-
Constitutive promoters have the following additional requirements: <br>
 
-
1. Three wells must contain BBa_J23101 and a reporter. It should be analogous to your constitutive promoter of interest. This is to enable reporting in relative promoter units.<br>
 
-
2. Three wells must contain just the media that you are using. In the parts name section, list this as "media_control".<br>
 
-
3. Three wells must contain the strain that you are using. In the parts name section, list this as "strain_control".<br>
 
-
</p>
 
-
<br>
 
-
<h3>Inducible Promoters</h3>
 
-
<p>
 
-
Inducible promoters have the <b>similar requirements as constitutive promoters, but</b> with two additional requirements: <br>
 
-
1. If applicable, three additional wells must contain the wild-type promoter and a reporter gene. The promoter of interest should be have an identical reporter gene attached. This is required because comparing the output of a constitutive promoter, BBa_J23101, to an inducible promoter is unfit in some applications. <br>
 
-
2. Have data over the entire range of fluorescence output by varying the inducer concentration from zero to saturation.
 
-
</p>
 
-
 
</div>
</div>
<div class="floatbox">
<div class="floatbox">
Line 86: Line 69:
     <tr>
     <tr>
       <td>
       <td>
-
       <a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/4/4e/Depotbutton_UCDavis.jpg" class="blur"></a>
+
       <a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/4/4e/Visitdepot_UCDavis.jpg" class="blur"></a>
       <a href="http://dilbert.cs.ucdavis.edu/Depot/"><h3>Visit the Depot</h3></a>
       <a href="http://dilbert.cs.ucdavis.edu/Depot/"><h3>Visit the Depot</h3></a>
       </td>
       </td>
Line 107: Line 90:
       </td>
       </td>
<td>
<td>
 +
      <a href="https://2013.igem.org/Team:UC_Davis/Database">
 +
<img src="https://static.igem.org/mediawiki/2013/4/42/UCD_2013_Depot_Icon.png" class="blur /">
 +
      <a href="https://2013.igem.org/Team:UC_Davis/Database"><h3>About the Depot</h3></a>
 +
      <p>Check out the motivations behind the Depot.
 +
      </p>
</td>
</td>
     </tr>
     </tr>
   </tbody></table>
   </tbody></table>
 +
</div>
 +
 +
<div id="sitemapbox" class="floatbox">
</div>
</div>
</body>
</body>
 +
<script type="text/javascript">
 +
      $("#sitemapbox").load("https://2013.igem.org/Template:Team:UC_Davis/site_map #sitemap1");
 +
</script>
</html>
</html>

Latest revision as of 02:01, 29 October 2013

Standards in the Depot

Although there have been differing methods of characterizing Biobricks, the vast majority of characterizations use the measurement of fluorescence and cell density in a microplate reader. The standards can accommodate some other types of characterizations, but are best suited to report data as described.

Additionally, The Depot defines an uploadable experiment as: empirical measurements of a response from a single part type in the same construct that are affected by the same set of user-controlled variables.


Uploading to The Depot requires the following:
1. The raw data file (.txt, .csv, .xls, .xlx) from the output of your machine. An example is shown here.
2. Standardized data file (csv) that reports your plate layout with information on how each well varies within the experiment. The linked tabular format that is partly shown here. Sheet two in the link contains a hypothetical example filled in.
3. Standardized data file (csv), that reports your measurements over time (ex: fluorescence, cell density, temperature) in the linked tabular format that is partly shown here. Sheet two in the link contains a hypothetical example filled in.
4. The metadata file (csv) that reports information on your experiment's conditions and settings in the linked tabular format that is fully shown here. Sheet two in the link contains a hypothetical example filled in.
The well-IDs follow the following naming system, where the columns are numbered and the rows are capitalized letters.


Visit the Depot

Data Standards

See the Depot's standards and data requirements so you can share your data as well.

Initial Population

See how we initially populated the Depot.

About the Depot

Check out the motivations behind the Depot.

Retrieved from "http://2013.igem.org/Team:UC_Davis/Database/Standards"