Team:UC Davis/Database/Standards

From 2013.igem.org

(Difference between revisions)
(added plate layout image)
 
(48 intermediate revisions not shown)
Line 2: Line 2:
<html>
<html>
<head>
<head>
 +
<style type="text/css">
 +
.black td{vertical-align:top;
 +
              text-align:justify;}
 +
#randcss5{clear:both;}
 +
</style>
</head>
</head>
<body>
<body>
-
<div><img src="https://static.igem.org/mediawiki/2013/d/d4/UC_Davis_2013ConstBanner.jpg" class="banner" width=967px height=226/>
+
<div>
 +
<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 class="floatbox2">
 +
<table class="showbox">
 +
  <tbody>
 +
    <tr>
 +
      <td>
 +
        <a href="http://dilbert.cs.ucdavis.edu/Depot/"><img src="https://static.igem.org/mediawiki/2013/4/4e/Visitdepot_UCDavis.jpg" class="blur"></a>
 +
      </td>
 +
    </tr>
 +
</table>
</div>
</div>
Line 11: Line 28:
<h1>Standards in the Depot</h1>
<h1>Standards in the Depot</h1>
<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 accomodate some other types of characterizations, but are best suited to report such characterizatoin data.  
+
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>
 +
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>
 
-
Characterization for all part types require four files:<br>
 
-
1. The raw data file (txt, csv, xls, xlx) from the output of your machine. <br>
 
-
2. Standardized data file (csv) that reports your plate layout in the linked tabular format that is partly shown here.<br>
 
-
<p><img src="https://static.igem.org/mediawiki/2013/c/cf/UCD_database_plate_layout.png" width=400px height=300px></p>
 
-
3. Standardized data file (csv), that reports your fluorescence and cell density measurements in the linked tabular format that is partly shown here.<br>
 
-
4. The metadata file (csv), which contains information on your experiment's conditions and settings.<br>
 
-
 
-
The following standards for specific part types inherit the requirements above in addition to their further requirements.
 
-
</p>
 
-
<h3>Constitutive Promoters</h3>
 
<p>
<p>
 +
<table class="black">
 +
Uploading to The Depot requires the following:
 +
<tr>
 +
<td><img src="https://static.igem.org/mediawiki/2013/6/66/UCDavis_exTecanraw.jpg" width=389 height=300 /></td>
 +
<td>
 +
1. The raw data file (.txt, .csv, .xls, .xlx) from the output of your machine. An example is shown here. </td>
 +
</tr>
 +
<tr>
 +
<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 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>
 +
<td>
 +
<img src="https://static.igem.org/mediawiki/2013/6/6e/UCD_fluo_celldensity.png" width=257px height=300px></td>
 +
<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>
 +
<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="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>
 +
<td><img src="https://static.igem.org/mediawiki/2013/7/74/UCD_welID.png"></td>
 +
<td>The well-IDs follow the following naming system, where the columns are numbered and the rows are capitalized letters.</td>
 +
</tr>
 +
</table>
 +
<p><br />
</p>
</p>
 +
</div>
 +
<div class="floatbox">
 +
  <table class="showbox">
 +
    <tbody>
 +
    <tr>
 +
      <td>
 +
      <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>
 +
      </td>
-
<h3>Inducible Promoters</h3>
+
      <td>
-
<p>
+
      <a href="https://2013.igem.org/Team:UC_Davis/Database/Standards"><img src="https://static.igem.org/mediawiki/2013/c/c6/UCD_2013_BCDD_Icon.PNG" class="blur"></a>
-
</p>
+
      <a href="https://2013.igem.org/Team:UC_Davis/Database/Standards"><h3>Data Standards</h3></a>
 +
      <p>See the Depot's standards and data requirements so you can share your data as well.
 +
      </p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td>
 +
      <a href="https://2013.igem.org/Team:UC_Davis/Database/Initial_Population">
 +
<img src="https://static.igem.org/mediawiki/2013/6/65/Depotpopbutton_UCDavis.jpg" class="blur /">
 +
<!--img src="https://static.igem.org/mediawiki/2013/6/63/UCD_2013_BCDD_Icon2.PNG" class="blur"--></a>
 +
      <a href="https://2013.igem.org/Team:UC_Davis/Database/Initial_Population"><h3>Initial Population</h3></a>
 +
      <p>See how we initially populated the Depot.
 +
      </p>
 +
      </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>
 +
    </tr>
 +
  </tbody></table>
 +
</div>
-
<h3>Other Part Types</h3>
+
<div id="sitemapbox" class="floatbox">
-
<p>
+
</div>
-
</p>
+
-
<h3>Metadata</h3>
 
-
</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"