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Team:UC Davis/Database/Standards
From 2013.igem.org
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<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=" | + | <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> |
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<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> | ||
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| - | 3. Standardized data file (csv), that reports your fluorescence and cell density measurements in the <a href=" | + | 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> |
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<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=" | + | <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> |
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Revision as of 22:14, 27 September 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 characterization 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.
All Part Types
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1. The raw data file (txt, csv, xls, xlx) from the output of your machine. An example is shown here. |
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2. Standardized data file (csv) that reports your plate layout in the linked tabular format that is partly shown here. |
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3. Standardized data file (csv), that reports your fluorescence and cell density measurements in the linked tabular format that is partly shown here. |
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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. |
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The well-IDs follow the following naming system, where the columns are numbered and the rows are capitalized letters. |
The following standards for specific part types inherit the requirements above in addition to their further requirements.
Constitutive Promoters
Constitutive promoters have the following additional requirements:
1. Three wells must contain BBa_J23101 in the same construct that your constitutive promoter of interest is in. This is to enable reporting in relative promoter units.
2. Three wells must contain just the media that you are using. In the parts name section, list this as "media_control".
3. Three wells must contain the strain that you are using. In the parts name section, list this as "strain_control".
Inducible Promoters
Inducible promoters have the same requirements as constituive promoters with two additional requirements:
1. If applicable, three wells must contain the wild-type promoter in the same construct that your promoter of interest is in. This is required because comparing the output of a constitutive promoter, BBa_J23101, to an inducible promoter is unfit in some applications.
2. Have data over the entire range of fluorescence output by varying the inducer concentration from zero to saturation.
