(r6) Barrick Lab :: ProtocolsStrainDatabase

<noautolink>
---+ Strain Database

---++ Table Description

Barrick lab strains are stored in a MySQL database, accessible after login or by this [[http://barricklab.org/adminer/?username=lab&select=strains][direct link %ICON{"external"}%]].

| *column* | *example* | *description* |
| strain | REL | Initials of strain designation |
| number | 606 | Number of strain designation |
| freezer | Barrick 1 | Freezer where sample is located. Choose from list. |
| rack | Barrick 3 | Rack where sample is located. Should be in format: [last name] [number] |
| box  | Barrick 4 | Rack where sample is located. Should be in format: [last name] [number] |
| container | 2 ml glass vial | Type of container used to freeze sample. Choose from list. |
| well | | Well number for samples frozen in microplates. |
| experiment | LTEE | Sample experiment. Choose from list. |
| population | | Sample population in experiment.) |
| time | 0 | Sample time point in experiment. |
| M/C | C | Mixed population or Clone sample |
| clone | | Designation of particular clone. Either a number or a letter. |
| description | Ara– ancestor clone used to begin the long-term experiment. | Full description of the strain. Include information about what strain it is derived from and whether this sample has been subcultured from different samples. |
| media | DM1000 | Media strain was grown in for freezing. |
| cryoprotectant | Glycerol | Choose from list. |
| source | REL | Stock center or other lab strain is from. |
| frozen | 2002-08-17 | Date when sample was frozen. | 

---++ Importing Files

When entering many (>10) samples, importing a .csv file is usually more convenient. CSV files require specific formatting, and the quickest way to get this format is to go the the strain database and export a single strain. Open up this file in excel, and fill in the appropriate data into the columns. The date column is somewhat tricky, as the database will only properly read the date entries if they are in YYYY-MM-DD. The easiest way to do this is "format cells" and change number type to "text". Ensure that the file type is still .csv and save the file. Go to the strain database click import and select the file. This method should allow for an easy way to upload large numbers of samples.

---++ Important Points

   * In population names, use the minus sign "–" character, rather than a hyphen "-" (option-hyphen on Mac). These must be entered consistently for searching to work.
      * e.g. Ara–3 NOT Ara-3

---++ Backing up the database

Periodically and before doing any complex SQL operations, backup the database.

In phpMyAdmin, select the "strain" table from the "lab" database. Then click on "Operations". In the "Copy table to" box select the "backup" database and name the new table "strain_YYYY_MM_DD", e.g. "strain_2011-05-31". Be sure the "structure and data" button is selected. Hit "go".

---++ Batch Editing

You can use MySQL commands by clicking on the SQL tab in phpMyAdmin.

Set up a SELECT statement that retrieves the items you want to change.

<verbatim>
SELECT * 
FROM  `strain_5-31-11` 
WHERE  `strain` LIKE  'JEB'
AND  `number` >=622
AND  `number` <=702
AND  `freezer` =  'Barrick 1'
</verbatim>

If you need to change multiple items at once, use something like following UPDATE statement.

<verbatim>
UPDATE `strain` 
SET `rack` = 'Barrick 1', `box` = 'Barrick 3'
WHERE  `strain` LIKE  'JEB'
AND  `number` >=622
AND  `number` <=702
AND  `freezer` =  'Barrick 1'
</verbatim>
Barrick Lab > ProtocolList > ProtocolsStrainDatabase
Contributors to this topic
JeffreyBarrick, CraigBarnhart, AlvaroRodriguez, AurkoDasgupta
Topic revision: r6 - 2012-08-10 - 23:07:29 - Main.AurkoDasgupta