Difference: ProtocolsStrainDatabase (7 vs. 8)

Revision 82016-04-07 - JeffreyBarrick

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META TOPICPARENT name="ProtocolList"

Strain Database

Table Description

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Barrick lab strains are stored in a MySQL database, accessible after login or by this direct link External site.
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Barrick lab strains are stored in a database on UT Box, accessible after login via this direct link.
 
column example description
strain REL Initials of strain designation
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source REL Stock center or other lab strain is from.
frozen 2002-08-17 Date when sample was frozen.
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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
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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.

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

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

UPDATE `strain` 
SET `rack` = 'Barrick 1', `box` = 'Barrick 3'
WHERE  `strain` LIKE  'JEB'
AND  `number` >=622
AND  `number` <=702
AND  `freezer` =  'Barrick 1'
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