Difference: ProtocolsStrainDatabase (4 vs. 5)

Revision 52011-06-06 - JeffreyBarrick

META TOPICPARENT	name="ProtocolList"

Strain Database

Table Description

Barrick lab strains are stored in a MySQL database, accessible after login or by this direct link .

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.

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.

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

Changed:

<
<

If you need to change multiple items at once use the following UPDATE statement.

>
>

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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