Changes between Version 1 and Version 2 of net.sf.basedb.meludi.notes1_2


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Timestamp:
Mar 16, 2015, 8:07:18 AM (3 years ago)
Author:
olle
Comment:

Added note about adding extraction protocols.

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  • net.sf.basedb.meludi.notes1_2

    v1 v2  
    33Updating to !MeLuDi 1.2 requires some manual changes to the items that already exist. This is due to the decision to exchange the annotation type `MutationAnalysis` option value "`KRAS_NRAS`" for two new values "`KRAS`" and "`NRAS`", since currently few samples have been registered with the former value, and new referral forms contain individual check boxes for the two latter choices. The affected sample items should have the `MutationAnalysis` annotation updated as part of the installation to have both values "`KRAS`" and "`NRAS`" selected, instead of "`KRAS_NRAS`", since the latter option will no longer be available. See ticket:725 for more information. Follow this procedure:
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    5 == 1. Update to !MeLuDi 1.2 ==
     5== 1. Exchanging Mutation Analysis option value "`KRAS_NRAS`" for "`KRAS`" plus "`NRAS`"
     6
     7=== a. Update to !MeLuDi 1.2 ===
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    79Among other things, this will add option values "`KRAS`" and "`NRAS`" for the `MutationAnalysis` annotation.
    810
    9 == 2. Exchange `MutationAnalysis` annotations for all relevant cases ==
     11=== b. Exchange `MutationAnalysis` annotations for all relevant cases ===
    1012
    1113Find all `Case` items that have value "`KRAS_NRAS`" for the `MutationAnalysis` annotation. Select each item in BASE, and open the `Edit` dialog. In the "`Annotations & parameters`" tab, select annotation `MutationAnalysis`, and check both values of "`KRAS`" and "`NRAS`", while unchecking "`KRAS_NRAS`". Click the "`Save`" button to store the changes.
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    13 == 3. Remove option value "`KRAS_NRAS`" for the `MutationAnalysis` annotation ==
     15=== c. Remove option value "`KRAS_NRAS`" for the `MutationAnalysis` annotation ===
    1416
    1517Select BASE menu option `Administrate -> Types -> Annotation types` to display a list of annotation types. Select the `MutationAnalysis` annotation type, and open the `Edit` dialog. In the "`Options`" tab, remove option "`KRAS_NRAS`" from the list of allowed values. Click the "`Save`" button to store the changes.
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     19== 2. Add extraction protocols ==
     20
     21The "Lab tracking protocol for Allprep isolation" wizard supports selecting an extraction protocol. Protocols for the extraction process have to be added into BASE by the administrator.