Changes between Version 2 and Version 3 of net.sf.basedb.meludi.notes1_3


Ignore:
Timestamp:
Jul 23, 2015, 8:13:09 AM (5 years ago)
Author:
olle
Comment:

Clarification of some entries.

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  • net.sf.basedb.meludi.notes1_3

    v2 v3  
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    55 a. Registration of extra material is now supported. Previously the number of extra QIAcube items was stored in a start plate annotation, and later on names for these items (optional). Extra material is now treated nearly as MeLuDI items, with some exceptions:[[BR]][[BR]]i. No case items are stored for extra material.[[BR]]ii. Extra material may be of types specimen, DNA, or RNA, and should be indicated by an added suffix to the core name ("." + number for specimens, ".d" for DNA, and ".r" for RNA).[[BR]]iii. Core names (name without added suffix) can be selected more freely, but may not start with "ML", in order not to be confused with MeLuDI items. The core name may not include special characters like a dot ".", comma, semicolon, or space.[[BR]]iv. The amount of initial information for an extra material is restricted to an arrival date and an optional comment.[[BR]]v. No storage location is stored for extra material.[[BR]][[BR]]
    6  b. DNA/RNA extraction wizards now store extract source item selections and parameters in an item list, instead of start plate annotations. This was motivated by the extracts not being placed on a start plate until the library preparation stage, where one wants to be free to select any DNA extract for a specific plate. Data is stored in an item list of type `Item.EXTRACT` as follows:[[BR]][[BR]]i. Data like dates and kit lot numbers are stored in start list annotations.[[BR]]ii. DNA/RNA extract source items are stored as members for the item list, while specimens are represented by their DNA child extracts.[[BR]]iii. A new annotation "`SamplePrepListIsProcessed`" is introduced to indicate if the item list is processed, i.e. concentrations and delta-Ct values are stored for the related extract items. (For start plates this was previously indicated by a set creation date, but creation events are not defined for item lists.)
     6 b. DNA/RNA extraction wizards now store extract source item selections and parameters in an "`ItemList`" record (referred to simply as "item list" in the following), instead of start plate annotations. This was motivated by the extracts not being placed on a start plate until the library preparation stage, where one wants to be free to select any DNA extract for a specific plate. Data is stored in an item list of type `Item.EXTRACT` as follows:[[BR]][[BR]]i. Data like dates and kit lot numbers are stored in start list annotations.[[BR]]ii. DNA/RNA extract source items are stored as members for the item list, while specimens are represented by their DNA child extracts.[[BR]]iii. A new annotation "`SamplePrepListIsProcessed`" is introduced to indicate if the item list is processed, i.e. concentrations and delta-Ct values are stored for the related extract items. (For start plates this was previously indicated by a set creation date, but creation events are not defined for item lists.)
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    88If no extra material has been used previously, the only needed extra step is to convert start plate items to start lists, and then delete the former. Otherwise, one has to choose how much information one wants to store for old extra items. At a minimum, previously used extra material should be registered, in order to allow it to be used with a start item list.