Changes between Version 1 and Version 2 of net.sf.basedb.meludi.notes1_3_2


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Timestamp:
Sep 24, 2015, 7:56:49 AM (5 years ago)
Author:
olle
Comment:

Completed information on MeLuDI 1.3.2 (and removed old stuff)

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  • net.sf.basedb.meludi.notes1_3_2

    v1 v2  
    2323Important!
    2424 i. MeLuDI v1.3.2 requires at least version 3.5.0 of BASE. If needed, update BASE before installing MeLuDI v1.3.2.
    25  ii. After installation of MeLuDI v1.3.2, run the installation wizard.
     25 ii. MeLuDI v1.3.2 has been tested successfully with Tomcat 8, but should still work with Tomcat 7.
     26 iii. After installation of MeLuDI v1.3.2, run the installation wizard.
    2627
    27 === b. Check what start plates contain information on extra material, and collect the information ===
     28== 2. Update processed start lists
    2829
    29 Select BASE menu option `Biomaterial LIMS -> Bioplates` to display a list of bioplates. Display values for name, `BatchNumberExtraQiacubeItems [A]`, and `ExtraQiacubeItemNamesListString [A]`. Filter name for "`LP%`" to display start plates, and annotation `BatchNumberExtraQiacubeItems [A]` for "`>0`" to show start plates with data for extra material. Note values of names for extra material in annotation `ExtraQiacubeItemNamesListString [A]`. If not present here, check for extra material names in paper copies of lab tracking protocol for Allprep isolation. Make a list outside the BASE/MeLuDI software of the extra material names for each start plate, or, if no names are stored, the number of extra items.
     30=== a. Update processed start lists with lot numbers from extracts ===
    3031
    31 === c. Check if any extra material names need to be modified ===
     32In section "Server administrator wizards" of the MeLuDI v.1.3.2 software, select the "Update processed start lists with lot numbers from extracts" wizard.
    3233
    33 If necessary, modify names for extra material according to the following:
    34 
    35  i. If more than one extra material item has the same name, modify some of them.
    36  ii. If some extra material names start with "ML", modify them.
    37  iii. If some extra material core names contain special characters dot ".", comma, semicolon, or space, modify them.
    38  iv. If some extra material core names consist entirely of digits, modify them.
    39  v. Construct names of extra material for start plates, where no names had been stored.
    40  vi. All previously used extra material were of type specimen, since they were QIAcube items. Therefore add a suffix "." + number to the core name. Start with number "1" for the first specimen having a specific core name, and increment the number for each new specimen with the same core name.
    41 
    42 The result is a list of extra material specimen names for the start plates, where the former can be used to register extra material in MeLuDI v.
    43 1.3.1
    44 === d. If needed, modify the start plate data to include the updated extra material names ===
    45 
    46 Select BASE menu option `Biomaterial LIMS -> Bioplates` to display a list of bioplates. Display values for name, `BatchNumberExtraQiacubeItems [A]`, and `ExtraQiacubeItemNamesListString [A]`. Filter name for "`LP%`" to display start plates, and annotation `BatchNumberExtraQiacubeItems [A]` for "`>0`" to show start plates with data for extra material. For each start plate:
    47 
    48  i. Click on the start plate name, to display info for the start plate.
    49  ii. Select tab "`Annotations`". Under primary annotations, for "View" select radio button "All annotations".
    50  iii. For annotation `ExtraQiacubeItemNamesListString`, click the "`Edit`" icon at the right end of the value field, to open an edit dialog window. In the edit dialog, enter new data or modify existing to get a comma-separated line of the extra material names for the start plate, that were constructed in the previous section. Make sure to use the specimen names ending in "." plus a number. Click the "`Save`" button in the edit dialog, to save the new values and close the dialog window.
    51 
    52 === e. Register (optionally modified) extra material names ===
    53 
    54 In section "Case registration" of the MeLuDI v.1.3.1 software, select the "Register new extra material" wizard. Enter data for the extra material specimens, whose names are included in the start plate annotation `ExtraQiacubeItemNamesListString`. Note that the core name without suffix should be entered in this wizard, since the suffix is added later, based on the chosen item type (here equal to specimen). Register the extra material. The wizard will now create the extra material specimens and child DNA and RNA extracts.
    55 
    56 == 2. Create start item lists
    57 
    58 === a. Create start item list from old start DNA plate ===
    59 
    60 In section "Server administrator wizards" of the MeLuDI v.1.3.1 software, select the "Create start lists from start DNA plates" wizard.
    61 
    62  i. Select the start plates you want to create start item lists for (normally all the plates).
    63  ii. Click "Register" to create the start lists.
     34 i. Select the processed start item lists you want to update (normally all the start lists).
     35 ii. Click "Register" to update the start lists.
    6436
    6537The following assumptions must be met for success:
     
    6941 3. All related specimens and extracts have already been created with the specified names.
    7042
    71 For each start plate, a start item list will be created, with the following properties:
     43Each selected processed start list will be updated as follows:
    7244
    73  a. The start list name is that of the start plate with prefix "`LP`" exchanged for "`SL`".
    74  b. All relevant start plate annotations are copied to corresponding start list annotations.
    75  c. Items named in start plate annotations are added as start list members (DNA child extracts represent specimens).
    76  d. An optional start plate creation date is stored in start list "`ListExtractionDate`" annotation.
     45 a. New start list lot number annotations will be set to values of the corresponding annotations for the first DNA extract.
     46 b. The new extraction operator annotation will not be set, as it was not defined for extracts prior to MeLuDI v1.3.2.
    7747
    78 The created start item lists can now be inspected using the "Lab tracking protocol/report copy" wizard.
    79 
    80 Storage of the start plate creation date in an item list annotation was chosen, as creation events are not defined for item lists. Since a set creation date for a start plate in MeLuDI v1.2.* indicates that the plate has been processed, i.e. that concentration and delta-Ct values have been registered for MeLuDI DNA/RNA, the created start list should also be marked as processed, by setting value of Boolean annotation "`SamplePrepListIsProcessed`" to `true`, if the start list does not contain any extra material. However, this should not be done for start lists with extra material, since concentration and delta-Ct values were only registered for MeLuDI items in v1.2.*, but not for extra material. Setting the value of annotation "`SamplePrepListIsProcessed`" to `true`, would prevent the start list from being opened in the "DNA/RNA registration/quantification" wizard, in order to register concentrations and delta-Ct values for the extra material.
    81 
    82 == 3. (Optional) Register quantification/QC values for extra material items
    83 
    84 If desired, concentration and delta-Ct values can now be registered for the new extra material items.
    85 
    86 === a. Store kit lot numbers for each start item list in a file ===
    87 
    88 The "DNA/RNA registration/quantification" wizard will display previously registered values for MeLuDI extracts in the input form as a practical side effect, so these values need not be re-entered. Unfortunately, the latter is not true for kit lot numbers. The following procedure is therefore recommended to register additional values for an item list:
    89 
    90  i. Open each start item list with extra material in the "Lab tracking protocol/report copy" wizard.
    91  ii. In step 2, after existing kit lot number values have been loaded, click button to download values to a reagent lot number file. Cancel this wizard when ready.
    92 
    93 === b. Register concentration and delta-Ct values for extra material items ===
    94 
    95  i. Open each start item list with extra material in the "DNA/RNA registration/quantification" wizard.
    96  ii. In step 2, select to import kit lot numbers from the file saved previously.
    97  iii. In step 3, enter the missing concentration and delta-Ct values for extra material, and complete the registration.
    98 
    99 == 4. After controlling the created start item lists, delete or rename the old start DNA plate items
    100 
    101 After controlling the created start lists, the start plates may be deleted. An alternative is to rename the plates by adding a new prefix (e.g. "`OLD_`"), so the names do not start with "`LP`". The start plates will reappear in the library preparation wizards, when they are to be filled with samples (though not necessarily the same samples as were previously related to it via annotations).
     48The updated start lists can now be checked in the "Lab tracking protocol/report copy" wizard.