Changes between Initial Version and Version 1 of net.sf.basedb.meludi.notes1_3

Jul 22, 2015, 4:43:01 PM (8 years ago)

Added information on MeLuDI 1.3


  • net.sf.basedb.meludi.notes1_3

    v1 v1  
     1= Updating to MeLuDI 1.3 =
     3Updating to MeLuDI 1.3 might require some manual changes for items that already exist. This is due to two decisions (See ticket:792 for more information):
     5 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 cases 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.)
     8If 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.
     10Follow this procedure:
     12== 1. Preparations for transferring old start DNA plate information to a start item list.
     14=== a. Update to MeLuDI 1.3 ===
     16Among other things, item lists with desired annotations are installed.
     18=== b. Check what start plates contain information on extra material, and collect the information ===
     20Select 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.
     22=== c. Check if any extra material names need to be modified ===
     24If necessary, modify names for extra material according to the following:
     26 i. If more than one extra material item has the same name, modify some of them.
     27 ii. If some extra material names start with "ML", modify them.
     28 iii. If some extra material core names contain special characters dot ".", comma, semicolon, or space, modify them.
     29 iv. If some extra material core names consist entirely of digits, modify them.
     30 v. Construct names of extra material for start plates, where no names had been stored.
     31 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.
     33The 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 v1.3.
     35=== d. If needed, modify the start plate data to include the updated extra material names ===
     37Select 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:
     39 i. Click on the start plate name, to display info for it the start plate.
     40 ii. Select tab "`Annotations`". under primary annotations, for "View" select radio button "All annotations".
     41 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.
     43=== e. Register (optionally modified) extra material names ===
     45In section "Case registration" of the MeLuDI v.1.3 software, select the "Register new extra material" wizard. Enter data for the extra material specimens, whose names are included in the start 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.
     47== 2. Create start item lists
     49=== a. Create start item list from old start DNA plate ===
     51In section "Server administrator wizards" of the MeLuDI v.1.3 software, select the "Create start lists from start DNA plates" wizard.
     53 i. Select the start plates you want to create start item lists for (normally all the plates).
     54 ii. Click "Register" to create the start lists.
     56The following assumptions must be met for success:
     58 1. The start plate contains a list of all related MeLuDI item names as annotation.
     59 2. The start plate contains a list of all related extra material names as annotation.
     60 3. All related specimens and extracts have already been created with the specified names.
     62For each start plate, a start item list will be created, with the following properties:
     64 a. The start list name is that of the start plate with prefix "`LP`" exchanged for "`SL`".
     65 b. All relevant start plate annotations are copied to corresponding start list annotations.
     66 c. Items named in start plate annotations are added as start list members (DNA child extracts represent specimens).
     67 d. An optional start plate creation date is stored in start list "`ListExtractionDate`" annotation.
     69The created start item lists can now be inspected using the "Lab tracking protocol/report copy" wizard.
     71Storage 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, it might be argued that annotation "`SamplePrepListIsProcessed`" for the created start list should be set to `true`, in order t0 indicate that the start list has been processed. However, this is normally only true for converted item lists without 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 have prevented using the DNA/RNA registration/quantification wizard to register the latter values for the start list.
     73== 3. (Optional) Register quantification/QC values for extra material items
     75If desired, concentration and delta-Ct values can now be registered for the new extra material items.
     77=== a. Store kit lot numbers for each start item list in a file ===
     79The "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:
     81 i. Open each start item list in the "Lab tracking protocol/report copy" wizard.
     82 ii. In step 2, after existing kit lot number values have been loaded, click button to download values to a reagent lot no. file. Cancel this wizard when ready.
     84=== b. Register concentration and delta-Ct values for extra material items ===
     86 i. Open each item list in the "DNA/RNA registration/quantification" wizard.
     87 ii. In step 2, select to import kit lot numbers from the file saved previously.
     88 iii. In step 3, enter the missing concentration and delta-Ct values for extra material, and complete the registration.
     90== 4. After controlling the created start item lists, delete the old start DNA plate items
     92After controlling the created start lists, the start plates may be deleted. The latter 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).