Changes between Version 9 and Version 10 of net.sf.basedb.meludi.background_software_info


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Timestamp:
Apr 26, 2016, 4:57:07 PM (4 years ago)
Author:
olle
Comment:

Renumbering sections and adding new material

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  • net.sf.basedb.meludi.background_software_info

    v9 v10  
    2020BASE was developed to be a web-based interface to a database with bio assay data. In order to simplify adapting the software/database to specific data storage needs, a system of annotation types was developed, making it easy to add storage of new variable data to an "annotatable" item. An annotation type is of a specific data type, e.g. integer, float, string; and is defined for a specific type of item, e.g. samples, extracts, bioplates, item lists, etc.
    2121
    22 === 1.5 Pipeline management ===
     22== 2 Pipeline management ==
     23=== 2.1 Description ===
    2324MeLuDI, like Reggie, is intended to simplify keeping track on what items are of interest in each step of the processing pipeline, e.g. by only including those items in selection menus for a particular step. In some cases, this is simple, since child items are created at registration in several steps, and will then be input items in the next step. One case where you might be interested in the details of how MeLuDI keeps track of what steps an item has passed, is when you want to undo a step in the BASE GUI by deleting child items created in the last step. Sometimes this is not enough to allow you to redo the last step in MeLuDI, since the needed items do not appear in selection menus, if the software still considers them to have passed the step in question.
    2425
    25 ==== 1.5.1 Wizard "Lab tracking protocol for FFPE extraction": Extract source items added to start list ====
     26=== 2.2 How some wizards perform their magic ===
     27==== 2.2.1 Wizard "Lab tracking protocol for FFPE extraction": Extract source items added to start list ====
    2628Extract source items (specimens or input extracts) added to a start list have their original quantity changed from `null` to 0.0. This will stop them from appearing in the extract source item selection menu, when the wizard is run again.
    27 ==== 1.5.2 Wizard "DNA/RNA registration/quantification": Processing a start list
     29==== 2.2.2 Wizard "DNA/RNA registration/quantification": Processing a start list
    2830A start list is regarded as processed, when quantification data for its extracts have been entered. This is indicated by setting value of Boolean item list annotation `Annotationtype.SAMPLE_PREP_LIST_IS_PROCESSED` to `true`.
    29 ==== 1.5.3 Wizard "Create new start DNA plate" Step 1: Processed start list to select DNA extracts from
     31==== 2.2.3 Wizard "Create new start DNA plate" Step 1: Processed start list to select DNA extracts from
    3032Only processed start lists with at least one DNA extract without an FPA child extract on a library plate will appear in the start list selection menu.
    31 ==== 1.5.4 Wizard "Create new start DNA plate" Step 2: DNA extracts on selected processed start lists
     33==== 2.2.4 Wizard "Create new start DNA plate" Step 2: DNA extracts on selected processed start lists
    3234Only DNA extracts without an FPA child extract on a library plate will appear in the DNA extract selection menu.
     35
     36=== 2.3 Some hints when correcting erroneous MeLuDI entries in BASE ===
     37==== 2.3.1 General ====
     38a. It is always a good idea to get a printout of the current state of MeLuDI, e.g. a lab protocol, before starting to change anything in BASE.
     39b. It is often a good idea to completely remove an erroneous item, and then re-create it with correct data in MeLuDI. Trying to modify item properties in BASE, may have side effects in the way MeLuDI treats the item. An exception is modification of comment text for an item, that normally can be made without software consequences.
     40==== 2.3.2 Wizard "Create new start DNA plate" Step 2 after registration: Remove an erroneously created start DNA plate
     41a. The following recommendation concerns removing the most recently registered start DNA plate.
     42b. Print a lab protocol (Plate layout) of the start DNA plate to be removed. This is preferred over a dilution protocol, since the former contains the name of the library preparation kit.
     43c. In BASE, delete the Bioplate and all *.fpa and *.fpb DNA extracts on the plate.
     44d. In MeLuDI wizard "Inspect/edit library preparation kit data", edit the entry for the library preparation kit used for the removed start DNA plate. At entry "Unused FPA plate locations", add the plate positions used for *.fpa DNA extracts on the removed plate to the list. Make sure that the plate positions are separated by a single comma. Save the changes.