wiki:net.sf.basedb.reggie.notes213

Updating to Reggie 2.13

The following items should be performed after updating to Reggie 2.13.

1. Flag some libraries and their parent RNA item

Due to a bug (see #508), libraries which got a Qubit concentration measurement of 0 ng/µl have been left in a dead end state. To ensure that new RNA is extracted in the future, a flag must be set manually and the parent RNA items must be added to the Flagged RNA list.

  1. To find the libraries in question go to the Biomaterial LIMS->Extracts page and filter on Type=Library and CA_Molarity=0.
  2. Edit each library item and set the annotation: Flag=ExcludedFromPool.
  3. Find the parent RNA item for each library and set the annotation: Flag=ExcludedFromPool.
  4. Add all parent RNA items to the Flagged RNA biomaterial list.
  5. Check that the selection list in the Create pooled libraries no longer include already registered library plates.

2. Fix PoolConc values for all *.dil extracts

Due to a bug (see #507), all *.dil extracts have been registered with an incorrect value for the PoolConc annotation. This need to be fixed by a manual export/import procedure.

  1. To find the libraries in question go to the Biomaterial LIMS->Extracts page and filter on name=%.dil.
  2. To avoid rounding errors in the exported data go to BASE->Preferences and set Decimals=all.
  3. Use the Table exporter plug-in to export a tab-separated file with Name and Original quantity columns.
  4. Download the exported file to your computer and open in a spreadsheet program.
  5. Add a new column PoolConc and use the following formula to calculate the values: =1000 * <quantity> / 5
  6. Save the results as a tab-separated file and upload it to BASE.
  7. Use the annotation importer to update the PoolConc values.

3. Register all *.dil extracts as destroyed

A decision was made to not store *.dil items after the pool has been created. Reggie has been updated to register this as an event attached to the *.dil items that remove all remaining quantity. Unfortunately there is no batch importer support for events, so existing *.dil items need to be fixed manually one by one.

  1. To find the libraries in question go to the Biomaterial LIMS->Extracts page and filter on name=%.dil and Remaining quantity>0
  2. Click on each one, copy the Original quantity value and then go to the Events tab.
  3. Create a new event and paste the copied value into the Used quantity field.
  4. Save, and repeat for all *.dil items in the main list.

4. Copy missing consent information from blood to case items

Due to a bug (see #511) consent information that has already been registered on blood samples with BloodSample=PreNeo has not been copied to cases that was registered at a later time. To fix this a manual crossmatch is required to find which cases are missing consent information that is available on a blood item.

  1. Find all cases with missing consent information. Export a list with the case names to a tab-separated file.
  2. Find all PreNeo blood items that has consent information. Export the blood name, Consent and ConsentDate columns to a tab-separated file.
  3. Use a spreadsheet program to crossmatch the case names with the blood names.
  4. Copy the found consent information to new columns in the list with cases.
  5. Save the result as a tab-separated file and upload it to BASE.
  6. Use the annotation importer to import values for Consent and ConsentDate to the cases.

5. Copy missing QiaCube annotations to FlowThrough items

Due to a bug (see #520) the four QiaCube annotations (QiacubeDate QiacubeOperator QiacubePosition QiacubeRunNo) was never set on FlowThrough items. The values are available on related RNA and DNA items, so it is easy to fix using a batch import.

  1. List all RNA extracts. Export a list with the names and the four QiaCube annotations to a tab-separated file.
  2. Edit the file and replace .r in all names with .f.
  3. Upload the file to BASE and use the annotation importer to import QiaCube annotation to the FlowThrough items.
Last modified 4 years ago Last modified on Oct 25, 2013, 9:28:20 AM