Opened 2 months ago

Closed 2 weeks ago

#1390 closed task (fixed)

Updates to wizards that assume tubes are marked with item name

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v4.39
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

Samples that have been handled externally and then transferred to the SCAN-B lab will most likely have a different text on the label on storage tubes. A new annotation TubeLabel was introduced in #1388 [6711].

Some wizards, for example, those that create lab protocols may have to use the TubeLabel text instead of the item name. Exactly which wizards that need to be updated have not yet been determined. It has to be done as part of this ticket.

Normally, these items will not show up in any wizard unless they are selected for re-processing at some step. This typically happens from the "Flagged RNA" wizard so we start from there and follow the lab processing step by step. In all cases we assume that when a material has been handled the produced new items will be labeled using the standard SCAN-B naming scheme.

Flagged RNA wizard
This wizard doesn't need the TubeLabel information for it's functionality, but it may be useful to display it as a reminder so that lab people can be notified beforehand. From this wizard it is possible to start a re-processing at 3 different levels:

  • Specimen → Partition wizard
  • Lysate → Pick lysate for re-extraction, and the other extraction wizards
  • RNA → Either the 'RNA normalization wizard' or the 'Create new library plate wizard'

Partition wizard
The wizard include all specimen marked for ReProcessing in the second list. It doesn't care about the storage location and works even if there is no information.

The "pick list" need to display TubeLabel information.

Step 2 need to display TubeLabel information. The wizard generates a "label" file for new tubes. The new labels are based on SCAN-B names.

Pick lysate for re-extraction
The wizard only include item in Lys% boxes. This may need to be changed since it is most likely that the external boxes are named differently. Registration will move selected items to ExtraLys% boxes so maybe it should allow boxes except ExtraLys%.

The protocol should include TubeLabel information.

Lab tracking protocol for Allprep isolation
The wizard only include lysates stored in ExtraLys% box. The wizard generates a "label" file for new tubes. The new labels are based on SCAN-B names.

The protocol should include TubeLabel information.

DNA/RNA/FlowThrough registration
The wizard only include lysates stored in ExtraLys% box. The wizard generates a "label" file for new tubes. The new labels are based on SCAN-B names.

The table in step 3 should include TubeLabel information.

The NanoDrop file uses SCAN-B names for new items.

RNA and DNA concentration normalization
Manual selection of RNA/DNA is possible. The protocol should include TubeLabel information. New labels for the pre-normalized tubes are created manually. It is assumed that the SCAN-B name is used for this.

Create new library plate
Manual selection of RNA is possible or auto-selection if the RNA is marked for re-processing. TubeLabel information doesn't have to be included and doesn't affect functionality.

Lab protocol for mRNA and cDNA preparation
TubeLabel information should be included in the lab protocol.

Lab protocol for external sequencing
TubeLabel information should be included in the lab protocol.

Protocols and labels for sample outtakes
TubeLabel information should be included in the lab protocol.

Lab protocol for extract destruction
TubeLabel information should be included in the lab protocol.

Change History (18)

comment:1 Changed 8 weeks ago by Nicklas Nordborg

Description: modified (diff)

comment:2 Changed 8 weeks ago by Nicklas Nordborg

Description: modified (diff)

comment:3 Changed 8 weeks ago by Nicklas Nordborg

Description: modified (diff)

comment:4 Changed 8 weeks ago by Nicklas Nordborg

Milestone: Reggie v4.xReggie v4.39
Status: newaccepted

comment:5 Changed 8 weeks ago by Nicklas Nordborg

In 6720:

References #1390: Updates to wizards that assume tubes are marked with item name

The "Flagged RNA" wizard has been updated. A new column "Label" was added to the table. It is possible to filter on that column to only display items with a different label.

The table has also been updated to use sticky headers so that the toolbar and filter doesn't disappear when scrolling the table.

comment:6 Changed 8 weeks ago by Nicklas Nordborg

In 6721:

References #1390: Updates to wizards that assume tubes are marked with item name

The partition wizard has been updated. The "Pick list" will include a "Label" column if there are any samples with a "TubeLabel?" annotation (it is hidden otherwise).

The partion registration form will also display the label close to the SCAN-B name of the item.

comment:7 Changed 7 weeks ago by Nicklas Nordborg

In 6722:

References #1390: Updates to wizards that assume tubes are marked with item name

The "Pick lysate for re-extract" wizard has been updated. It will display an extra column with the label on the tube.

comment:8 Changed 7 weeks ago by Nicklas Nordborg

In 6723:

References #1390: Updates to wizards that assume tubes are marked with item name

The "Lab protocol for AllPrep? isolation" has been updated. It will display an extra column with the label on the tube.

comment:9 Changed 7 weeks ago by Nicklas Nordborg

In 6724:

References #1390: Updates to wizards that assume tubes are marked with item name

Empty positions in the Allprep protocol may also need the label column.

comment:10 Changed 7 weeks ago by Nicklas Nordborg

In 6725:

References #1390: Updates to wizards that assume tubes are marked with item name

The "RNA/DNA/FlowThrough registration wizard" has been updated.

comment:11 Changed 7 weeks ago by Nicklas Nordborg

Description: modified (diff)

comment:12 Changed 7 weeks ago by Nicklas Nordborg

In 6726:

References #1390: Updates to wizards that assume tubes are marked with item name

The RNA and DNA normalization wizards have been updated.

comment:13 Changed 7 weeks ago by Nicklas Nordborg

In 6727:

References #1390: Updates to wizards that assume tubes are marked with item name

The Lab protocol for mRNA and cDNA preparation has been updated. The list view has an extra column for the label information. The plate view doesn't have room for both name and label so on that protocol only the label is printed.

comment:14 Changed 7 weeks ago by Nicklas Nordborg

Description: modified (diff)

comment:15 Changed 7 weeks ago by Nicklas Nordborg

In 6728:

References #1390: Updates to wizards that assume tubes are marked with item name

The Lab protocol for external sequencing has been updated. The list view has an extra column for the label information. The plate view doesn't have room for both name and label so on that protocol only the label is printed.

comment:16 Changed 7 weeks ago by Nicklas Nordborg

In 6730:

References #1390: Updates to wizards that assume tubes are marked with item name

The Pick list protocol for sample outtake has been updated. An extra column with the label has been added.

comment:17 Changed 7 weeks ago by Nicklas Nordborg

In 6731:

References #1390: Updates to wizards that assume tubes are marked with item name

The lab protocol for extract destruction has been updated. The protocol now has a column with the label.

comment:18 Changed 2 weeks ago by Nicklas Nordborg

Resolution: fixed
Status: acceptedclosed
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