Opened 17 months ago

Closed 15 months ago

Last modified 13 months ago

#1135 closed task (fixed)

Design MIPs plate wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.23
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Similar to the wizard for designing mRNA plates but with a lot less freedom.

Typically, a MIPs plate should allow placing aliquots from one or several aliquot plates column-wise. Empty wells at the end of a column are left empty and cannot be filled one-by-one manually as in the mRNA plate wizard.

Pool layouts are not needed since typically at least one entire plate, and sometimes two or more plates, are pooled in a single pool.

We can assume that all aliquots are pre-normalized. If not, they should be taken through the DNA pre-normalization wizard (#1129) first.

Change History (24)

comment:1 Changed 17 months ago by Nicklas Nordborg

In 5389:

References #1133: Re-organize the Reggie front page

Added lots of wizards to the "MIPs library preparation and analysis" section. The wizards will be implemented in other tickets. See #1130, #1135, #1136, #1137, #1138 and more to come.

comment:2 Changed 17 months ago by Nicklas Nordborg

Status: newaccepted

comment:3 Changed 17 months ago by Nicklas Nordborg

In 5390:

References #1135: Design MIPs plate wizard

Started to work on this wizard. So far it will only display an empty plate and generate a new name for it.

A new plate type, MIPs plate, has been defined and it will create plate names as MIPsPlate0001, MIPsPlate0002, ...

comment:4 Changed 17 months ago by Nicklas Nordborg

In 5392:

References #1135: Design MIPs plate wizard

Implemented selection of source aliquot plates and a simple auto-layout of the selected plates on the MIPs plate. Lots of things still missing:

  • No protocol for target quantity and volume
  • No checks for remaining quantity
  • No extra information about the aliquots (eg. bed, target, etc)
  • No preliminary (or final?) barcode selection
  • No registration

comment:5 Changed 17 months ago by Nicklas Nordborg

In 5413:

References #1135: Design MIPs plate wizard

Display more information for each well on the MIPs plate: remaining quantity, volume (or NDConc), BEDFile, Target, etc.

comment:6 Changed 17 months ago by Nicklas Nordborg

In 5414:

References #1135: Design MIPs plate wizard

Added "Normalization protocol" selection field. Target amounts and volumes are used to generate some warnings if the remaining quantity and concentration of the aliquot is not matched. It should cover at least some cases, but there are probably other issues depending on the flexibility of the protocol.

comment:7 Changed 17 months ago by Nicklas Nordborg

In 5417:

References #1135: Design MIPs plate wizard

Implemented registration of the plate. It will create the "MIPsPlate" and child "Library" items (with suffix .lib just as usual).

Registration of used quantities are not yet implemented. Additional book-keeping for aliquot plates is also needed. An initial attempt is made to set PlateProcessing=Disabled if all aliquots has been placed. This must be extended so that we can support "splitting" an aliquot plate on two MIPs plates if needed.

comment:8 Changed 17 months ago by Nicklas Nordborg

In 5418:

References #1135: Design MIPs plate wizard

Started to implement tracking of quantities. It's easy if the pre-normalization matches the target for the protocol, but the wizard should be able to handle other (expected and unexpected) situations as well, so this probably need more specifications.

comment:9 Changed 17 months ago by Nicklas Nordborg

In 5419:

References #1135, #1136 and #1137.

Added a counter query for some more MIPs-related wizards. A MIPs plate without a creation date is in the lib-prep process and it should show up in the "Lab protocol" wizard and in the "MIPs library registration" wizard.

comment:10 Changed 17 months ago by Nicklas Nordborg

In 5440:

References #1135 and #1136. Added functionality for displaying the aliquot plate name in the plate view (similar to how pools are displayed).

comment:11 Changed 16 months ago by Nicklas Nordborg

In 5446:

References #1135: Design MIPs plate wizard

Implemented functionality for checking BEDFile values in a column. Normally, all aliquots in a column should have the same BED. If not, a warning is displayed.

Consecutive columns that all have the same BED are grouped into pool-like display in the plate preview.

Aliquot plates are also grouped in a second row.

comment:12 Changed 16 months ago by Nicklas Nordborg

(for some reason the message was omitted from the commit so I paste it here)

In [5448]:

References #1135: Design MIPs plate wizard

Removed the "Normalization protocol" parameter from this wizard. Aliquots that have a registered remaining quantity are assumed to be fully consumed.

Updated the wizard with the new data fields (see [5447]).

comment:13 Changed 16 months ago by Nicklas Nordborg

In 5454:

References #1135: Design MIPs plate wizard

Fixed problems with overfilling a plate. This is now handled and a message is displayed that not all aliquots could be placed on the MIPS plate.

Implemented "Move up/down" buttons for re-arranging the order of selected aliquot plates. The layout of the MIPS plate is automatically re-done.

comment:14 Changed 16 months ago by Nicklas Nordborg

In 5455:

References #1135: Design MIPs plate wizard

Fixed a problem with empty pool/plate rows not being hidden if removing all selected plates from the selection list.

comment:15 Changed 16 months ago by Nicklas Nordborg

In 5457:

References #1135: Design MIPs plate wizard

Set PlateProcessing=DesignMIPs on aliquot plate that was not fully used on the MIPs plate. This should help us to find it again so that the remaining aliquots can be placed on the next MIPs plate.

comment:16 Changed 16 months ago by Nicklas Nordborg

In 5458:

References #1135: Design MIPs plate wizard

Added a special dialog for selecting aliquot plates. It will make it possible to select aliquot plates that are annotated with PlateProcessing=AddAliquots|DesignMIPs and not marked as destroyed.

The query for selecting aliquots from the plates now also have a filter to only return aliquots without child items. This should solve the problem with an aliquot plate being split accross two MIPs plates. The exception is that if the plate is marked with AutoProcessing=ReProcess all aliquots are selected no matter how many child items they have.

comment:17 Changed 16 months ago by Nicklas Nordborg

In 5459:

References #1135: Design MIPs plate wizard

Added a "preview" of the clicked plate in the "Select aliquot plate" dialog. It uses icons and colors to indicate the coordinates with aliquots and also if an aliquot has already been used or not. There are probably room for improvements...

comment:18 Changed 16 months ago by Nicklas Nordborg

In 5460:

References #1135: Design MIPs plate wizard

Added a MIPS pool row to the preview in the "Select aliquot plates" dialog.

comment:19 Changed 16 months ago by Nicklas Nordborg

In 5481:

References #1130, #1135, #1136. Introduced soft line-breaks in sample names. This should make it possible to print the lab protocol on a single sheet even if the sample names are a bit longer.

comment:20 Changed 16 months ago by Nicklas Nordborg

In 5483:

References #1130, #1135, #1136. Synchronized some missing styles and remove the prefix from external sample names in the plate view lab protocol in order to save space.

comment:21 Changed 16 months ago by Nicklas Nordborg

In 5520:

References #1135: Design MIPs plate wizard

Added support for pool colors.

comment:22 Changed 15 months ago by Nicklas Nordborg

In 5526:

References #1130, #1135, #1142, #1146. Fixing and getting rid of some 'TODO' entries in the code.

comment:23 Changed 15 months ago by Nicklas Nordborg

Resolution: fixed
Status: acceptedclosed

comment:24 Changed 13 months ago by Nicklas Nordborg

In 5603:

References #1135: Design MIPs plate wizard

Changes related to the renaming of MIPS_Pool to MIPS_Panel.

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