Opened 18 months ago

Closed 15 months ago

Last modified 12 months ago

#1129 closed task (fixed)

DNA pre-normalization

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

Description (last modified by Nicklas Nordborg)

We are about to start processing DNA. In preparation for this we need a pre-normalization functionality that is similar to the pre-normalization done for RNA.

  • The extraction registration wizard should be updated with functionality to mark DNA that should be pre-normalized. Flagging is not needed.
  • A 'DNA concentration normalization' wizard is needed. It should have more or less the same functionality as the RNA counterpart. Flagging is not needed. We probably need to define new protocol and annotation types to hold target amounts and volumes. The default target amount and volume is 500ng in 10µl.
  • We may also need an additional label if we decide to store the pre-normalized DNA in tubes. The other option is to store the DNA in plates which requires new functionality for creating plates and assigning positions to the pre-normalized DNA.

Change History (16)

comment:1 Changed 18 months ago by Nicklas Nordborg

In 5356:

References #1129: DNA pre-normalization

The extraction registration wizard has been updated with a "pre-normalize" option for DNA. If selected, it will set AutoProcessing=PreNormalizeDNA on the DNA. It will not check remaining quantity except if it is 0 (or less). In this case the DNA is flagged with NotEnoughRemainingQuantity.

comment:2 Changed 18 months ago by Nicklas Nordborg

In 5357:

References #1129: DNA pre-normalization

Added a "Flagged DNA" list. Not actually needed at the moment, but maybe in the future.

comment:3 Changed 18 months ago by Nicklas Nordborg

In 5358:

References #1129: DNA pre-normalization

Added a link to DNA normalization wizard on the front page and a counter for number of items.

comment:4 Changed 18 months ago by Nicklas Nordborg

Description: modified (diff)

comment:5 Changed 18 months ago by Nicklas Nordborg

In 5359:

References #1129: DNA pre-normalization

Started to work on the "DNA normalization" wizard. It is more or less a clone of the RNA normalization wizard.

There are some new types:

  • DNANormalizedAliquot (Extract)
  • DNANormalization (Protocol)
  • DNATargetAmount (Annotation type)
  • DNAMinimalAmount (Annotation type)
  • DNATargetVolume (Annotation type)

The final registration has not been implemented. Plate positions are not assigned to the normalized DNA.

The normalized_rna.css has been renamed to normalized_extract.css since it can be used to style both the DNA and RNA normalization protocols. The RNA normalization wizard must be updated.

comment:6 Changed 18 months ago by Nicklas Nordborg

In 5360:

References #1129: DNA pre-normalization

Updated the RNA normalization wizard to use the renamed css file.

comment:7 Changed 18 months ago by Nicklas Nordborg

Status: newaccepted

comment:8 Changed 17 months ago by Nicklas Nordborg

In 5361:

References #1129: DNA pre-normalization

Added functionality for selecting a plate for the normalized DNA aliquots. A new plate type has been defined: PreNormalizedDNA plate. In the second step of the wizard the user is allowed to select among existing plate that still has enough free wells remaining or to create a new plate.

DNA aliquots are laid out automatically filling all rows in a column before moving on to the next column. The wizard will automatically skip DNA that has too low concentration as indicated by the selected protocol (default value is 500ng in 10µl). Changing the protocol or plate will re-do the calculations and plate layout.

comment:9 Changed 17 months ago by Nicklas Nordborg

In 5362:

References #1129: DNA pre-normalization

Implemented registration of the pre-normalized DNA aliquots.

comment:10 Changed 17 months ago by Nicklas Nordborg

In 5407:

References #1129: DNA pre-normalization

Added PlateProcessing annotation which is intended to be used for controlling how pre-normalized DNA plates can be used. AddAliquots is currently the only defined value which is required for the DNA pre-normalization wizard to be able to add aliquots to the plate. At some later stage the value will change to something else to enable it for MIPs plate design.

comment:11 Changed 16 months ago by Nicklas Nordborg

In 5449:

References #1129: DNA pre-normalization

Enabled the MIPS_Pool annotation for protocols (DNANormalization). In the pre-normalization wizard the value from the selected protocol will be copied to the normalized aliquots.

comment:12 Changed 16 months ago by Nicklas Nordborg

In 5456:

References #1129: DNA pre-normalization

Added a separate counter on the index page for the number of pre-normalized DNA that plates that are in the SCAN-B lab (assuming that PlateProcessing=AddAliquots indicates that the plate has not yet been picked for MIPs).

Fixed the filter for getting the list of currently active plates for storing pre-normalized DNA since.

Set creation date on pre-normalized DNA plates when the plate is created.

comment:13 Changed 16 months ago by Nicklas Nordborg

In 5482:

References #1129: DNA pre-normalization

Pre-normalized DNA plates should start with NormDNA to keep the names shorter.

comment:14 Changed 15 months ago by Nicklas Nordborg

Resolution: fixed
Status: acceptedclosed

comment:15 Changed 13 months ago by Nicklas Nordborg

In 5591:

References #1129: DNA pre-normalization

The DNA/RNA/Flowthrough registration wizard now checks if there are any normalization protocols available. It uses this information to decide if the "pre-normalize" checkboxes should be selected or not initially.

comment:16 Changed 12 months ago by Nicklas Nordborg

In 5602:

References #1129: DNA pre-normalization

Changes related to the renaming of MIPS_Pool to MIPS_Panel.

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