Opened 17 months ago

Closed 15 months ago

Last modified 13 months ago

#1136 closed task (fixed)

MIPs plate lab protocol

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

Description

In the RNA pipeline there are three protocols that are plate-based, one for dilution/normalization, one for barcode assignment and one for pooling.

In the MIPs pipeline the aliquots are already normalized and pooling is done for entire plats(s). So, we need a protocol for the mapping between aliquot plate positions and MIPs plate positions and barcode assignment. We may also need information about the "protocol" (BED-file, target).

In any case, details about which information to include and where to find it must be worked out.

Change History (12)

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

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:3 Changed 17 months ago by Nicklas Nordborg

Status: newaccepted

comment:4 Changed 17 months ago by Nicklas Nordborg

In 5424:

References #1136: MIPs plate lab protocol

Started to work on the protocol. It is based on the mRNA protocol for the RNA-seq pipeline. Details about what to include and not on the protocol have not been decided yet.

comment:5 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:6 Changed 16 months ago by Nicklas Nordborg

In 5450:

References #1136 and #1137. Added some date and operator annotations that are more relevant for the MIPs pipeline (Hybridization and PCR). The lab protocols have been updated as well as the library registration wizard.

comment:7 Changed 16 months ago by Nicklas Nordborg

In 5451:

References #1136: MIPs plate lab protocol

Updated the lab protocols to display the new data variables added in [5447]. Column-wise checks are made for MIPSpool and volume.

comment:8 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:9 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:10 Changed 16 months ago by Nicklas Nordborg

In 5521:

References #1136: MIPs plate lab protocol

Added support for pool colors.

comment:11 Changed 15 months ago by Nicklas Nordborg

Resolution: fixed
Status: acceptedclosed

comment:12 Changed 13 months ago by Nicklas Nordborg

In 5604:

References #1136: MIPs plate lab protocol

Changes related to the renaming of MIPS_Pool to MIPS_Panel.

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