Opened 7 years ago

Closed 7 years ago

#386 closed task (fixed)

Qiacube/nanodrop wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v2.6
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

The Qiacube machine is used with Lysate extracts to create RNA, DNA and FlowThrough items (also extracts). We need a wizard to register information about this process. It needs to keep track of used quantities, bioplate positions, and several annotations:

  • QiaCubeDate
  • QiaCubeRunNo
  • QiaCubePosition
  • QiaCubeOperator

After the extraction the NanoDrop machine is used to measure the following annotations (on RNA and DNA):

  • NDConc
  • ND260by230
  • ND260by280

The Lysate wizard (#388) is used first to create the lab protocol. This wizard will start by finding the Lysate extracts that was used (eg. they have a date but no child RNA or DNA items items without a creation date). Information about the lysis and Qiacube steps are recorded with protocol, operator, actual date, quantities, etc.

The second step generates a file with sample names that can be imported to the NanoDrop machine to map wells to samples.

The third step create child items (DNA, RNA and FlowThroguh?) for the Lysate items. The data file generated by the NanoDrop machine should be used to import the ND* annotations.

Change History (13)

comment:1 Changed 7 years ago by Nicklas Nordborg

Description: modified (diff)

comment:2 Changed 7 years ago by Nicklas Nordborg

(In [1639]) References #386: Qiacube/nanodrop wizard

The major function in the wizard are in place. Error handling is not yet fully implemented and it is not possible to change some default values (eg. Lysate/DNA/RNA volumes, Qiacube position, etc.)

The wizard uses the '8x12' array format for the Sample ID file that should be imported to the NanoDrop? software.

The NanoDrop? output file is read directly by the browser and require HTML5 feature that may not be implemented in all browsers (Firefox 12 is working).

comment:3 Changed 7 years ago by Nicklas Nordborg

Status: newassigned

comment:4 Changed 7 years ago by Nicklas Nordborg

(In [1642]) References #386: Qiacube/nanodrop wizard

Imporved wizard GUI. Old steps are now hidden as we move on to the next step. A legend makes it possible to display/toggle the older steps if needed.

Added popup dialog for modifying volumes and comments.

More error handling in the final step.

comment:5 Changed 7 years ago by Nicklas Nordborg

(In [1643]) References #386: Qiacube/nanodrop wizard

Use the Qiacube position to order the sample names in the Sample ID file that should be imported to the NanoDrop? software.

Improved error handling when reading the file exported from the NanoDrop?. Checking well location agains sample names, checking for missing columns or missing values. Checking that values have been imported for all samples.

comment:6 Changed 7 years ago by Nicklas Nordborg

(In [1647]) References #386: Qiacube/nanodrop wizard

Fixes an issue with parsing files that are using Mac-style linebreaks \r instead of \n.

comment:7 Changed 7 years ago by Nicklas Nordborg

(In [1648]) References #386: Qiacube/nanodrop wizard

Some minor changes to the last step in the wizard:

  • Display the storage box position in the table
  • Display 260/280 and 260/230 values as tooltips when moving the mouse over the RNA/DNA concentration values
  • Gray background in the concentration columns to indicate that they are loaded from the file
  • Use the 'Highlight' color when a comment is set to make it more clear. Display the actual comments as tooltips.
  • Fixed issue with forgotten comments if opening the edit dialog twice.

comment:8 Changed 7 years ago by Nicklas Nordborg

(In [1653]) References #386: Qiacube/nanodrop wizard

Some more enhancements to this wizard:

  • Check if the browser support the FileReader API in javascript
  • Show NanoDrop? position for each DNA/RNA sample
  • Generate fake test data in debug mode
  • Make forms 150px wider

comment:9 Changed 7 years ago by Nicklas Nordborg

(In [1654]) References #386: Qiacube/nanodrop wizard

The "generate fake data" button should be hidden to begin with.

comment:10 Changed 7 years ago by Nicklas Nordborg

(In [1655]) References #386: Qiacube/nanodrop wizard

Move the 'Storage position' column to the 'Lysate' section in the table.

Generate random data with 2 decimals only.

comment:11 Changed 7 years ago by Nicklas Nordborg

(In [1660]) References #386: Qiacube/nanodrop wizard

Add link to the 'Create aliquots on Bioanalyzer/Caliper? plates' wizard. The wizard starts at step 2 for selecting the plate and then step 3 to verify the locations.

comment:12 Changed 7 years ago by Nicklas Nordborg

Description: modified (diff)

comment:13 Changed 7 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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