Opened 8 years ago

Closed 7 years ago

#364 closed task (fixed)

Put RNA aliquots on bioplate to be used by the Caliper machine

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v2.4
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The Caliper machine takes 8x12 plates for batch processing 96 extracts at a time. Aliquots are put on the plate at regular intervals, and it will usually take a couple of weeks to fill up a plate.

We need a reggie wizard that is able to pick RNA extracts that has not yet been processed and put aliquots on the current plate or on a new plate. New plates should automatically be generated with a naming convention and a running number.

Each use of the wizard should generate a "bioplate event" with protocol information, dates, etc. Used quantity can be different for each processed RNA extract and there may also be other values that need to be entered for each aliquot.

It is also possible that external RNA is used on the plate. Since we don't have any information about that in the BASE installation the wizard must allow "empty" wells on the plate.

The general outline of the wizard is:

  1. Show a list of unprocessed RNA and allow the user to select which one to process in this event. An advanced mode should also allow the user to select already processed RNA since the procedure may have to be repeated a second or third time.
  1. Let the user select an existing plate or create a new plate to use in this event.
  1. For each selected RNA, allow the user to select position and other values. There should be a function that can suggest default positions, but it must be possible to override by the user.
  1. Save everything to BASE.

Change History (15)

comment:1 Changed 8 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 7 years ago by Nicklas Nordborg

(In [1543]) References #364: Put RNA aliquots on bioplate to be used by the Caliper machine

Main features of the wizard has been implemented. Lots of minor details and error handling is not yet implemented.

comment:3 Changed 7 years ago by Nicklas Nordborg

(In [1549]) References #364: Put RNA aliquots on bioplate to be used by the Caliper machine

Adding two more annotation type checks (NDConc and QCHiSense)

comment:4 Changed 7 years ago by Nicklas Nordborg

(In [1551]) References #364: Put RNA aliquots on bioplate to be used by the Caliper machine

Add option for 'HiSense?' to each aliquot. Use 'NDConc' value for automatic default checked/unchecked. Need to get information about the limiting value that should be used (currently hard-coded at 50ng/μl).

The wizard can now handle the case were no protocol can be found.

comment:5 Changed 7 years ago by Nicklas Nordborg

(In [1552]) References #364: Put RNA aliquots on bioplate to be used by the Caliper machine

  • Added functionality for creating new quality control plates.
  • A bit more error handling and usability improvements, but the last step still need more checking when selecting wells

comment:6 Changed 7 years ago by Nicklas Nordborg

(In [1553]) References #364: Put RNA aliquots on bioplate to be used by the Caliper machine

More error handling and usability improvements. Should be working ok now, without any major issues.

comment:7 Changed 7 years ago by Nicklas Nordborg

(In [1554]) References #364: Put RNA aliquots on bioplate to be used by the Caliper machine

  • Fixed a problem with the barcode field.
  • The validation of column coordinate was off by 1.
  • Adding a file with RNA extracts for testing.

comment:8 Changed 7 years ago by Nicklas Nordborg

(In [1557]) References #364, #365 and #366. Added a short note about the new wizards to the README.

comment:9 Changed 7 years ago by Nicklas Nordborg

(In [1560]) References #364: Put RNA aliquots on bioplate to be used by the Caliper machine

  • Suffix '.qc' instead of '.qc1' for first RNAQC aliquot
  • Queries should be filtered to only return items shared to the current project

comment:10 Changed 7 years ago by Nicklas Nordborg

(In [1573]) References #364: Put RNA aliquots on bioplate to be used by the Caliper machine

Display bioplate location in the list when selecting RNA extracts.

comment:11 Changed 7 years ago by Nicklas Nordborg

(In [1583]) References #364, #365, #366, #370. Show a message and animated 'loading' icon when waiting for JSON request to return data from server

comment:12 Changed 7 years ago by Nicklas Nordborg

(In [1613]) References #364: Put RNA aliquots on bioplate to be used by the Caliper machine

Change the default HiSense? limit to 35 (from 25).

comment:13 Changed 7 years ago by Jari Häkkinen

The wizard should check that a position on the plate is not used more than once while the form is filled. Currently the check is done when the Create button is pressed.

comment:14 Changed 7 years ago by Nicklas Nordborg

(In [1615]) References #364: Put RNA aliquots on bioplate to be used by the Caliper machine

There is now a check for duplicate positions after each coordinate has been entered. The suggestion algorithm is now also taking the actually used positions into account instead of simply assuming that everything is filled in order.

comment:15 Changed 7 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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