Opened 8 years ago

Closed 8 years ago

Last modified 7 years ago

#473 closed task (fixed)

Register library processing results

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.12
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

This wizard is the last step in #423. In the lab, the library preparation first needs a number of test rounds for finding the correct parameters (eg. depending on humidity, etc.) and quality control. After that a complete plate is processed.

The wizard should be able to register each test round with at least a PDF file and a comment.

The complete plate (if successful) registration need to provide data files from the Caliper and Qubit runs. Details need to be investigated, but we'll need at least a PDF and a CSV file to parse for annotations.

(It should be possible to mark specific positions as failed and their parent RNA should then be flagged for re-processing -- TODO in a later release)

The wizard should also have support for a completely failed plate which also results in all parent RNA being flagged.

Change History (26)

comment:1 Changed 8 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 8 years ago by Nicklas Nordborg

(In [1895]) References #473: Register library processing results

Started with the QC part of the registration.

comment:3 Changed 8 years ago by Nicklas Nordborg

(In [1902]) References #473: Register library processing results

Added annotations for storing concentration from Qubit measurements (QubitConc) and fragment sizes from Caliper (CA_SIZE).

comment:4 Changed 8 years ago by Nicklas Nordborg

(In [1903]) References #473: Register library processing results

Added two test data files that matches the data in the 'mrna.txt' file that can be used to create a new Mrna plate. The test files should work if this is the first plate that is created and the wells with errors (duplicates, not-found, etc.) are cleared.

  • LibPlate0001_Caliper_out.csv: Data from the Caliper run on the entire plate, but not for the Stratagene extracts.
  • LibPlate0001_Qubit_out.csv: The file is created by Reggie and the operator enter concentration values for each extract. This is how the final file would look like and it is then uploaded to BASE again.

comment:5 Changed 8 years ago by Nicklas Nordborg

(In [1904]) References #473: Register library processing results

Prepared the CaliperPlateImporter implementation for importing data to other plate types (eg. with different prefix than CaliperPlate).

Added possibility to provide external lookup for setting more annotations for each sample. The idea is to pre-parse the Qubit data file and then for each sample in the Caliper file lookup the corresponding concentration in the Qubit file. This way we don't have to duplicate lots of error checking in a QubitPlateImporter class.

comment:6 Changed 8 years ago by Nicklas Nordborg

(In [1905]) References #473: Register library processing results

Add possibility in the LookupConverter to throw an exception if a value is not found.

comment:7 Changed 8 years ago by Nicklas Nordborg

(In [1906]) References #473: Register library processing results

Added functionality to import Caliper (size) and Qubit (concentration) data. The original quantity of the library is calculated assuming that the final volume is 10µl after the aliquots have been taken for Caliper and Qubit.

Also added the CA_Molarity annotation which is calculated using the formula: 1000 * 1000 * (1/649) * QubitConc? * (1/CA_Size)

Removed ng/µg from Qubit file since it may cause issues if opened in programs not automatically using UTF-8.

comment:8 Changed 8 years ago by Nicklas Nordborg

(In [1908]) References #473: Register library processing results

It should now be possible to register all three types of library plate processing results:

  • QC checks (can be done several times)
  • Full plate - success
  • Full plate - failed

Removed the "Assign barcode" event since it is no longer needed when the library plate is pre-created without date.

comment:9 Changed 8 years ago by Nicklas Nordborg

Description: modified (diff)

comment:10 Changed 8 years ago by Nicklas Nordborg

(In [1909]) References #473: Register library processing results

Add support for importing Caliper results from a re-mapped 384-well plate. Added a fiel with testdata in that format. Same values and extracts as the regular file.

comment:11 Changed 8 years ago by Nicklas Nordborg

(In [1925]) References #472, #473 and #479. Added QubitConcAfterSpeedVac annotation which should be used for Qubit concentration measurements after SpeedVac?. The original Qubit concentration should always be stored in the QubitConc annotation.

The exported template file entering Qubit concentration values have been modified so that it is possible to enter both values. The test data file has been updated and a few entries now have two values.

The importer have been modified to check for both values and use the latest in when calculating molarity, original quantity, etc.

The pooling lab protocol have been updated to check if QubitConcAfterSpeedVac annotation exists or not.

comment:12 Changed 8 years ago by Nicklas Nordborg

(In [1930]) References #472 and #473. Use 'ng/ml' in Qubit files since that is what is shown in the display on the Qubit. The importer converts to 'ng/µl'.

comment:13 Changed 8 years ago by Nicklas Nordborg

(In [1931]) References #473: Register library processing results

Split the library registration wizard into two. One for registering QC results and one for the final registration of the complete plate.

comment:14 Changed 8 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

comment:15 Changed 8 years ago by Nicklas Nordborg

(In [1961]) References #473: Register library processing results

The library registration now uses 'local storage' to temporarily save the form. In case the registration fails for any reason (common: data files are not correctly formatted), the saved data is used to re-populate all input fields so that the user doesn't have to enter all values again.

comment:16 Changed 8 years ago by Nicklas Nordborg

(In [1962]) References #473: Register library processing results

The importer for Qubit concentration values now accepts files that have been mangled through any *Office program. Eg. it accapts tab or comma as separator and quoted values.

Added a second test data file which have commas and quotes.

comment:17 Changed 8 years ago by Nicklas Nordborg

(In [1963]) References #473: Register library processing results

The Caliper importer now has an option to allow matching samples using the location coordinate. The reason is that the Caliper software for some reason seems to forget the sample name for a few positions and only output the location. There is a limitation so that at most half of the samples on a plate can be matched this way. Otherwise there is a risk that a file can be imported to a plate that it doesn't belong to.

comment:18 Changed 8 years ago by Nicklas Nordborg

(In [1964]) References #473: Register library processing results

Forgot to re-enable call to commit after testing.

comment:19 Changed 8 years ago by Nicklas Nordborg

(In [1968]) References #473: Register library processing results

Swithced order of file selection so that the Qubit file is selected first. This makes it possible to validate that file at the same time the Caliper Well Table file is validated.

comment:20 Changed 8 years ago by Nicklas Nordborg

(In [1969]) References #473: Register library processing results

Qubit test data files should have correct unit (ng/ml) and instruction.

comment:21 Changed 8 years ago by Nicklas Nordborg

(In [1984]) References #473: Register library processing results

Save comments in LibPlate description.

comment:22 Changed 8 years ago by Nicklas Nordborg

(In [1986]) References #473: Register library processing results

Show warning if trying to register a library plate without any quality control PDF files attached to it. Registration is still possible.

Added "manual select" functionality for registering quality control PDF:s to a library plate. This allows a PDF file to be attached to a plate at any time.

comment:23 Changed 8 years ago by Nicklas Nordborg

(In [1989]) References #473: Register library processing results

Set file description that includes the plate name if no description already exists. This is also automatically applied to Caliper RNA QC files since it is using the same importer.

comment:24 Changed 8 years ago by Nicklas Nordborg

(In [1991]) References #473: Register library processing results

Automatically set the working directory to /home/SCANB/LibPlateQC when opening the "Browse" dialog.

comment:25 Changed 8 years ago by Nicklas Nordborg

(In [1992]) References #436 and #473. Added subtypes for 5 different files produced or used by Bioanalyzer, Caliper and Qubit. The wizards use those subtypes as a filter when selecting files so that it should be easier to find the correct files.

comment:26 Changed 7 years ago by Nicklas Nordborg

(In [2002]) References #473: Register library processing results

Added date and operator fields to the library preparation registration wizard. Already registered plates should be fixed manually.

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