Generate a lab protocol for RNA -> cDNA processing

[Nicklas Nordborg]

This is part of the RNA->cDNA processing group of wizards (see #422).

The protocol is needed before the actual lab work is started. The RNA selection wizard (#424) has created a child bioplate with the next set of RNA items to be processed.

This wizard should generate a list with the following information:

• Fields for date, operator, comments, etc.
• RNA name and storage location
• Work plate location
• Quantities to use (depends on QC)
• .... more?

[Nicklas Nordborg]

(In [1745]) References #425: Generate a lab protocol for RNA -> cDNA processing

Two variants of the protocol can be created. One with a list layout and aone with a plate layout.

[Nicklas Nordborg]

(In [1771]) References #425: Generate a lab protocol for RNA -> cDNA processing

Changes to the servlet method for finding current mRNA plates.

[Nicklas Nordborg]

(In [1789]) References #422, #424 and #425. Renamed 'Stratagene' to 'Stratagene.r' to follow the general naming convention for RNA items.

[Nicklas Nordborg]

(In [1792]) References #424, #425 and #436. Added a 'comments' field on the mRNA plate design wizard. The comment is included in the lab protocol and in the final mRNA registration wizard.

[Nicklas Nordborg]

(In [1793]) References #425: Generate a lab protocol for RNA -> cDNA processing

Include empty wells in the list protocol. Added some notes about print settings for list vs. plate layout. Restrict width of screen layout to better see how the printed version will look (also fixed on the Histology and Allprep protocols).

[Nicklas Nordborg]

(In [1794]) References #425: Generate a lab protocol for RNA -> cDNA processing

Added an optional field to enter the current Stratagene concentration. If it is used, the wizard will automatically calculate volumes to use as for the regular RNA items. If not used, the wizard will add a remark about how much RNA to use (eg 1.1 or 1.22 depending on QC).

[Nicklas Nordborg]

(In [1795]) References #424 and #425. Do not use 'pool' in the wizards/lab protocols since that may be confusing. Pools are not created until later.

[Nicklas Nordborg]

(In [1800]) References #424 and #425. Added support for marking wells as used by an 'External' RNA item not tracked by BASE. This will be indicated in the lab protocols, but information about concentration and volumes to use must be picked from another source.

[Nicklas Nordborg]

(In [1802]) References #424 and #425. Changed plate design to use 5 pools of 16 on each plate. This leaves just 1 column on each side free for extra biomaterial.

[Nicklas Nordborg]

(In [1807]) References #424 and #425. Added support for selecting different pooling layouts. It should be relatively easy to add more layouts in the future. Most of the functionality is in the 'pools.js' file which define the available layouts using some properties and some customization methods. The selected layout is stored as an annotation PoolSchema on the mRNA bioplate. The annotation is then copied to the cDNA plate when that is created. The layout is also used in the plate-view lab protocol.

The barcode layout wizard (#456) will use the selected pool schema as a starting point, but it should also be possible to change and select variants so that all barcodes are used evenly.

[Nicklas Nordborg]

(In [1809]) References #424, #425 and #456. Restructure the plate-handling javascript so that it is easier to re-use on different pages.

The barcode wizard now display the intended barcodes, but it is still only visual and there is not yet possible to change or save the information.

[Nicklas Nordborg]

(In [1817]) References #425: Generate a lab protocol for RNA -> cDNA processing

Show comments in the lab protocol.

[Nicklas Nordborg]

(In [1818]) References #425: Generate a lab protocol for RNA -> cDNA processing

Also show the comments for Stratagene and External RNA.

[Nicklas Nordborg]

(In [1891]) References #425: Generate a lab protocol for RNA -> cDNA processing

No files are needed by lab intruments. The only file we want in BASE is the PDF file from the BioAnalyzer quality control in the mRNA step.

[Nicklas Nordborg]

(In [1898]) References #425: Generate a lab protocol for RNA -> cDNA processing

Added possibility to register an 'externalId' and 'NDConc' annotation on external mRNA items which will then be used in the lab protocols. The registration has to be done using the regular BASE interface after the mRNA plate has been created.

IMPORTANT! Do not change the 'name' on external items since then they will not be recognized as external anymore.

[Nicklas Nordborg]

(In [1916]) References #425: Generate a lab protocol for RNA -> cDNA processing

Changed title to include the plate name and protocol type since it gives better file names when printing to PDF.

[Nicklas Nordborg]

(In [1919]) References #425: Generate a lab protocol for RNA -> cDNA processing

• Changed order of columns in the list protocol.
• Use white background in the plate layout.
• Amount of water is right-aligned in each cell.
• Samples with no storage box (eg. stratagene) now have an empty line so that volumes are aligned vertically.
• Latest stratagene concentration is stored and re-used the next time.

[Nicklas Nordborg]

(In [1927]) References #425, #457, #479. Format comment text with line breaks.

[Nicklas Nordborg]

(In [1929]) References #424, #425, #457, #479. Re-designed protocols to make the header section a bit more compact when the comment text is large. Display a warning when the remaining RNA quanitity is below 1.5 times the required amount (eg. 1.1µg or 1.22µg).

[Nicklas Nordborg]

(In [1944]) References #425: Generate a lab protocol for RNA -> cDNA processing

The protocol wizard now find out the actual regular quantity and marks all higher that that as items selected for QC.

[Nicklas Nordborg]

(In [1996]) References #425: Generate a lab protocol for RNA -> cDNA processing

Adding more date and operator fields to the lab protocol.