Opened 6 years ago

Closed 6 years ago

#479 closed task (fixed)

Generate lab protocol for pooling

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

Description

This is a wizard in the pooling and flow cell processing group of wizards (#478). The wizards should start with selecting a Library bioplate and then generate one or more lab protocols with the information that is needed to create the pools and prepare the flow cell.

It has yet to be decided what should be included in the lab protocol.

Change History (13)

comment:1 Changed 6 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 6 years ago by Nicklas Nordborg

(In [1911]) References #479: Generate lab protocol for pooling and flow cell preparation

First version of a pooling lab protocol. Don't know how useful it is, but the numbers that are needed should be there. Still not clear exactly how the 'Speedvac' step is performed and how that should affect numbers. We probably also need to pre-created the pool library items in an earlier step. Don't know if it is possible to do when finalizing the registration of the library preparation or if one more wizard is needed (eg. similar to 'Create new mRNA plate' and 'Assign barcodes to cDNA plate').

comment:3 Changed 6 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:4 Changed 6 years ago by Nicklas Nordborg

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

comment:5 Changed 6 years ago by 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).

comment:6 Changed 6 years ago by Nicklas Nordborg

(In [1948]) References #479: Generate lab protocol for pooling and flow cell preparation

Rearranged column order in list view so that work plate location is next to the volumes column.

Only show one of the 5µl and 10µl volumes. If the amount of extract is less than 1µl the 10µl values are used otherwise the 5µl values.

comment:7 Changed 6 years ago by Nicklas Nordborg

(In [1950]) References #479: Generate lab protocol for pooling and flow cell preparation

The limit for 5 vs 10 µl should be 1.0.

comment:8 Changed 6 years ago by Nicklas Nordborg

(In [1959]) References #479 and #485. Re-worked the process of selecing libraries for pooling. The first step will now create the PooledLibrary item and link to the used libraries with quantities. All calculations are base on pooling 5µl/2nM of each library. If a larger mix is required for a library dis is registed as a special item with .dil as a suffix. All items are registered without a creation date to indicate that it has yet to be done in the lab.

The lab protocol will use as much information as possible from the database.

Lots of error handling is still needed, and special cases are probably not well supported yet.

comment:9 Changed 6 years ago by Nicklas Nordborg

(In [1965]) References #479: Generate lab protocol for pooling and flow cell preparation

Fixed bug in calculations for list view. Some style changes to the list view protocol. Better document title for saving to pdf.

comment:10 Changed 6 years ago by Nicklas Nordborg

(In [1973]) References #479: Generate lab protocol for pooling and flow cell preparation

Do not show form until information about pools have been loaded.

comment:11 Changed 6 years ago by Nicklas Nordborg

(In [1975]) References #485 and #479. Only use 1 decimal in lab protocols for pooling. Use the rounded values when calculating molarity and other values for the pool.

comment:12 Changed 6 years ago by Nicklas Nordborg

(In [2003]) References #479: Generate lab protocol for pooling and flow cell preparation

Redisign of the protocol so that it looks similar to the mRNA and library preparation protocols.

comment:13 Changed 6 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
Summary: Generate lab protocol for pooling and flow cell preparationGenerate lab protocol for pooling

The pooling part is ok so far.

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