Opened 6 years ago

Closed 6 years ago

Last modified 5 years ago

#503 closed enhancement (fixed)

Change pooling strategy

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.13
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The current pooling protocol has a problem with libraries that have a low concentration. Part of the problem can be solved by looking at the entire pool as a group instead of only a single lib at a time when calculating how much EB to use.

The current target volume and concentration is 5µl and 2nM. Libraries with a concentration lower than 2nM cause the final pool concentration to decrease since we can't use more than 5µl. If we instead can use up to 10µl (all) for some libraries but decreasing the amount of EB used for the other libraries the total pool volume and concentration can be kept at optimal level in more cases.

Change History (9)

comment:1 Changed 6 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 6 years ago by Nicklas Nordborg

(In [2027]) References #503: Change pooling strategy

The new implementation works like this:

  1. Use the target volume and target molarity to calculate the amount of each library to take. The resulting value is rounded to one decimal. The result may be higher that the target volume if the concentration is low.
  2. Libraries with high concentration are special cases and are always mixed to 2nM in double the target volume.
  3. Sum up everything and spread out the remaining EB volume equally among all libs. Rounding issues are considered and added to the last lib which may get a higher EB volume.
  4. The selected target volume is stored as an annotation on the pool since the value is needed again when generating the lab protocols.

There is currently not enough checking for extreme cases, eg. if there are many libraries with low concentration the final EB volume may be negative.

NOTE! Since the new implementation is very different from the old, case is needed when installing this update. Pools that have been created with the old Reggie wizard should be completed in the lab and registered before installing this update. Otherwise the lab protocols may show incorrect mixing values.

The incorrect calculations for 'dil' (see #507) items have been fixed.

comment:3 Changed 6 years ago by Nicklas Nordborg

(In [2040]) References #503: Change pooling strategy

Better handling of the special case when the total EB volume is negative. This is probably an indication that the libraries are too bad to be sequenced. In the GUI a warning message is displayed and the pool summary is calculated as if EB volume is 0. Pool creation is still possible. The lab protocol wizard has also been fixed so that 0 is displayed for all EB volumes in this case.

comment:4 Changed 6 years ago by Nicklas Nordborg

(In [2041]) References #503: Change pooling strategy

Implemented option to select 'Dynamic' or 'Fixed' pooling strategy, where 'Dynamic' is the new implementation and the 'Fixed' is the old. This should make it possible to register data that is in the backlog even after this release.

comment:5 Changed 6 years ago by Nicklas Nordborg

(In [2042]) References #503: Change pooling strategy

Added support for writing comments for each pool in the create pool wizard. The comments are displayed on the lab protocols.

comment:6 Changed 6 years ago by Nicklas Nordborg

(In [2043]) References #503: Change pooling strategy

Fixed bug in volume calculation when a max volume was not set.

comment:7 Changed 6 years ago by Nicklas Nordborg

(In [2053]) References #503: Change pooling strategy

Updates to the pooling lab protocol to make it clearer how EB should be mixed with libraries. When dynamic mixing strategy is used, no EB is displayed for individual libraries. Instead, the final EB is calculated and added to the pool after all libraries. The exception is high-concentration libraries that must be mixed to double volume before adding them to the pool. This is always displayed as a special "Remark" and not in the volume/eb columns.

comment:8 Changed 6 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

comment:9 Changed 5 years ago by Nicklas Nordborg

(In [2104]) References #503: Change pooling strategy

Destroy *.dil items after pool has been completed. Existing *.dil items need to be fixed manually, by creating an event for the *.dil item removing all remaining biomaterial.

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