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A message is shown when to change source plates in the transfer_dilution_hal.pro protocol, but not for the first one. Change this so it's easier to spot mistakes.

Affected file(s)

• rna_prep_v1203.pro

Description

After the 1st and 2nd strand synth mix plates have been prepared and are loaded into the MiniHub, the user is asked to put them in the fridge. In some or possibly all occasions the MiniHub is rotated before the instruction and pause making the plates hard to access.

Solution

Is there a way to prevent any further MiniHub activity between the loading of the plates and the pause?

Protocol: TruSeq PCR-free

Description: Waste overfills during prep, this problem was introduced with d592edd.

Solution: Replace waste plate with empty one after size selection but there are no available large slots in the MiniHub so how to do this?

1. Add centrifugation after mixing sample and reagents
2. Add tRobot incubation
3. Add possibility to do final hold
4. Add sealing of plate before 1–3 and at end (conditionally, if last protocol in runset)
5. Add PCR cleanup to runset

Affected files:

• [transfer_dilution_v1403.pro](/jgruselius/bravo-protocols/blob/master/Protocol Files/facility/transfer/transfer_dilution_v1403.pro) (production)
• [transfer_dilution_v1403.pro](/jgruselius/bravo-protocols/blob/master/Protocol Files/development/jgr/transfer_protocols_eval/transfer_dilution_v1403.pro) (development)
• [jgr_lib_v1405.js](/jgruselius/bravo-protocols/blob/master/Protocol Files/facility/transfer/jgr_lib_v1405.js) (production)
• [jgr_lib_v1405.js](/jgruselius/bravo-protocols/blob/master/Protocol Files/development/jgr/scripts/jgr_lib_v1405.js) (development)

Description:

When all buffer transfers are 0 volume (i.e. final volume = sample volume for all transfers) this will create an empty array for the buffer transfer objects. This can not be handled properly by the VWorks protocol.

Probably the same problem will occur in the case of an empty source transfer array.

How to fix:

Make sure the TransferManager class handles these cases properly then skip zero-length transfer arrays in the .pro file.

Affected protocols:
ca_purification_96_v1202.pro (master), ca_purification_runset_v1202.pro (master),
ca_purification_96_v1202.pro (production), ca_purification_runset_v1202.pro (production)

Description:
When the elution is done with small volumes (seemingly less than 20 µL) there is a risk that the eluate is not transferred from the plate where the beads are collected to the final plate. The reason for this being that the droplet is not in the center of the well and is missed by the tip.

Possible fixes:

• Disable shaking during elution (implemented)
• Manually spin down elatuate before transfer
• Do not allow elution volumes less than 20 µL
• Change plate from current round-bottomed to conical

Affected file(s)

• transfer_v1506.pro
• transfer_dilution_v1506.pro
• transfer_adapter_v1301.pro

Description

The protocol accepts instructions where the transfer volume is above what the tip can hold potentially causing liquid to be aspirated into the tip filter.

Solution

Set a tip capacity value in the .pro file and limit transfer volumes to this.

Affected protocols:

• transfer_dilution_v1303.pro (master)
• transfer_dilution_lims_v1303.pro (master)

Description:
More complicated than the aliquotation protocol since the dilution protocol allows whole-plate transfers. What consequence does this have for using multiple tip boxes?

Affected protocols:

• truseq_pcr-free_setup5.pro (development)

Description:

Use another bead solution plate for the two last purifications in the runset in order to get the desired size separation. Switch the plate in the setup protocol prior to the first of the two purifications.

Affected file(s):

• jgr_lib_v1303.js (development)
• jgr_lib_v1404.js (development)
• jgr_lib_v1303.js (master)

Description:

It turns out 0-volumes are represented by an empty string in CSV files generated by the normalization process in Clarity LIMS. The parsing function can't handle an empty string where a volume is expected.

• Add back the initial bead clean-up (truseq_nano.rst, truseq_nano.js)
• Remove the use of a second bead plate (truseq_nano_setup5.pro)

1. Add centrifugation after mixing sample and reagents
2. Add tRobot incubation
3. Add possibility to do final hold
4. Add sealing of plate before 1–3 and at end (conditionally, if last protocol in runset)

Also changed:

• “With-bead” protocol in adapter ligation (beads are added once, then kept after elution and present in following reactions).
  • Implemented and tested but did not work good.
• Related to above; CA purification is separated into three modules: Bead wash, purification, elution.
  • Implemented and tested but did not work good either.
• The RoboCut size selection will be swapped out for a regular CA purification.

• Part 1: mRNA purification, fragmentation and cDNA synthesis
• Part 2: A-tailing, adapter ligation

Affected protocol(s):

• nextera_capture_hyb.pro
• nextera_capture_elute.pro

Description
Use different plates in the hybridization setup and the elution protocol depending on the number of columns of samples. By using an Eppendorf twin.tec PCR plate with conical wells the dead volume can be kept to a minimum without the same risk of pipetting errors as with the Nunc deep well plates.

Affected protocols:
truseq_ligation_v1202.pro (master)
truseq_ligation_v1202.pro (production)
truseq_ssrna_ligation_v1.0.pro (production)

Description:
The ligation mix is not distributed properly from the reagent to the reaction plate. After this step some wells are missing liquid.

Cause:
The viscosity and small volume of the ligation mix causes it to form droplets on the end of the tips during dispense that sometimes fail to detach.

Possible fixes:

• Lowering of dispense height (implemented)
• A pause was introduced to allow the operator to confirm that the mix was transferred properly (this should be removed when the problem is solved)

Affected protocols:
qpcr-384_setup_ver2.pro

Description:
Standards should be put in the first two columns and samples in columns 3 – 2 * n, where n is the number of columns of samples

In recent preps there have been beads left in several wells after the SPRI purifications. Try:

• Increase elution volume but don't transfer all of it
• Increase magnet time in elution

Affected protocols:

• jgr_lib_v1303.js (master)

Description:

• Methods for resetting tipbox state, i.e. create new Tipbox instances
• Methods for checking whether a new tipbox is needed

Affected protocols:

• Transfer protocols
  • transfer_adapter_v1301.pro
  • transfer_dilution_v1403.pro
  • transfer_v1304.pro
• TruSeq PCR-free protocols
  • illumina_double-spri.pro
  • illumina_spri.pro
  • truseq_pcr-free_ligation.pro
  • truseq_pcr-free_reaction.pro
• TruSeq RNA protocols
  • rna_prep_v1203.pro
  • truseq_ssrna_adenylation_v1.2.pro
  • truseq_ssrna_ligation_v1.0.pro
• SureSelect^XT protocols
  • A-Tailing_XT_Illumina_v1.5.pro
  • AMPureXP_XT_Illumina_runset_v1.5.pro
  • AMPureXP_XT_Illumina_v1.5.pro
  • AdapterLigation_XT_Illumina_v1.5.pro
  • Aliquot_Libraries_v1.5.pro
  • EndRepair_XT_Illumina_v1.5.pro
  • Hybridization_v1.5.pro
  • LibraryPrep_XT_Illumina_v1.5.rst
  • Post-CaptureIndexing_XT_Illumina_v1.5.pro
  • Pre-CapturePCR_XT_Illumina_v1.5.pro
  • SureSelectCapture&Wash_v1.5.rst
  • SureSelectCapture_v1.5.pro
  • SureSelectWash_v1.5.pro
• ThruPLEX protocols
  • illumina_spri.pro
  • thruplex.pro
  • thruplex_pcr.pro
• Nextera XT protocols
  • nextera.pro
  • nextera_pcr.pro
• Nextera Rapid Capture protocols
  • nextera.pro
  • nextera_capture_elute.pro
  • nextera_capture_hyb.pro
  • nextera_capture_wash.pro
  • nextera_intermission1.pro
  • nextera_intermission2.pro
  • nextera_intermission3.pro
  • nextera_pcr.pro
  • nextera_spri.pro
• AMPureXP protocol
  • illumina_spri.pro
• qPCR setup protocol
  • qpcr-384_setup_ver2.pro
• CA purifiation protocol
  • ca_purification_96_v1202.pro
• RoboCut protocol
  • robocut2_v1202.pro

Description:

Define source plate processes to have barcode on east side.

Affected protocols:
transfer_v1303.pro (master)

Description:
Try to use Change Instance task to accomplish this

A deadlock is triggered when:

1. Moving UsedTips from Bravo-3 to Bravo-8
2. Moving Nunc plate from Bravo-7 to Bravo-3

Rename jgr_lib_v1***.js to something like transfer_lib.js and keep a single version. This is to reflect that the code is only used for the transfer protocols.

Make a separate protocol file for full-plate setups, started in qpcr-384_setup_12_cols.pro

Affected protocols:

2ul-aliquotation.VWForm
general_transfer.pro

Description:

The liquid is not always dispensed successfully because a small volume is transferred to an empty plate.

Description:
The robot performs liquid transfers with 0 µL volume. The parsing function should ignore these. This problem lies in jgr_lib_v130*.js script files.

1. Add centrifugation after mixing sample and reagents
2. Add tRobot incubation
3. Add possibility to do final hold
4. Add sealing of plate before 1–3 and at end (conditionally, if last protocol in runset)

Description

Add an option to select the AB-0800 PCR plate as destination plate in the transfer protocols. This plate type will be used to send samples for genotyping.

Description

LIMS container ID's are of format 27-nnnnn which are sorted alphabetically by the transfer file parser because it contains the non-numeric - character. This is confusing when placing plates in the correct order on the robot because it's logical to assume 27-987 goes before 27-1234.

Solution

Implement a special case sort in transfer_lib.js when plate ID's match the LIMS format.

Affected protocols:

• All the transfer protocols

Description:

There may be an issue with tips sometimes, though very rarely, getting attached to the underside of the flat part of the head due to static electricity. A workaround for this could be to change which side of the head tips are mounted on. By using A12 instead of A1 and picking tips from the left side of the box, the head should not come in contact with other tips in the box.

This requires:

• Changing head mode in the .pro files
• Moving where labware are placed so that the wells are accessible
• Rewrite the TipBox class in transfer_lib.js

Affected protocols:

• transfer_dilution_v1303.pro (master)
• transfer_dilution_lims_v1303.pro (master)

Description:
Add support for multiple source plates as in the aliquotation variant.

• (Script) Sort transfers on plate ID before creating transfer objects
• (Script) Set first dilution transfer of each plate to use a new tip
• (VWorks) Go through iteration loop, make sure tip handlings works

Affected protocol(s):

covaris_transfer.pro (master)

Decription:

To avoid clogging the tips with residue foil, use separate tips for piercing the seal and pipetting.