2022.05_3 Artifact Release

RELEASE DATE: May 17, 2022

Enhancements (New Features and Functionality)

DE-3759 PerkinElmer LabChip GXII Touch
  • IDS

    • namespace: common
    • slug: plate-reader-perkinelmer-labchip
    • version: v4.0.0
    • changelog:
      • Add support for <experiment-name>_WellTable.csv export files
      • Add support for <experiment-name>_Data_<sample-label>.csv export files
      • Add support for <sample-name>_<experiment-name>_Egram_<sample-label>.Tif export images
      • Add support for <sample-name>_<experiment-name>_Gel_<sample-label>.Tif export images
      • Add field systems[*].software
      • Move field samples[*].location.holder.plate_file to methods[*].file_name
      • Remove requirement for field results[*].chip_id
      • Add field methods[*].assay_name
      • Add field methods[*].size_unit
      • Add field methods[*].concentration_unit
      • Add field methods[*].data.frequency
      • Add field methods[*].data.start_time
      • Add field methods[*].data.end_time
      • Add field methods[*].ladder_sizes[*]
      • Add field methods[*].size_unit
      • Move field results[*].acquisition_time to results[*].time.acquired
      • Add field results[*].analysis_error
      • Add field results[*].calibration.slope
      • Add field results[*].calibration.intercept
      • Add field results[*].ladder_quality_score
      • Add field results[*].peak_count.total
      • Add field results[*].peak_count.expected
      • Add field results[*].peak_count.filtered
      • Add field results[*].electropherogram_image
      • Add field results[*].gel_image
      • Add field results[*].total_concentration
      • Convert field results[*].peaks[*].concentration from type number to value_unit_object
      • Add field results[*].time.zero
      • Rename field results[*].well_position to results[*].position to maintain key consistency with join field source samples[*].location.position
      • Move field results[*].peaks[*].signal_noise to results[*].signal_noise as signal_noise values are unique per well, not per peak
      • Move field results[*].peaks[*].comments to results[*].comments as comments are unique per well, not per peak
      • Add top level field datacubes to capture raw data from <experiment-name>_Data_<sample-label>.csv files
      • Rename results[*].plate_index to results[*].holder_index and set as required
      • Remove requirement for field results[*].peaks[*].number
      • Remove requirement for field results[*].peaks[*].index
      • Remove requirement for field results[*].peaks[*].type
      • Remove requirement for field results[*].peaks[*].concentration
      • Remove requirement for field results[*].peaks[*].expected_protein
      • Remove requirement for field results[*].peaks[*].baseline
      • Remove requirement for field results[*].peaks[*].signal_noise
      • Remove requirement for field results[*].peaks[*].height
      • Remove requirement for field results[*].peaks[*].area
      • Remove requirement for field results[*].peaks[*].full_width_at_half_maximum
      • Remove requirement for field results[*].peaks[*].migration_time
  • Protocol

    • namespace: common
    • slug: perkinelmer-labchip-gxii-touch-raw-to-ids
    • version: v2.2.0
    • changelog:
      • Update to use task script common/perkinelmer-labchip-gxii-touch-raw-to-ids:v4.0.0
  • Task Script

    • namespace: common
    • slug: perkinelmer-labchip-gxii-touch-raw-to-ids
    • version: v4.0.0
    • changelog:
      • Use IDS versionv4.0.0
      • Add support for more export files
        • *_WellTable.csv
        • *_Data_<well-label>.csv
        • *_Electropherogram_<well-label>.tif
        • *_Gel_<well-label>.tif
DE-3752 Xcalibur - ProteoWizard raw to mzML
  • Protocol

    • namespace: common
    • slug: proteowizard-msconvert
    • version: v1.0.0
    • changelog:
      • First release
        • msconvert command line arguments are captured via pipeline config on TDP
DE-3548 Shimadzu -- Can not output chromatograms data for some LCD data files
  • Task Script

    • namespace: common
    • slug: shimadzu-windows
    • version: v1.0.5
    • changelog:
      • Add ChannelNumber to LSSChromatogramObjectNumber object, since some of the chromatogram data is reading by channel number now.
      • Add a new checking for the number of LSS and PDA chromatogram objects. We could read a number from Shimadzu API and compare it with number of objects in our list and make sure those two numbers are equal. If not, output error message.
      • Update Shimadzu API from 3.5.0 to 3.8.1
      • Add unit test project.
      • Update all the sample files.

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