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

Protocol

• namespace: common
• slug: proteowizard-msconvert
• version: v1.0.0
• changelog:
  • First release
    • msconvert command line arguments are captured via pipeline config on TDP

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.