Description

This package contains configuration and plugins to import results from the Agilent Bioanalyzer 2100 Expert Software into SLIMS.

The package contains the following entities:

  • Two plugins:
    • Bioanalyzer result import
      • The result import plugin can import Peak concentration and Region concentration result files in the XML format.
    • Bioanalyzer sample sheet export
  • Two tests:
    • Bioanalyzer peak concentration (ng/μl)
    • Bioanalyzer region concentration (pg/μl)
  • Ten custom fields on Result:
    • Observation: A field of type Text box.
    • Fragment size: A field of type quantity and dimension DNA/RNA length, with default unit BP.
    • Average size: A field of type quantity and dimension DNA/RNA length, with default unit BP.
    • Molarity: A field of type quantity and dimension molarity, with default unit M.
    • Area: A field of type quantity and dimension scalar, with default unit blank.
    • Height: A field of type quantity and dimension scalar, with default unit blank.
    • % Total: A field of type decimal number.
    • Start base pair: A field of type quantity and dimension DNA/RNA length, with default unit BP.
    • End base pair: A field of type quantity and dimension DNA/RNA length, with default unit BP.
    • Peak width: A field of type quantity and dimension scalar, with default unit blank.
  • Two custom fields on Content: 
    • Comment: A field of type Short text.
    • Rest. Digest: A field of type Checkbox.
  • A grid template: 
    • Bioanalyzer sample sheet

How to use the package

Pre-requisites

  • The results should be exported from Agilent Bioanalyzer 2100 Expert Software in XML format.
  • Units: The package contains the minimum necessary units for the tests’ configuration (e.g. nt, bp, nmol/l…). However, it is recommended to install the SI Unit package and the Molar concentration unit packages.
  • SLIMS GATE must be running.

Configuration

Result import plugin

The plugin is configured to have two flows (flowConfigurations):

  • bioanalyzerElectrophoresisPeakConcentrationImportResult (import the Peak Concentration)
  • bioanalyzerElectrophoresisRegionConcentrationImportResult (import the Region Concentration)

The following parameters are set to the specifics needed for the Bioanalyzer import:

  • fileProperties:
    • xPathToSamples: “/Chipset/Chips/Chip/Files/File/Samples/Sample” is the XPath where samples are searched in the file.
    • ignoreTree: Samples missing a value for Name are ignored (without causing an error).
  • fileHeaders: The list of test properties imported from the file and their mapping to SLIMS fields.
    • Peak Concentration test will import the Concentration as the result value (with the unit found in the file “/Chipset/Chips/Chip/AssayBody/DAAssaySetpoints/DAMAssayInfoMolecular/ConcentrationUnit”) and the following properties as result fields:
      • PercentTotal
      • Area
      • Height
      • PeakWidth
      • Molarity
      • FragmentSize
      • Observations
    • Region Concentration test will import the RegionConcentration as the result value (with the unit found in the file “/Chipset/Chips/Chip/AssayBody/DAAssaySetpoints/DAMAssayInfoMolecular/ConcentrationUnit”) and the following properties as result fields:
      • AverageSize
      • StartBasePair
      • EndBasePair
      • PercentTotal
      • RegionMolarity

Sample Sheet Export Plugin

The proposed configuration of the plugin is for the assays that have the following columns: “Sample Name,” “Sample Comment,” “Rest. Digest,” and “Observation.” The assays concerned are: DNA 1000, DNA 7500, DNA 12000, and High Sensitivity DNA Assay.

It is possible to adapt the configuration of the plugin for the assays that have the columns “Sample Name” and “Sample Comment” for the following assays: Eukaryote Total RNA Nano, Eukaryote Total RNA Pico, mRNA Nano, mRNA Pico, Plant RNA Nano, Plant RNA Pico, Prokaryote Total RNA Nano, Prokaryote Total RNA Pico, and Small RNA.

To adapt it, the following configuration changes are needed, but only involve the parameter “thymeleafTemplate”:

  • First line (defining the headers of the columns) needs to be adapted like this in order to have only two column headers:
    • replace: “Sample Name\”,\”Sample Comment\”,\”Rest. Digest\”,\”Observation\” by: “Sample Name\”,\”Sample Comment\”
  • In the loop over the columns we need to change the boundary:
    • replace “2” with “1”

    • It should looks like:

      thymeleafTemplate: "\
        \"Sample Name\",\"Sample Comment\"\
        [# th:each=\"row,rowIter:${grid.rows}\"]\
           [# th:each=\"column,columnStat:${row.columns}\" th:if=\"!${rowIter.first}\"]\
              [(${columnStat.index} < 1 ?(${column.value} == null ?'':${column.value}) + ',': '' )]\
              [(${columnStat.index} == 1 ?(${column.value} == null ?',':${column.value}+','):'')]\
           [/]\n\
        [/]\
        \n\
        \"Chip Lot #\",\"Reagent Kit Lot #\"\n\
        ,\n\
        \n\
        \"QC1 Min [%]\",\"QC1 Max [%]\",\"QC2 Min [%]\",\"QC2 Max [%]\"\n\
        ,,,\n\
        \n\
        \"Chip Comment\"\
        "

You can use the tests and SLIMS GATE flows in any “Result” protocol step of your workflow.

Where to Look Next

These references have further information on how to configure or use the package contents after the initial installation and integration.

  • SLIMS Administration Manual:
    • Miscellaneous > Plugins Module
    • Miscellaneous > Fields > Custom Fields
    • Electronic Lab Notebook > Tests and Test groups
    • Reporting and Grids > Grid templates
    • Workflows
  • Plugin configuration details can be requested from your Agilent SLIMS Administrator.