Normalization Buffer Volumes

Available from: Clarity LIMS v1.0

This section discusses the normalizationBufferVolumes script, which is used to calculate buffer volumes.

Script Overview

The normalizationBufferVolumes script generates a comma-separated file — Normalization buffer volumes.csv — file that holds the calculated buffer volumes information. The generated file is a attached to the Library Normalization step in the LIMS.

The script calculates the 'Volume of Dilution Buffer (uL)' as follows:

  • "Volume of Dilution Buffer (uL)" = ( ("Source Volume (uL)" * "Source Conc.") / "Destination Conc." ) - "Source Volume (uL)"

⚠️ The script

  • requires that input samples to the step have Concentration and Conc. Units UDFs.

  • only supports Conc. Units of nM.

Script Parameters

Parameter

Description

-u {username}

(Required) LIMS login username (Requires admin credentials)

-p {password}

(Required) LIMS login password

-i {URI}

(Required) LIMS process URI

-c {filename}

(Required) Normalization Buffer Volumes CSV file name

Command Line Example

Example
bash -l -c "/opt/gls/clarity/bin/java -jar \
/opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:normalizationBufferVolumes \
-i {processURI:v2:http} \
-u {username} \
-p {password} \
-c {compoundOutputFileLuid0}

Configuration

The following step UDFs are configured on the Library Normalization step:

  • Library volume (ul) transferred to DESTINATION plate: Numeric, Default = 10

  • Normalized conc. (nM): Numeric, Default = 2

  • Maximum destination container volume (ul): Numeric, Default = 800

The inputs to the step must have values for the following sample UDFs:

  • Concentration: Numeric

  • Conc. Units: Single Line Text

Rules & constraints

  • One sample input generates one sample output and one shared result file.

  • The CSV file header contains the date and a record of the user who generated the file.

  • The contents of the CSV file are ordered by source plate and then source well.

Additional information

Other scripts you may find useful:

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