A San Francisco-based company that performs cancer tissue genomic analysis sought to increase laboratory throughput, efficiency, and automation with GenoLogics Clarity LIMS. After success with the initial implementation, they decided to upgrade to the newest version and automate additional assays.  As part of the upgrade, they also wanted to integrate BarTender® with Clarity LIMS.  The LIMS team engaged CSols Inc. to perform the Clarity LIMS upgrade, automate new assays, and integrate BarTender® label automation.


The primary goal of the project was to upgrade Clarity LIMS to leverage new functionality, incorporate new version functionality, and integrate BarTender®. All previously automated assays and processes needed to function appropriately in the new LIMS.


  1. Tight project schedule for the upgrade and the related enhancements
  2. Minimal client resources were available to support the upgrade and BarTender® integration
  3. There were few subject matter experts (SMEs) available to develop, implement, and test the new assay configuration
  4. Access and security parameters between BarTender®
  5. Security and permission settings did not overlap between the BarTender® windows server and Clarity LIMS server
  6. Both Python and Groovy were in use for existing extensions and integrations of Clarity LIMS

CSols’s Role in the Solution

To overcome these challenges, CSols

  • Provided project management services
    • Developed work breakdown structure
    • Scheduled tasks
    • Facilitated communications among stakeholder groups
    • Managed internal and contractor resources
      • Added CSols resources to ensure that all milestones were met
    • Performed requirements gathering and documentation
      • Developed functional requirements specifications (FRS)
    • Supported Clarity LIMS version upgrade
      • Documented upgrade changes
      • Migrated steps, scripts, services, and setup data to the new version
    • Developed and implemented Clarity LIMS enhancements
      • Developed Clarity LIMS workflow for a new assay
        • Automated plate mapping
      • Developed and implemented new Illumina® HiSeq instrument interface
      • Developed and implemented BarTender® integration


  • Optimized workflows in the upgraded version increased laboratory effectiveness
  • Newly implemented features improved laboratory efficiency
  • Robust integrations of BarTender® and Illumina® HiSeq increased scientist and technician productivity
  • Additional Clarity LIMS capabilities improved the user experience, leader to greater system utilization
  • CSols’s effective project management maximized the consulting budget: the project was completed 60 hours under budget

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