The Semaphore Solution:

The Semaphore Solution: An integrated LIMS for a Large Scale Molecular & Genomic Pathology Hospital Laboratory


About the Laboratory

This large scale Molecular and Genomic Laboratory is connected to a hospital, and as such is responsible for the analysis of a high volume of clinically significant samples. This highly complex, state of the art laboratory runs many different types of analyses and is staffed with a large team.

Executive Summary

Genomic laboratories have complex workflows. From accessioning through to analysis, the number of possible interactions between sample, staff, and instrument can be overwhelming.  Many labs purchase Laboratory Information Management System (LIMS) software planning to streamline, regulate, and document workflows. LIMS systems are often employed directly out of the box with great success, but sometimes they require extra configuration to best support the specific needs of complex genomic laboratories.

Semaphore Solutions understands that when it comes to LIMS, one size does not fit all. As an Illumina Partner, Semaphore specializes in BaseSpace Clarity LIMS implementation, configuration, and support. With years of experience in Clarity configuration, Semaphore’s development team is expert at building laboratory solutions. Our team members are also experts at integrating LIMS with Electronic Medical Record systems (EMR’s) via HL7.

An American hospital laboratory found their needs exceeded out of the box LIMS capabilities, and asked Semaphore Solutions for a customized BaseSpace Clarity LIMS. 

Challenges Semaphore Addressed

Like many other complex genomic laboratories, this lab found that tasks such as repetitive paperwork, data entry, and by-hand calculations took time away from lab technicians doing their actual job: analyzing clinical samples.

They needed a LIMS that aligned with their workflow while eliminating redundancy and streamlining process. They also required a LIMS that could be fully integrated into their existing EMR and LIS. Semaphore worked closely with the lab management staff to help them meet all of these requirements. Through teamwork and an open, iterative process, Semaphore was able to provide a custom solution that spanned the entire laboratory workflow: 

The Semaphore Solution

Accessioning: Semaphore developers are proficient in HL7, allowing them to build a custom User Interface and integrate it with pre-existing Laboratory Information Systems (LIS’s) and Electronic Medical Records (EMR’s). The integration with the pre-existing LIS enables Accessions staff to continue working with the software they already know and trust, but with the advanced functionality of BaseSpace Clarity LIMS.

Sample Processing: All extraction protocols are batched to increase efficiency and reduce lag time. A barcode is generated for each sample to allow for easy re-extraction later on.

Analysis Preperation: Semaphore automates plate assignments, reagent calculations, and dissolution tables. The automation of repetitive tasks reduces the potential for human error while saving time and money.

Benchtop Support: Bench notes are automatically generated and displayed on tablets to ensure placement tables, calculations, notes, and reminders are kept handy at each workstation. Comprehensive, easily accessible bench notes enable lab technicians to remain focused on the task at hand.

Instrument integration: Bi-directional instrument integration enables lab staff to skip data entry and get straight to work. Output automatically feeds back into the LIMS, enabling quick turnaround between testing and delivering results.

Internal Documentation: An internal tracking report is generated for each sample, simplifying retroactive reporting of analytic factors. Tracking reports are especially useful for audits and accreditation.


This Large Scale Molecular & Genomic Pathology laboratory required a customized, fully integrated LIMS to track and manage complex daily workflow. Semaphore’s dedicated development team were able to meet their needs by creating custom solutions across all stages of the laboratory workflow.


  • A reduction in repetitive tasks enabled lab technicians to focus more on sample analysis and less on paperwork.

  • Batched protocols increased efficiency and reduced accession-to-report time.

  • Internal tracking mechanisms allowed for transparency into all lab processes, ensuring consistency and quality.

  • Integration with pre-existing EMR  and LIS  simplified accessioning and enabled ordering physicians to view results sooner.

Technologies: PCR, NanoDrop, Mass Spec, HL7, Assays

Order and Resulting Integration
We integrate Clarity LIMS with order and results systems, laboratory information systems (LIS), requisition provisioning (ERP), CRM, project management or in-place custom portals. No matter your workflow, we can deliver on your integration requirements.

Analysis Pipeline Integration
We support your analysis pipeline solution. No matter how complex, our software professionals provide efficient solutions for ensuring your sequencing data securely enters your analysis platform of choice.

Commercial Off the Shelf (COTS) Implementation
Implementing a new system is complex. Your business includes many pieces of software that needs to connect. We support you as you select your COTS and help integrate the missing pieces.

Business Analysis 
An effective software solution requires a solid business analysis. Our team excels in providing relevant documentation and requirements to the right stakeholder. 

Software Architecture 
A software solution is reliable, maintainable and scalable. This requires smart and robust software architecture. Our team develops well-designed and appropriate architecture for each software solution. 

Integrations Services
Your technology solution or system has several moving parts. We provide integration services for complex solutions. We enable complicated systems to reliably to communicate with each other. We ensure the reduction of manual errors and the creation of greater efficiencies.  

Software Modernization
Technology improves everyday and programming frameworks and languages shift. The day arrives when your software solution needs an update. We understand the complexity of a software upgrade for your business processes and staff. We provide software modernization services customized to your business requirements. 

User Experience Design 
We offer User Experience (UX) design services to our clients. Our professional team collaborates with customer stakeholders to develop effective user interfaces. 

“Semaphore provides software expertise for Helix’s Clarity LIMS implementation. They have provided excellent project management, technical leadership, and quality software development that was crucial to the successful launch of our high volume lab. It’s refreshing to collaborate with an attentive team during complex implementations.”

Tony Le, Product Manager