A Free Open-Source Library for BaseSpace Clarity LIMS

Built for Developers. Optimized for Laboratories.

A Modern Python Library for Clarity LIMS

After years of BaseSpace Clarity LIMS implementations and extensions, we are pleased to share a free open-source library for Clarity LIMS users built by our LIMS engineers. The Semaphore Clarity Library makes complex sample management easier, letting you easily codify your lab process. BaseSpace Clarity LIMS enables thorough customization to your laboratory environment through the use of the Rapid Scripting Application Programming Interface (API). Reduce the effort to write scripts, allowing rapid automation of workflows.


Simplify file-based integration between Clarity and lab Instruments.


Dynamically create pools while avoiding adapter conflicts.


Plate sample replicates in a specific layout.


Organize samples to different workflows based on sample properties.


Generate worksheets without leaving Clarity. No more copy-pasting values to and from Excel.


Apply custom quality control (QC) flags applicable to your laboratory standards.

Build Auto Workflow Tests

Our library provides developers auto testing tools for building workflow scripts that push samples through Clarity steps without user interaction. These scripts enable developers to automate regression testing, which is critical to ensuring current and new code and features are not adversely affected by updates made in a workflow. Improve your lab with confidence and assure that new code changes will not have side effects on the existing functionalities. 

Increase Automated Workflows

Incorporate the Semaphore Clarity Library at any stage of your Clarity implementation. Improve laboratory efficiency by replacing manual processes with automatic scripted processes. For example, use scripts to replace calculations performed in Excel and then are manually inputted into Clarity. Our library enables LIMS developers to create automated workflows and to build workflows based on business rules. Allow your lab technicians to manage standard laboratory processes, such as rework, with very little manual LIMS interaction. 

Scale Clarity LIMS

Quickly adapt your LIMS as your laboratory grows.  New scripts (EPPs, DSAs, and shell scripts) can be developed and tested with minimal effort.   We built the library to be flexible regardless of the stage of your implementation and there is no need to replace any existing code. Your developers can extend your BaseSpace Clarity LIMS implementation with confidence. 

Take advantage of a library that our LIMS engineers have refined over years implementing Clarity LIMS. Clarity developers can skip the boilerplate, letting them spend more time on the laboratory’s business needs.

We deliver software services to support our clients’ growth.

Software Development, DevOps, Quality Assurance, Architecture User, and Interface/User Experience.

We offer additional services in Project Management, Business Analysis and Process Consultation. We are available to augment a software team with a single expert, or provide a full team to complete and maintain feature or project.

Semaphore is trusted by these incredible partners

“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 exciting to work with such an attentive and collaborative team, especially during complex design and implementations."

Tony Le, Product Manager

Let’s start the conversation

We build Next Generation Sequencing (NGS) Information Systems for leading genomics laboratories across the world. Let our software experts support your team in reaching their laboratory goals.

Contact us for a free consultation.

1 (844) 744-3577 ext 1

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Victoria, BC V8W 1C4