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LIMS Implementation
Lab Software

A Free Open-Source Library

for BaseSpace Clarity LIMS

by

The Semaphore Team

A Modern Python Library for Clarity LIMS

Built for Developers. Optimized for Laboratories.

Learn More on Github.

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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.

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“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, Helix

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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.

Explore our blog

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Six Types of Software Requirements in Lab Informatics and When to Use Them

Before labs implement new software, they should document everything the software needs to do. These “requirements” will ensure the software does what the lab intends. However, not all requirements are created equal. Different types serve different purposes throughout the software lifecycle.

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The Importance of Data Integrity in the Laboratory: Adhering to FDA Standards and ALCOA Principles

In today’s highly regulated laboratory environment, maintaining data integrity is not just a matter of good practice—it’s essential for compliance, reliability, and the overall success of lab operations. For lab managers and IT support staff, ensuring data integrity means safeguarding data’s accuracy, completeness, and consistency throughout its lifecycle.

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