Custom Lab Application

A Hand-Crafted Solution for a Sample Accessioning Bottleneck

Manifest Import Tool

Executive Summary

Semaphore collaborated with a contract research organization (CRO) to design and build an application that lets users upload manifest CSV files and automatically import the data into the LIMS. A custom user interface streamlines the mapping of columns in the customer manifest file to the appropriate LIMS fields, resulting in a significant reduction in the time required to accession samples and great improvement in the quality of data entering the LIMS. Once a manifest is uploaded, the application validates the data at each step of the accessioning process, and tracks all edits before fully accessioning samples into the LIMS.

Challenges Semaphore Addressed

Labs that perform sequencing in support of scientific research or clinical trials generally receive their samples in a batch of tens or hundreds of samples accompanied by a sample manifest. The manifest, usually a CSV or Excel file, provides the lab with the sample metadata required to successfully process samples and report results.

Sample manifests can arrive in many different formats and labs often have to dedicate significant manual effort to edit them into a standard format that can be accessioned into their LIMS. We designed and built a solution to drastically reduce the cost and time required to accession batches of samples while also reducing errors associated with manual processes.

The Semaphore Process

Collaboration & Trust: The Semaphore team worked with the CRO laboratory team using a collaborative, agile process. By providing periodic demos of completed work, the teams were able to develop mutual trust, which was key to accelerating the project to success. 

Quality-First: Semaphore’s commitment to software engineering best practices during software building and testing supported the lab team’s high standards for laboratory quality control. Validation measures were built into the application to ensure completeness and accuracy of data, as well as adherence to HIPAA regulations.

Expert Training & Support: Semaphore thoroughly trained the CRO lab team in how to use the application. During the warranty period when the project revealed gaps in the client’s workflows, we helped their team identify and overcome the issues so that everything is now running smoothly. Additionally, we trained their internal development team so that they can maintain the application themselves.

The Semaphore Solution

Our manifest import tool application not only addressed manifest format inconsistency during sample accessioning, but also provided several key features that improved downstream business processes such as bioinformatics and data delivery. 

Key features of the app include:

  • A dashboard that allows managers to track the manifest file status.
  • An easy-to-use interface with Excel-like functionality to assist in editing of manifest data including trim, combine, and apply all functions.
  • Auto-save of in-progress work.
  • Compatibility with barcode scanners. 
  • Ability to map the physical location of individual samples within their boxes or racks.
  • Validation of data types and completeness.
  • No data deletion to satisfy HIPAA compliance.
  • Validated database.
  • Full filterable audit log. 
  • Integration with freezer management.
  • Ability to report back results in the same key-pair values that the customer submitted the sample data in.
  • Single source of truth established for incoming manifests from clients, eliminating multiple versions of Excel.


The new application provides a significantly faster method for importing patient sample data into the LIMS and one that is much less prone to error. Most importantly, perhaps, the lab staff report that the application is easy to use and has become a valuable tool in their day-to-day work. 

The client has been thrilled to see:

  • A significant boost in productivity.
  • More efficient processes.
  • Fewer data input errors.
  • Reduced costs.
  • Employees freed up to work on more complex and interesting problems.

By replacing manual processes with automatic data import, the lab has also seen an increased efficiency for creating and delivering custom data outputs for clients, and the lab is also now in a better position to scale throughput.

Interested in a custom lab application?

Laboratory System Integration
We integrate laboratory information management systems (LIMS), laboratory information systems (LIS), order and results systems, requisition provisioning, Enterprise Resource Planning (ERP), Customer Relationship Management (CRM), project management and custom portals. No matter your workflow, we make it happen.

Analysis Pipeline Integration
We support your analysis solution. Our software professionals provide efficient solutions for ensuring sequencing data securely enters your analysis platform of choice, and final reports are delivered to the right place.

Instrument Integration
Automating the exchange of setup information and result data with instruments increases laboratory efficiency and accuracy. We have experience integrating the full range of molecular diagnostic instruments, from QC instruments to sequencers to automated liquid handlers.

Electronic Medical Record (EMR) Systems Integration
EMR integration ensures that critical test and patient information enters the laboratory efficiently and error-free, and results are communicated accurately and quickly. Whether using EPIC, Cerner or another EMR system, we can integrate your laboratory systems via HL7.

Laboratory Scalability
Increasing sample throughput requires significant automation of laboratory processes and information management. Our team builds and maintains some of the highest throughput NGS labs in the world and can apply that experience to help you achieve your throughput goals.

Order Management
In addition to tracking physical samples, clinical diagnostic laboratories need to efficiently manage the orders that accompany samples. From the physician portal to the dashboard that manages order status, our customized system ensures that your lab’s orders are processed efficiently and accurately.

Business Solutions
We build custom solutions that support business process related to the laboratory workflow including Order and Result Portals, HIPAA Compliant Databases, Panel Selection Websites, Project Management Dashboards. If you can’t find off-the-shelf solutions, talk to us about how we efficiently build solutions that exactly match your requirements.

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We understand that laboratory software needs change over time. Let us support your team with a single developer or full team.

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