GUI for Massively Demultiplexed Pathogen Detection

Cross-Platform, Easy-to-use, Clean Interface

Project Information


The ability to detect the presence of a disease causing pathogen is the first step in formulating the treatment and containment strategy. Traditional pathogen detection methods rely upon the identification of agents that are already known to be associated with a particular clinical syndrome. The emerging field of metagenomics has the potential to revolutionize pathogen detection by allowing the simultaneous detection of all microorganisms in a clinical sample through the use of next-generation DNA sequencing. Over the last 20 years, the scientific community has designed individual DNA-based molecular diagnostics tests for most diseases of interest. Often times simple pathogen detection is not possible and scientists have to design test panels to detect different strains/types of a known disease. Every single test in this pathogen screening panel can adversely interact with each other and create inaccurate results. Hundreds of thousands of potential interactions need to be monitored, evaluated, and optimized during the panel design process. In short, the computational expertise needed to design such diagnostic tools is not always found in clinicians tasked with outbreak investigations.

Problem Overview

The Fofanov Lab at Northern Arizona University, has designed and implemented a software application that automatically reviews the possible interactions that arise during panel creations, scores the quality of potential panels and generally helps the user design a better diagnostic panel. This application has been widely used by researchers at NAU, but because of the Command Line Interface the application is not truly appealing to the larger biology community.


To ensure that this software is widely available to users of varying technical expertise, Dr. Fofanov and Dr. Furstenau decided to task our team with the implementation of Graphical User Interface for this application. This GUI will create a more intuitive user interface which will eliminate the challenges faced by non-technical users when using a command line based application.


Client Information

The Fofanov Bioinformatics Lab

The Fofanov Lab is part of The School of Informatics, Computing, and Cyber Systems (SICCS) at Northern Arizona University. The lab's primary area of research is in Bioinformatics. To learn more click here .


Viacheslav Fofanov, Ph.D.

Primary Contact

Tara Furstenau

Pipeline Developer
Fofanov lab
Fofanov Lab is housed in School of Informatics, Computing, and Cyber Systems (Building #90)


Cross Platform

Compatible with Mac, Linux and Windows


Easy-to-use interface


Fast loading times


Output visualizations for analysis purposes


Ability to go back and forth between analysis stages

Appealing UI

Intuitive navigation and smart window design

Design Process



Images of various stages in the development of Primacy


Our Team

A. Turan Naimey

Team Lead

Alex Lacy

Documentation Manager

Chance Nelson

Dev Ops Specialist

Austin Kelly

GUI Front End Specialist

Contact Us

Northern Arizona University
Flagstaff, AZ 86011

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