Bio::Neos Provides Data Visualization & System Streaming Expertise with VCMap
Bio::Neos, Inc., a custom software consulting company based in Coralville, Iowa, provides full software design and development services to healthcare companies, life sciences researchers, and other scientific groups. With our strong history of providing our software development services for scientists throughout the nation, along with our scientific advisory board's decades of experience in bioinformatics research, our team is uniquely positioned to understand the problem space of our clients and provide the ideal software solutions to address them.
The Challenge
Several doctors at both the Medical College of Wisconsin (MCW) and Iowa State University (ISU) shared the desire to create a platform that would allow for the comparison of genetic elements across species. After thorough communication, the group decided to take action and created a basic Java application called VCMap. With time, it became apparent that the application needed to be overhauled, so they applied for a USDA grant – which they received. While the biological expertise was taken care of, VCMap was in need of external assistance to update the guided user interface (GUI) and quantitative trait locus (QTL) visualization.
The Solution
Beginning in 2009, Bio::Neos was approached by the VCMap group. Several features were necessary in order to modernize the VCMap genome application. First of all, the system needed to “facilitate genomic visualization that enables discovery of genetic elements responsible for quantitative trait variation.”* Secondly, the GUI must provide chromosomal viewing which optimizes QTL visualization and comparison with other species. Finally, the software and backend database must provide the functionality to allow for a plethora of annotation types to be shared across species.
The Results
With this framework, the Bio::Neos team drew from its rich background in system streaming and data visualization to create a fully-functioning and user-friendly platform. This system allowed users to choose between phenotype annotations, load their private annotations or genomic research data to help compare species, and compare different species map types. VCMap filled a “gap in the need for genomics viewers to compare QTL and annotations across species at a chromosomal level with multiple map types.”* VCMap delivered “more options to view annotations, QTL and private data, and selected subsets of this information that most other viewers cannot accommodate.”* Additionally, due to VCMap’s desktop operation design, private data never needs to be shared over the internet, leaving users with a more secure system.
*Koltes, J., Davis, S., & Hu, Z. (2012, July 04). Retrieved August 12, 2020, from https://www.animalgenome.org/VCmap/manual/v3/#3.0Bio
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