Partners: Hal Holmes, Misa Winters, and Cifeng Fang
SSEC Engineers: Aniket Fadia and Carlos Garcia Jurado Suarez
Research Goals and Domain
Genetic testing is routinely relied upon to detect the illegal trafficking of wildlife, the introduction of invasive species and pathogens, as well as monitor disease spread or outbreaks that can devastate the health of our ecosystems and communities.
Software Problem
Few commercial diagnostic developers feel an incentive to address the huge need for new tests and focus on only a small number of human diseases. There are major technical barriers in accessing reference genetic data necessary to develop tests, as these data are dispersed across public and private databases, resulting in inaccuracies or unreliable metadata. As such, the creation of new assays using these data is time-consuming and inefficient.
Software Solution
SSEC worked with Conservation X Labs to build an easy-to-use platform that enables researchers to rapidly create genetic tests for every pest, pathogen, or species in the field. The Streamlit application aggregates data from a variety of different databases and provides downstream steps in selecting various parts of the genome, loading files, and allowing for downloads as well as file manipulation.
Impact
These tools will streamline development of tests and assays, resulting in ~3x efficiency gains in the assay development process. Everyone from geneticists and assay designers to epidemiologists and resource managers will benefit from this platform, enabling better monitoring and protection of vulnerable ecosystems.