Rachel Karchin, professor of biomedical engineering at Johns Hopkins University, is among this year’s cohort of scientists selected to receive funding from the Chan Zuckerberg Initiative. Through this program, $3.8 million in funding will be shared among 23 projects that support open source software essential to biomedical research, enabling software maintenance, growth, development, and community engagement.
Karchin and her team are developing OpenCRAVAT, an open source, scalable decision support system for genomic research. Because large-scale genomic studies identify hundreds of small differences in genes between individuals, researchers must determine which of these variants are mostly likely to contribute to the disease or trait being studied. OpenCRAVAT helps researchers prioritize which variants and genes to pursue for further studies through a dynamic graphical user interface that allows users to easily download tools from an extensive resource catalog, create customized pipelines, run jobs at speeds that exceed current variant annotation services, and explore results in a richly detailed viewing environment. The system is designed to be open and modular in order to maximize community and developer involvement. As a result, it is being actively developed, and continues to grow larger every month.
“With this grant, OpenCRAVAT will strive to improve several aspects of biomedical research — to better understand the impact of genetic variants, improve bioinformatics education, and increase the engagement of the scientific community on variant annotation and interpretation,” said Kymberleigh Pagel, assistant research scientist in the Karchin lab and principal developer of OpenCRAVAT.