Description

The Research Software Engineer will lead the creation and development of biologically tailored software and applications for integration with Breeding Insight's core software platform to enhance breeding decisions for USDA-ARS specialty plant and animal breeders. This position, in concert with the science and software engineering teams, will work as part of a national initiative within the USDA-ARS to extend the application and use of genotypic information to routine development of specialty crops and animals. Breeding of specialty crops and animals has lagged behind major crops and livestock in funding and technology advances, though these specialty species together have equal economic value to the major crops and provide valuable nutrition and flavor to diets. One of Breeding Insight’s aims is to accelerate breeding efforts by integrating the use of phenomics (trait analysis) with genomics and integrated web-based software to increase the rate of genetic gain to create healthy, nutritious, and sustainable specialty crops and animals.  Breeding Insight currently supports 18 ARS breeding programs.

The Research Software Engineer will have expertise in creating biological software with easy-to-use user interfaces for isolated analyses and data visualization, such as, but not limited to, image analysis phenotypic data extraction, interpreting sensor and/or drone data as phenotypes, and data visualization in user-friendly interfaces.  The Research Software Engineer will also participate in weekly meetings, annual site visits, and provide breeder support. Through the process of supporting these programs, the Research Software Engineer will gain the experience necessary to set use-case and development priorities.

The Research Software Engineer will be a highly visible person central to the success of Breeding Insight and will report to the Breeding Coordinator. The Breeding Insight project integrates a team of USDA-ARS breeders (based at research locations across the US), with a scientific team and a software development team.

Characteristic Duties and Responsibilities/Anticipated Division of Time:

• Coordinates with breeders at multiple breeding locations across the US to understand their breeding objectives, data analytic needs, and to manage project deliverables. 30%
  
• Works with PIs and breeders at USDA centers and universities to develop workflows for genomic-phenomic data analyses, specify use-cases that clearly spell out the computational and interface requirements of the breeders, and form project plans to develop key capabilities and integrate Breeding Insight into each breeding program. 25%
• Overall, combines these communications into a regular process in conjunction with the development cycle implemented by the software team to ensure a well-defined roadmap of new methods and features. 25%
• In communication with breeders, designs and helps execute evaluation experiments and analyses of features introduced by Breeding Insight on which follow-up requirement documents are based. 20%

Required Qualifications:

A Ph.D. in the field of quantitative genetics, molecular breeding, plant or animal genetics, biological informatics, molecular biology, or related field, plus three years’ postdoctoral or equivalent post PhD experience is required. This position will be recruited based on core competency in several different areas, including a demonstrated proficiency creating applications with user-friendly UIs for data analyses and visualization.  The ability to develop pipeline analyses for large data sets and interpret results for efficient decision making is required.  Must be proficient in Python, shell scripting, R, RShiny (or similar), JupyterHub and JupyterNotebook.  Must have some experience in linkage mapping, QTL studies, genomic selection, bioinformatics, and project management.  Experience with multiple animals or crops, and experience working with diverse teams are preferred. Knowledge of information technologies, analytics, and methods appropriate for polyploid genomic data and/or image analysis are beneficial.  Above all, the incumbent must have demonstrated exceptional verbal and written communication skills. 

This position is a two-year term appointment with the possibility of extension contingent upon continued funding.

Remote or hybrid remote work arrangements within the United States possible under appropriate circumstances.