Cornell University, Institute of Biotechnology

Program ID:Cornell-Institute of Biotechnology-BIBIOSOFTWARE [#22018, WDR-00032206]
Program Title: Research Software Engineer, Breeding Insight Program
Program Type:Non tenure-track faculty
Location:Ithaca, New York 14853, United States [map] sort by distance
Subject Areas: Molecular Biology
Bioinformatics / Biological Informatics
Genetics / Plant, animal, Quantitative
Appl Deadline: finished (2022/07/01, finished 2023/10/21)
Description:   URMs Remote  

*** this program has been closed and new applications are no longer accepted. ***

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:

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. 

Familiarize yourself with Cornell’s COVID-19 workplace guidance as well as the university’s COVID-19 services and information

Employment Assistance:

For specific questions about the position or application process, please contact the Recruiter listed in the job posting or for general questions email

If you require an accommodation for a disability in order to complete an employment application or to participate in the recruiting process, you are encouraged to contact Cornell University's Office of Institutional Equity and Title IX at voice (607) 255-2242, or email at

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EEO Statement:

Diversity and Inclusion are a part of Cornell University’s heritage. We are a recognized employer and educator valuing AA/EEO, and we do not tolerate discrimination based on any protected characteristic, including race, ethnic or national origin, citizenship and immigration status, color, sex/gender, pregnancy or pregnancy-related conditions, age, creed, religion, actual or perceived disability (including persons associated with such a person), arrest and/or conviction record, military or veteran status, sexual orientation, gender expression and/or identity, an individual’s genetic information, domestic violence victim status, familial status, marital status, or any other characteristic protected by applicable federal, state, or local law. We also recognize a lawful preference in employment practices for Native Americans living on or near Indian reservations in accordance with applicable law. 

Cornell University embraces diversity and seeks candidates who will contribute to a climate that supports students, faculty, and staff to all identities and backgrounds. We encourage individuals from underrepresented and/or marginalized identities to apply.

Pay Ranges:

The hiring rate of pay for the successful candidate will be determined considering the following criteria:

  • Prior relevant work or industry experience.
  • Education level to the extent education is relevant to the position.
  • Academic Discipline (faculty pay ranges reflects 9-month annual salary)
  • Unique applicable skills.

Application Materials Required:
Submit the following items online at this website to complete your application:
And anything else requested in the description.

Further Info:
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