Breeding Insight is hiring!
Join us in the first large-scale public-sector effort to systematically apply genomic information to the breeding of specialty crops and animals. Our dynamic, multidisciplinary team of specialists at Cornell University is growing!
IT Team Positions
We seek an Applications Developer III to join a software engineering team as a part of the Breeding Insight platform project. With the support of the USDA-ARS, the Breeding Insight platform at Cornell University is the first large-scale public-sector effort to systematically apply genomic information to the breeding of specialty crops and animals. The project will develop and implement breeding and genomic data management systems to enhance the capacity of public-sector breeding programs to deliver increased rates of genetic gain. The breeding, genomic, and phenotypic data management systems will include databases, analytics, and decision support tools for breeders. A wide range of open source tools and platforms have already been built for breeding efforts in major crops and animals. This project will leverage these software development efforts, and focus on integration, cloud deployment, and ease of use for small breeding programs.
The developer in this role will code, test, debug, document and maintain highly complex programs or systems that make up the Breeding Insight platform stack under the direction of senior developers. They will collaborate with other software development teams to co-develop features needed by both teams. This role will offer software support in the form of analyzing and amending software errors in a timely and accurate fashion, performing code reviews for peers, and maintaining, updating, and improving existing applications.
This developer will ensure that test cases mimic external interfaces, implement automated testing routines to test functionality and stress, validate test routines and schedules, and evaluate code to ensure that it is valid, is properly structured, meets industry standards and is compatible with browsers, devices, or operating systems.
The incumbent will be part of a team of database/application developers and DevOps engineers, and will report directly to the Breeding Insight platform Lead Developer.
The project team at Cornell will be responsible for rapid cycle development of software, deployment in the cloud, coordination of genomic profiling, and integration with related initiatives at Cornell, nationally, and internationally. Tool development will be structured around a clear development cycle. Tool deployment will be followed by feedback from the breeders for further customization and improvement, mediated by application specialists. The success of the project will depend on tools and algorithmic solutions becoming fully integrated into the ARS and US breeding programs. Long-term success will be based on evidence of a measurable increase in the rate of genetic gain in the breeding programs. Funding for the effort is initially focused on tool development and developing genomic resources, but if successful will expand to large scale implementation across all breeding programs.
Science Team Positions
The Breeding Insight Biometrics Coordinator will lead the integration of statistical analyses from genotypic and phenotypic data to provide breeding-decision support efforts for USDA-ARS specialty plant and animal breeders. The Coordinator, in concert with the science and software engineering teams, will work as part of a national initiative to extend the application of genotypic information to routine development of specialty crops and animals. Breeding of specialty crops and animals has lagged behind major crops and livestock, 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 natural variation 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 Biometrics Coordinator will have expertise on applying genetic principles to enable interpretation of biological phenomena and provide information that guide strategies and optimize resources in specialty breeding programs.
The Biometrics Coordinator is responsible for working directly with the breeders to assist them in implementing optimal experimental and trial design, data processing for statistical analyses, and contribute to breeding decisions support tool creation at BI. The Biometrics Coordinator will also participate in weekly meetings, annual site visits, and provide breeding decision support. Through the process of supporting these programs, the Biometrics Coordinator will gain the experience necessary to set use-case and development priorities.
The Biometrics Coordinator 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.
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.
We are looking to hire one researcher with a background in bioinformatics of phenomic data. Strong skills in scripting and pipeline development are necessary, as are proven written and verbal communication skills. Researchers with experience in human, animal, and non-model organisms are especially encouraged to apply.
The successful researcher will work as part of the Breeding Insight program at Cornell University to collaborate with USDA-ARS breeders on a diversity of research projects across multiple breeding programs within USDA. Primary responsibilities for this position include:
- Developing customized image analysis pipelines to extract quantitative phenotyping data for key breeding targets
- Performing statistical analyses and extracting actionable interpretations from phenotyping data
- Preparing reports, manuscripts, and presentations of research results.
This position reports to the Executive Administrative Assistant and is tasked with providing various types of technical support to both Breeding Insight Coordinators and ARS specialty crop breeders. This position also works closely with the Communications and Training Lead, Data Curators, as well as interacting with the Biotechnology Resource Center core facilities at the Institute of Biotechnology and service providers. This is an in-person or hybrid position located in Ithaca, NY (cannot be fully remote).
Primary responsibilities include:
- Traveling to USDA-ARS locations within the US and assisting ARS breeders for short-term surge support including tissue sampling prep, tagging plants, digitizing records, phenotyping support (including set up of equipment), and providing additional support as needed.
- Assisting BI Coordinators to provide support where needed for a short duration either remote or on-site, prioritized by breeding cycle demands.
- Assisting in non-standard protocol development, recommendation of modifications for optimization, and deployment.
- Assisting BI Coordinators with scheduling, designing, and developing complex experiments for genomic and phenomic data collection.
- Collection of tissue samples for DNA, RNA, protein, and metabolite extractions with moderately complex record keeping.
- Managing the BI order tracking database and assisting breeders with sample submission to service providers and/or coordinating shipments from collaborators of large-scale, multi-collaborator projects.
- Procurement of laboratory supplies, maintenance of available inventory, and management of supplies disbursement to breeding groups.
- Assisting the Communications and Training Lead in BI-led training workshops (remote, virtual, or hybrid) and creating and maintaining SOPs for BI-deployed technologies and services.
- Occasionally assist the Data curation team in preparing data for loading into BreedBase and retrieval of stored data for downstream applications.
About Breeding Insight
Breeding Insight (BI) is a U.S. Department of Agriculture (USDA) and Agricultural Research Service (ARS) initiative hosted at Cornell University in Ithaca, New York.
The Breeding Insight initiative was launched in 2018 to level the playing field in the genomics era, creating new opportunities for specialty breeders in assimilating tools, technologies, and methods to catalyze the routine and accessible use of genomic insights. We integrate phenomics (trait analysis), genomics (genotypic data), data management, and software tools to help breeders increase the rate of genetic gain and create more healthy, nutritious, and sustainable specialty crops and animals.
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