Details
Posted: 24-Jul-22
Location: Ithaca, New York
Salary: Open
Internal Number: WDR-00032539
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Bioinformatics Programmer/Analyst II
Programmer/Analyst II - Band E
Buckler Lab - https://www.maizegenetics.net/
Cornell Institute of Biotechnology - Research Division
We seek a programmer to join the Buckler Lab team at Cornell's Institute for Genomic Diversity. We are a genetics lab involved in plant genetics, genomics, and bioinformatics with numerous national and international collaborations and efforts. We work to address three main questions: How can we use genetics to make agriculture more efficient and share those efficiencies globally? How can we reduce the impact of agriculture on the environment? How does genetic variation give rise to phenotypic variation?
The Buckler group develops and maintains various software tools for genomic data storage and analysis used by the lab, plant breeders, and the genetics community in general. One key tool, the Practical Haplotype Graph (PHG), is a graph-based representation of a pangenome and associated imputation tools. The PHG is primarily written in Java and Kotlin and interacts with a SQL database system (Postgres or Sqlite) and has a BrAPI compliant Web Service written in Kotlin using the Ktor Framework. The PHG also makes use of a number of alignment tools (Anchorwave, Minimap2, and BWA Mem) as well as standard Bioinformatic tools like samtools or bcftools and is packaged into a Docker Image for easy deployment.
This position will be responsible for deploying the PHG in multiple crop species and making it accessible and usable to the breeding community by setting-up and maintaining web servers. A qualified candidate will be able to assist with coding, testing, debugging, and maintaining the tool for tasks of low to moderate complexity. The candidate will also work with our collaborators to define new use cases and implement them. The developer will be part of a team of four programmers and will also contribute (with the guidance of senior leads) in the development and deployment of other software tools used by the Buckler lab and our projects.
Excellent written and verbal communication skills, organizational skills, and attention to detail are required. Teamwork, flexibility, and an aptitude for working with a diverse group (both in background and skill set) is especially important in this office/lab environment.
Specific responsibilities include:
- Deploying the PHG system in a number of different plant species
- Assisting the other Buckler Lab programmers to update and maintain the PHG code base
- Updating and adding new features to the PHG web service of low to moderate complexity
- Unit testing and code review
- Preparing demos for lab members as well as for both national and international collaborators.
What we need:
- Bachelor's degree with up to 2 years of relevant experience in bioinformatics, computer science or a related field (or equivalent combination).
- Experience with Java, Kotlin and/or Python.
- Experience with SQL DBs such as Postgres, SQLite, etc.
- Ability to write clean, scalable/modular code though source control. GIT required
- Comfortable with Linux environment.
- Highly organized with time management skills.
- Strong communication skills
- Ability to work in a team
- Mindset for continuous learning and improvement
Additional qualifications that would be extra helpful for the position:
- Experience with Container Technologies like Docker, Singularity or Conda.
- Familiarity with Software development practices (Scrum meetings, Agile development, etc.
- Experience Deploying Web Services
- Experience Deploying Docker Containers to servers
- Background or interest in biology or relevant sciences
- Experience using Genomic Assembly and Alignment tools
This is a full-time two-year term appointment with the possibility of renewal contingent on continued funding and successful performance.
This position is a Programmer/Analyst II classification with a hiring range of $63,974 to $70,708, with initial pay considering university, unit and department equity, as well as individual compensable factors.
Benefits and reward include:
- Comprehensive health care options, generous retirement contributions, access to wellness programs, and employee discounts with local and national retail brands, and more.
- Our leave provisions include three weeks of vacation and 13 holidays: Martin Luther King, Jr. Day, Memorial Day, Juneteenth, Independence Day, Labor Day, Thanksgiving and the day after, and an end of the year winter break from December 25-January 1.
- Impressive educational benefits include tuition-free Part-Time Study and Employee Degree Program, heavily discounted eCornell courses and certificate programs, tuition aid for external education, and Cornell Children's Tuition Assistance Program.
To apply for this opportunity: please submit BOTH a cover letter and resume/CV for full consideration, ideally as one combined PDF document. You can upload documents either by "dragging and dropping" them into the dropbox or by using the "upload" icon on the application page. For more detailed instructions on how to apply to a job at Cornell, visit How We Hire on the HR website. If you are an internal employee, please log in to Workday.
Please note: No visa sponsorship available for this position.
University Job Title:
Prog Analyst II
Job Family:
Information Technology
Level:
E
Pay Rate Type:
Salary
Company:
Endowed
Contact Name:
Emily Sampson
Number of Openings:
1
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Prior relevant work or industry experience.
Education level to the extent education is relevant to the position.
Unique applicable skills.
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Diversity and Inclusion are a part of Cornell University's heritage. We are a recognized employer and educator valuing AA/EEO, Protected Veterans and Individuals with Disabilities. We also recognize a lawful preference in employment practices for Native Americans living on or near Indian reservations. Cornell University is an innovative Ivy League university and a great place to work. Our inclusive community of scholars, students, and staff impart an uncommon sense of larger purpose, and contribute creative ideas to further the university's mission of teaching, discovery, and engagement.
2022-07-22-07:00
