"Scientific Programmer - PACC"

Position Summary

The Genomic & Bioinformatics Analysis Resource (GenBAR) of the Columbia Precision Medicine Initiative, is a unique interdisciplinary research environment specializing in human genetics and genomics. GenBAR is a key part of Columbia University's Precision Medicine Initiative to create a cohesive, university-wide research and teaching environment for human genetics/genomics. Together with academic and industrial partners, we aim to drive innovation in genomic medicine through vibrant research and apply them towards clinical applications that can directly benefit patients. Columbia University’s Precision Medicine Initiative has established a genetics/genomics sequencing and analysis facility as a core part of this mission.

We are looking for a highly motivated Scientific Programmer to join a talented group of bioinformatics scientists/statisticians and programmers to develop our NGS data pipeline.

Responsibilities

• Assist in the design, development, and implementation of novel pipelines and methods for analyzing Next-Generation Sequencing (NGS) data.
• Contribute to the development of new platforms and solutions for large integrative analysis of genomic data.
• Assist GenBAR staff and affiliates with data access, analysis, and interpretations; collaborate and consult with GenBAR researchers to analyze problems and recommend solutions to meet the computational needs for a wide range of biological research.
• Establish and maintain rigorous coding and testing standards to ensure code quality, readability, and maintainability.
• Provide project support for pipeline and iLab initiatives.
• Mentor and onboard new team members.
• Perform other projects and duties as assigned.

Minimum Qualifications

• Requires a bachelor’s degree or equivalent, plus two years of related experience
• Master’s degree would substitute for experience
• Solid understanding of genetics, bioinformatics, and statistics as applied to NGS datasets
• Extensive experience with AWS step functions, AWS Lambda, AWS Batch and AWS HealthOmics.
• Demonstrated problem-solving skills, desire and ability to work effectively within a team, including strong organization and communication skills.

Preferred Qualifications

• Extensive knowledge of programming languages in either Java/C++ or 3+ years of Python in a production setting
• Experience in unit testing using pytest framework.
• An understanding of a wide range of data systems and platforms, such as data warehouses and data lakes, relational databases, such as MySQL and PostgreSQL, and NoSQL databases
• Experience in Unix/Linux, Bash Shell, Git
• Experience with job schedulers (SLURM, Sun Grid Engine, etc.)
• Willingness and initiative to seek out and learn novel tools, methods, and technologies within a quickly evolving field.

Other Requirements

• Successful completion of applicable compliances and systems training requirements

Job Type: Officer of Administration

Regular/Temporary: Regular

Hours Per Week: 35

Salary Range: $75,000 - $80,000

The salary of the finalist selected for this role will be set based on a variety of factors, including but not limited to departmental budgets, qualifications, experience, education, licenses, specialty, and training. The above hiring range represents the University's good faith and reasonable estimate of the range of possible compensation at the time of posting.