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Programmer

Systems Biology

Programmer

  • 532720
  • Medical Center
  • Systems Biology
  • Full Time
  • Opening on: Dec 13 2022
  • Grade 104
  • Job Type: Officer of Administration
  • Bargaining Unit:
  • Regular/Temporary: Regular
  • End Date if Temporary:
  • Hours Per Week: 35
  • Salary Range: $90,000 - $100,000
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.
 

Position Summary

The Programmer will work in the J.P. Sulzberger Columbia Genome Center and the Columbia Single Cell Analysis Core, which are housed in the Department of Systems Biology (DSB). The Center and Core provide experimental and computational genomics services to both internal Columbia users and external users.  Genome Center experimental services include various bulk RNA-seq protocols and sequencing of pre-prepared libraries from individual labs. Single Cell Core services primarily use the 10x Genomics platform for single-cell RNA-seq, single-cell ATAC-seq, joint single-cell RNA/ATAC-seq (multi-ome), and joint single-cell RNA/VDJ-seq.  Computational services include basic data processing (e.g. alignment, quality control, quantification, and demultiplexing), basic data analysis (e.g. unsupervised clustering, visualization, and differential expression), and custom bioinformatics projects involving more sophisticated analytical methods (e.g. trajectory inference, gene regulatory network inference).

This position will involve computer programming, developmental operations, data management, and systems administration to support the computational pipelines and infrastructure in the Center and Core, which are used to provide basic data processing and analysis of RNA-seq and single-cell genomic data.


Responsibilities

Maintaining Computational Pipelines for Basic Data Processing and Analysis:

  • Maintain computational pipelines for analyzing RNA-seq and single-cell genomic data, working in collaboration with bioinformatics analysts.
  • Procure appropriate computing and storage equipment or cloud-based resources.
  • Collaborate with bioinformatics analysts to develop software for analyzing RNA-seq and single-cell genomic data.

Data Management:

  • Maintain the data storage, curation, and data sharing / web-based data release infrastructure for genomic data generated by the Center and Core.

Systems Administration:

  • Maintain cluster- and cloud-based computing infrastructure and programming environments for bioinformatics analysis.
  • Perform other tasks as requested.

Minimum Qualifications

  • Bachelor’s degree in computer science, bioinformatics, engineering, or equivalent in education and experience; plus three years of related experience.

Preferred Qualifications

  • Master’s degree in computer science, bioinformatics, engineering, or equivalent in education and experience, plus two years of related experience.
  • Experience working in a core facility, with software development, bioinformatic pipeline development (e.g. Airflow, Django) and bioinformatics and/or genomic analysis.
  • Strong verbal communication, software development, and use and administration of cluster and cloud-based computing environments.
  • Excellent communication skills and teamwork.

Other Qualifications

  • Demonstrated experience in computer programming, software development, systems administration, and data management.
  • Programming: Fluency with at least one general-purpose programming language (e.g. C/C++, Rust, Java, Ruby, Perl, Python) and one language for scientific computing (R, MATLAB, Python).
  • Experience using a Linux-based operation system.
  • Experience working in cluster and cloud-computing environments (e.g. Amazon Web Services).

Equal Opportunity Employer / Disability / Veteran

Columbia University is committed to the hiring of qualified local residents.

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