Computational Research Lab Mgr

Columbia University
US - New York - New York
July 24, 2024

Job Type:
Officer of Administration
Bargaining Unit:
Regular/Temporary:
Regular
End Date if Temporary:
Hours Per Week:
35.00
Standard Work Schedule:
Building:
Salary Range:
$85,000.00 - $110,000.00

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

Columbia University's Department of Systems Biology is seeking a highly motivated genomics and computer science expert to join the Rabadan lab. The incumbent will take part in a cutting-edge project on untangling the molecular biology of cancer. The overarching approach is to generate and analyze deep whole exome and whole genome from public and private data sets and develop visualization tools for these data. The incumbent will also develop and maintain a software pipeline for the analyses of genomic sequencing data. The job would require the candidate's active participation in the design and implementation of these pipelines as well as interaction with collaborators in applying the pipelines toward achieving the goals of specific sequencing projects. The person will work in a highly multidisciplinary and supportive environment and will work directly with members of the lab in meeting assigned objectives under the supervision of the Principal Investigator.

The incumbent will also oversee the research staff technician position within the Rabadan Lab, who will be coordinating research computational efforts, as well as oversee genomic data coordination for various working groups within the Program for Mathematical Genomics (PMG) group. The position will report to the Principal Investigator of the Rabadan Lab.

Responsibilities

Design and implement bioinformatics pipelines, as well as maintain and operate existing in-house pipelines and tools. Including generating and analyzing deep whole exome and whole genome from both public and private data sets and developing visualization tools for these data. (30%)

Manage and administer local and cloud computing infrastructure. This includes managing and maintaining files, workflows, and files on HPC cluster operations - Manitou and Amazon Web Services including user accounts and permissions, and cost management. (20%)
Supervises data analyst staff duties and conduct quality assurance on project processes, activities, and tasks from the research staff technician; Review the genomic data coordination for various working groups within the Program for Mathematical Genomics (PMG) group. (15%)
Maintain lab-generated software. (10%)
Provide support and training on data pipelines, protocols, and database tools for all team member projects. (10%)
Coordinate and assist with implementation and improvement of data management and data processing protocols. (5%)
Assist and advise principal investigators and lab research team members with data management needs. (5%)
Perform other duties as assigned and/or requested. (5%)

Minimum Qualifications

Bachelor's degree or equivalent in Computer Science, Engineering, or Physics, plus 4 years of related experience.
Experience with Linux, Python, scripting, and/or cluster computing (primarily with the Oracle Grid Engine (SGE).

Preferred Qualifications

Master's degree preferred.
Supervisory experience preferred.
The candidate should have excellent programming and communication skills.
The candidate must be proactive in making suggestions for better system design and documentation and must be actively involved to ensure projects achieve their goals.
Skills in web design and graphical design are a plus.
Experience in Docker, Adobe Creative Suite (photoshop and Illustrator, for designing scientific figures), and scientific writing.
Experience with Amazon web services (EC2, S3, Glacier, IAM, Batch, AWS Organizations, etc.) is a plus.
Prior experience with existing sequencing technologies and their application as a tool for understanding cancer genetics are a plus.
Experience with Bioinformatics Software tools, such as BLAST, BWA, Samtools, Bowtie, and Trinity, and how to access data cohorts is a plus.
Experience with Version control software (git) is a plus.
Experience with backend web development, primarily in Django (with some forays into Flask and database stuff, like Postgres, as well) is a plus.
Experience with frontend web development, primarily in Javascript, HTML, and CSS (with some forays into Javascript frameworks like Vue and Angular) is a plus.

Equal Opportunity Employer / Disability / Veteran

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

Read the full job description and apply online on the recuiter's web-site

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