Bioinformatics Software Engineer – Pathology

Job Posting Number: 9937

Information Technology
New York, NY
September 28, 2017
Company Overview:

At Memorial Sloan Kettering (MSK), we’re not only changing the way we treat cancer, but also the way the world thinks about it. By working together and pushing forward with innovation and discovery, we’re driving excellence and improving outcomes.

For the 26th year, MSK has been named a top hospital for cancer by U.S. News & World Report. We’re treating cancer, one patient at a time. Join us and make a difference every day.

Job Details:

The Clinical Bioinformatics group within the department of Pathology specializes in analyzing next-generation sequencing data to characterize the spectrum of genetic mutations in patient tumors. Analysis of this genomic data is guiding treatment decisions and the enrollment of patients onto clinical trials of novel targeted therapies.

The clinical data management system has rapidly grown from 40TB to approximately 1PB with a dozen production servers and over a dozen software systems and pipelines. As a Bioinformatics Software Engineer, you will work in a highly collaborative environment directly impacting patient care. You will be responsible for supporting production-scale analysis of clinical next-generation sequencing data on patient samples, building new and extending existing production systems, providing technical support, and participating in various aspects of the software development life cycle. You will also participate in developing full-stack web applications, RESTful web APIs, for our clinical variants sign out system.

Additional responsibilities include but are not limited to:

  • Performs software development and support for the clinical Bioinformatics group.
  • Participates in testing, implementing, designing, and deploying NGS clinical diagnostics pipelines and systems.
  • Develops software systems using a mix of the following: Python, Perl/CGI, JavaScript, Ruby, and PL/SQL.
  • Installs necessary and relevant software. Stays current with new software versions, patches and security.
  • Works to develop visualizations for clinical bioinformatics as well as provides support for clinical bioinformatic databases.
  • Works with clinical bioinformatics to integrate engineered software and various platforms for computational pipeline efficiency.
  • Develops and maintains user interfaces for reporting of output from data pre-processing and data analysis pipelines.
  • Works with UNIX systems administrator to configure new and existing software packages for security, performance and maintainability.
  • Sets up technical evaluation studies for the optimization of database schemas, SQL queries.
  • Participates in building proper production, development, and integration environments and assists in unit/functional, regression, and system testing
  • Develops plug-ins, RESTful APIs, and Web interfaces for the clinical systems. Also, facilitate smooth integration to group-wide systems.
  • Strictly and systematically manages the database schema release management and the software release management.

You Are:

  • Capable of building strong customer relationships and delivering customer-centric
  • A good decision-maker, with proven success at making timely decisions that keep the organization moving forward.
  • Able to work effectively in an environment notable for complex, sometimes contradictory
  • Consistently achieving results, even under tough
  • Adept at planning and prioritizing work to meet commitments aligned with organizational
  • Adept at building partnerships and working collaboratively with others to meet shared objectives and goals.
  • An effective communicator, capable of determining how best to reach different audiences and executing communications based on that understanding.
  • Resilient in recovering from setbacks and skilled at finding detours around
  • Able to operate effectively, even when things are not clear or the way forward is not
  • Adept at learning quickly, applying insights from past efforts to new situations.

Requirements:

  • Bachelor’s Degree with 2-4 years of computer and sequencing data experience. Master’s with 0-2 years experience preferred.
  • Next generation sequencing and cancer genetics experience preferred.
  • Experience with production systems and building data warehouse products and reporting systems is desirable.
  • Experience with full stack web development especially with Flask application framework and MySQL database integration is desirable.
  • Experience with front end data visualizations, especially with D3 library is desirable

This position requires cross-disciplinary and strong analytical skills as well as broad experience using computational methods, databases, software and hardware. #LI-G

#LI-SK1

MSK is an equal opportunity and affirmative action employer committed to diversity and inclusion in all aspects of recruiting and employment. All qualified individuals are encouraged to apply and will receive consideration without regard to race, color, gender, gender identity or expression, sexual orientation, national origin, age, religion, creed, disability, veteran status or any other factor which cannot lawfully be used as a basis for an employment decision.

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