Senior Bioinformatics Software Engineer – Memorial Sloan Kettering – New York, NY

Sep 21st, 2016 | By | Category:
Job ID: 5983
Job date: 2016-09-19
End Date:

Company : Memorial Sloan Kettering 

Country :

Role : Research Scientist 

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Job Description:
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 Senior 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.
Bachelor’s Degree with 4+ years of computer and sequencing data experience. Master’s 2+ years experience preferred. Some Next generation sequencing and cancer genetics experience required. 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.


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