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BACKGROUND

For over 130 years, the people of Memorial Sloan Kettering have been relentless pioneers in our single-minded focus on the prevention and cure of cancer. We are known for intensely innovative research that never stops, as well as for thoughtful, compassionate, and responsive patient care that treats the individual first.

Today, Memorial Sloan Kettering is the nation's number one hospital in cancer care (U.S. News & World Report, 2014-15) because of our unified commitment to the people we serve. Find your life's calling at a place that's finding a better way.

RESPONSIBILITIES

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 plug-ins, RESTful WebServices, and Web interfaces to our clinical laboratory information management system (LIMS).

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, Java, 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.
Collaborates with team members, and follows proper database techniques to maintain LIMS schema, facilitate LIMS data migration tasks.
Works with UNIX systems administrator to configure new and existing software packages for security, performance and maintainability.
Performs data integrity checks for the NGS clinical LIMS data. Setups monitoring/alert systems to automate this.
Research, design, and implement continuous integration frameworks as health-check for production clinical LIMS.
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 LIMS system. Also, facilitate smooth integration to group-wide systems.
Strictly and systematically manages the database schema release management and the software release management.
Writes scripts to monitor the clinical LIMS database backups, and archiving when appropriate.

REQUIREMENTS

Bachelor's Degree with 2-4 years of computer and sequencing data experience. Master's with 0-2 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.

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

LOCALE

New York, New York

COMPENSATION

Competitive

HOW TO APPLY

Please apply through our website - http://www.mskcc.org/jobs and search by job title or Job ID 3074

POLICY

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.

Federal law requires employers to provide reasonable accommodation to qualified individuals with disabilities. Please tell us if you require a reasonable accommodation to apply for a job or to perform your job. Examples of reasonable accommodation include making a change to the application process or work procedures, providing documents in an alternate format, using a sign language interpreter, or using specialized equipment.

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