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Opportunity: Bioinformatics Software Engineer (#3697) @ Memorial Sloan-Kettering -- New York, NY (US)
Submitted by Gina Schaefer; posted on Tuesday, January 14, 2014
BACKGROUND:
Memorial Sloan-Kettering Cancer Center is a world renowned organization dedicated to the progressive control and cure of cancer through programs of patient care, research, and education.

The Molecular Diagnostics Laboratory within the Department of Pathology is applying next-generation sequencing techniques to characterize the spectrum of genetic mutations in patient tumors. These genomic data are guiding treatment decisions and the enrollment of patients onto clinical trials of novel targeted therapies.

As a Bioinformatics Software Engineer, you will support production-scale analysis of clinical next-generation sequencing data on patient samples, build new and extend existing production systems, provide technical support, and participate in various aspects of the software development life cycle. Also, you will participate in developing plug-ins, RESTful WebServices, and Web interfaces to our clinical laboratory information management system (LIMS).

RESPONSIBILITIES:
* 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:
Education: Bachelor's Degree required, Master's preferred

Experience: 2-4 years of computer and sequencing data experience, 0-2 years for a Masters candidate. Some Next generation sequencing and cancer genetics experience. This position requires cross-disciplinary and strong analytical skills as well as broad experience using computational methods, databases, software and hardware.

LOCALE:
New York City

COMPENSATION:
Competitive

HOW TO APPLY:
Please apply on our website mskcc.org/jobs and search for Job ID 3697 or use the following link: [link]

POLICY:
MSKCC 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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