Bioinformatics Software Engineer

Job Locations USA-NY-New York
Posted Date 1 month ago(2/12/2018 2:46 PM)
Requisition ID
Information Technology

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 27th year, MSK has been named a top hospital for cancer by U.S. News & World Report. We are proud to be on Becker’s Healthcare list as one of the 150 Great Places to Work in Healthcare in 2016, as well as Glassdoor’s annual Employees’ Choice Awards 2017. We’re treating cancer, one patient at a time. Join us and make a difference every day.

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 at our group has rapidly grown from 40TB to a private cloud of 2PB, and is managed by over a dozen production servers that facilitate automatic processing of data, increasingly complex genomic databases and modern web applications that help in visualizations. Clinical bioinformatics group is revolutionizing the health level exchange systems to integrate genomic and biomedical systems.


We are looking for a talented and self-driven bioinformatics software engineer to help us to continue being the pioneer in pathology software systems. As a Bioinformatics Software Engineer, you will work in a highly collaborative environment, engineer clinical and research software systems that directly impact patient care, and will be responsible for building the next-generation clinical informatics systems. You will also participate in developing high throughput data processing pipelines, petabyte scale data management, microservices oriented RESTful APIs, genomic and analytic data portals, department-wide messaging/queuing system, and socket based TCP/IP servers.


Responsibilities include but are not limited to: 


  • Take part in the developing cutting-edge software systems for clinical diagnostics and to support existing clinical bioinformatics software.
  • Work on full-stack components for various clinical bioinformatics software system.
  • Implement and follow the best practices in software development, code versioning, software testing, and deployment.
  • Develop and maintain clinical bioinformatics databases which uses MySQL, MongoDB, GraphDB, and hybrid technologies. Be willing to learn and implement efficient database design methodologies.
  • Take part in technical discussions including but not limited to code reviews, and build/release management.
  • Work with UNIX systems administrator to configure new and existing software packages for security, performance and maintainability.
  • Participate in building proper production, development, and integration environments and assists in unit/functional, regression, and system testing.
  • Develop and maintain software systems that interface with other departmental and/or institutional systems through RESTful APIs, web interfaces, and socket based client/servers.
  • Participate in designing and developing department-wide messaging queue, enterprise search platforms, and other enterprise-level informatics systems.
  • Proficient in using a mix of bleeding edge software technologies/tools: Python, Flask/Dgango, Java, React, Angular, D3, Node.js, JavaScript, message queues, search engines, MySQL, MongoDB, PL/SQL, and AWS-like systems.


You are:

  • Capable of building strong customer relationships and delivering customer-centric products
  • A good decision-maker, with proven success at making timely decisions that keep the organization moving forward.
  • Able to work effectively in a fast-paced environment solving for complex problems, consistently achieving results, even under tough situations.
  • Adept at planning and prioritizing work to meet commitments aligned with organizational goals
  • 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 problems.
  • Adept at learning quickly, applying insights from past efforts to new situations.


You need:


  • Bachelor’s Degree with 0-2 years of computer and sequencing data experience. Master’s preferred. 
  • Experience with full stack web development especially with Python/Java/Ruby, Flask/Spring/Django, MySQL/MongoDB/GraphDB, React/Angular/Node.js/JavaScript is required.
  • Next generation sequencing and cancer genetics familiarity preferred but not required.
  • Experience with building front end data visualization portals, high volume data processing, messaging queues, and enterprise search engines is desirable


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




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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