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Software Developer

Job ID 2209 Date posted 07/30/2020

Brookhaven National Laboratory is a multipurpose research institution funded primarily by the U.S. Department of Energy’s Office of Science. Located on the center of Long Island, New York, Brookhaven Lab brings world-class facilities and expertise to the most exciting and important questions in basic and applied science—from the birth of our universe to the sustainable energy technology of tomorrow. We operate cutting-edge large-scale facilities for studies in physics, chemistry, biology, medicine, applied science, and a wide range of advanced technologies. The Laboratory's almost 3,000 scientists, engineers, and support staff are joined each year by more than 4,000 visiting researchers from around the world. Our award-winning history, including seven Nobel Prizes, stretches back to 1947, and we continue to unravel mysteries from the nanoscale to the cosmic scale, and everything in between. Brookhaven is operated and managed by Brookhaven Science Associates, which was founded by the Research Foundation for the State University of New York on behalf of Stony Brook University, and Battelle, a nonprofit applied science and technology organization.

Organizational Overview

Organizational Overview

Brookhaven National Laboratory (BNL) is a scientific, extreme scale Data Laboratory in the US, New York State, Long Island. With over 140 PB of archived data, the Scientific Data & Computing Center (SDCC) at BNL hosts the largest scientific data archive in the US, and the 3rd largest worldwide. The SDCC stores and processes scientific data from local facilities such as the Relativistic Heavy Ion Collider (RHIC), and the National Synchrotron Light Source II (NSLS II), the Center for Functional Nano Materials and the Atmospheric Radiation Measurement program. The SDCC is the largest computing center for the ATLAS experiment at CERN, and the data center outside of Japan for the particle physics experiment Belle II.

As a result, we have a lively, fast growing data science research program at BNL, with a specific focus on the challenges presented by the analysis, interpretation, and use of data at extreme scales and in real time. The data science program is accompanied by significant computational modeling research effort, in support of the design, planning, analysis, and interpretation of experiments and their results. The Computational Science Initiative (CSI - provides a laboratory-wide umbrella for these activities, bringing together computer scientists, applied mathematicians, and domain scientists to carry out leading edge research, convert research results into practical solutions that advance domain science, and provide the necessary computing infrastructure services and training to support efficient operation.

CSI is now looking for a software developer to work in a multi-disciplinary team, delivering exciting software solutions for the System Biology Knowledgebase (

Position Description

Essential Duties and Responsibilities:

  • Work on issues of diverse scope; may include working with other KBase members to implement software to meet stakeholder needs; working with users of the analysis software to ensure that their needs are being met as well as to test and debug applications.
  • Maintain accurate documentation and source-code control for all work-product.
  • Execute full lifecycle software development.
  • Write well-designed, testable, efficient code.
  • Produce specifications and determine operational feasibility.
  • Integrate software components into a fully functional software system.
  • Develop software verification plans and quality assurance procedures.
  • Document and maintain software functionality.
  • Tailor and deploy software tools, processes and metrics.
  • Comply with project plans and industry standards.

Position Requirements

Required Knowledge, Skills and Abilities:

  • Bachelor’s Degree or equivalent plus 3 years of software development experience or MS degree plus 1 year of software development experience or PhD in Computer Science or related discipline (Training experience is considered at PhD level)
  • Experience on bioinformatics, computational biology, microbiology and bio- or chemical engineering discipline (two or more years)
  • Experience with modern practices of open collaborative software development, including code review, the GitHub pull request model, etc.
  • Experience in designing interactive applications
  • Demonstrated high analytical skills and programming skills (highest preference for Java or Python but open to C/C++)
  • Familiarity with software engineering practices that include testing, documentation, source code management and release procedures
  • Demonstrated ability to work collaboratively with programmers, engineers, postdocs, graduate students, and undergraduates from diverse backgrounds
  • Excellent writing, interpersonal communication, and analytical skills

Preferred Knowledge, Skills, and Abilities:

  • Graduate degree in bioinformatics, computational biology, microbiology and bio- or chemical engineering discipline or a software related degree program
  • Familiarity with Agile software practices (e.g., Scrum, Kanban)
  • Experience in bioinformatics software design and engineering, mathematical analysis and comparative and functional genomics
  • Experience with developing applications to display/visualize scientific (preferably biological) data
  • Experience with scientific analysis tools such as R, Matlab, or Mathematica
  • Experience with Jupyter Notebook, Docker
  • The ability to obtain and maintain a DOE “Q” security clearance

Other Information:

  • At Brookhaven National Laboratory we believe that a comprehensive employee benefits program is an important and meaningful part of the compensation employees receive. Our benefits program includes, but is not limited to:
    • Medical Plans
    • Vacation
    • Holidays
    • Dental Plans
    • Life Insurance
    • 401(k) Plan
    • Retirement Plan
    • Swimming Pool, Weight Room, Tennis Courts, and many other employee perks and benefits

Brookhaven National Laboratory (BNL) is an equal opportunity employer that values inclusion and diversity at our Lab.We are committed to ensuring that all qualified applicants receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, status as a veteran, disability or any other federal, state or local protected class.

BNL takes affirmative action in support of its policy and to advance in employment individuals who are minorities, women, protected veterans, and individuals with disabilities.We ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment.Please contact us to request accommodation.

*VEVRAA Federal Contractor

Brookhaven employees are subject to restrictions related to participation in Foreign Government Talent Recruitment Programs, as defined and detailed in United States Department of Energy Order 486.1. You will be asked to disclose any such participation at the time of hire for review by Brookhaven. The full text of the Order may be found at:

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