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Bioinformatics Software Engineer

Company: Frederick National Laboratory
Location: Bethesda
Posted on: January 13, 2022

Job Description:

Bioinformatics Software Engineer

Job ID: req1854
Employee Type: exempt full-time
Division: Biomedical Informatics & Data Science
Facility: NIH
Location: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA

The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc. The lab addresses some of the most urgent and intractable problems in the biomedical sciences in cancer and AIDS, drug development and first-in-human clinical trials, applications of nanotechnology in medicine, and rapid response to emerging threats of infectious diseases.

Our core values of accountability, compassion, collaboration, dedication, integrity, and versatility serve as a guidepost for how we do our work every day in serving the public's interest.

Position Overview:


The Frederick National Laboratory is dedicated to improving human health through the discovery and innovation in the biomedical sciences, focusing on cancer, AIDS and emerging infectious diseases.

The Biomedical Informatics and Data Science (BIDS) directorate works collaboratively and helps to fulfill the mission of Frederick National Laboratory in the areas of biomedical informatics and data science by developing and applying world leading data science and computing technologies to basic and applied biomedical research challenges, supporting critical operations, developing and delivering national data resources, and employing leading-edge software and data science to effectively enable and advance clinical trials.

The Advanced Biomedical Computing Sciences (ABCS) is a part of the Biomedical Informatics and Data Science (BIDS) Program at Leidos Biomedical Research, Inc. The ABCS provides technology development, scientific consultation, collaboration and training, and high-performance computing support to the NCI and NIH scientists and staff.


Software Engineer III will:

  • Work independently and with management to identify and define technical requirements for tasks and timelines
  • Design, build, test, and deploy scalable and fault-tolerant solutions on-premise (HPC environments) and the Cloud (AWS, Azure, or GCP)
  • Develop, document, and maintain version controlled quality code in adherence with established design patterns
  • Mock, develop, and enhance interactive UI designs and elements based on customer requirements
  • Build docker and singularity containers for various genomic workflows
  • Provide efficient solutions to reproducible workflow orchestrations on the cloud and local HPC
  • Automate and perform rigorous unit testing both, in the cloud and on-premise
  • Author and manage technical documentation that concisely describes design and implementation details
  • Report project status regularly to management and customers
  • Manage, publish and maintain code repository (eg. GitHub), container repository (eg. DockerHub) and pipeline repository (eg. Dockstore)
  • Respond to new feature requests, assist issues raised by userbase and perform program tuning as needed
  • Plan code and resource-bundle release cycles prioritizing high-demand customer feature requests
  • Candidates selected for interview will be requested to provide a GitHub repository or samples of code snippets for evaluation. The Software Engineer III is expected to work effectively as a member of a team; coordinate activities among other groups located at the Bethesda, Frederick, Rockville and Gaithersburg NCI campuses; follow sound scientific practices and maintain effective documentation of activities and analyses

    To be considered for this position, you must minimally meet the knowledge, skills, and abilities listed below:
    • Possession of a Bachelor's degree in Computer Science, Math or Biomedical Science related field from an accredited college or university or four (4) years related experience in lieu of degree. Foreign degrees must be evaluated for U.S. equivalency
    • Must be able to obtain and maintain a public trust clearance

      Candidates with these desired skills will be given preferential consideration:
      • Knowledge of open-source bioinformatics tools and workflows for analysis of Next-Generation sequencing datasets
      • Experience working with high performance clusters and cloud technologies
      • Understanding of the basic architectural principles for developing on the cloud and PaaS Services
      • Certification as an AWS Solutions Architect, Cloud Security Certification, and/or OpenStack Administrator Certification is a plus
      • Experience with one or more pipeline management frameworks like Snakemake, WDL etc. along with execution engines like Cromwell
      • Experience developing web-based application front ends utilizing one or more frameworks (eg. HTML, RShiny, Flask and Dash/Plotly)
      • Experience with building and orchestrating containers (Docker/Singularity) using technologies like Kubernetes
      • Experience building reliable and scalable applications using cloud technologies like AWS Step Functions, AWS Batch, etc.
      • Knowledge of building highly distributed, fault-tolerant and scalable frameworks to process large datasets
      • Knowledge of agile methodology for software project management
        • Extensive experience with open-source technology, software development and system engineering
        • Experience in one or more programming languages such as Python, PHP, Javascript, C/C++, R
        • Solid understanding of application programming in a shared-access, git concurrent-use environment, version control, etc.
        • Working knowledge of relational and non-relational databases
        • Ability to work effectively with a team on complex projects with strict requirements, yet take ownership and work independently on large portions of a project with little supervision
        • Strong communication (written and verbal) and organizational skills

          Equal Opportunity Employer (EOE) - Minority/Female/Disabled/Veteran (M/F/D/V) - Drug Free Workplace (DFW)


Keywords: Frederick National Laboratory, Bethesda , Bioinformatics Software Engineer, IT / Software / Systems , Bethesda, Maryland

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