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Bioinformatics Software Engineer II/III

Frederick National Laboratory for Cancer Research
Bethesda, MD
Start date
May 17, 2023

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Engineering, Information Technology, Bioinformatics, Science/R&D
Required Education
Bachelors Degree
Position Type
Full time

Job Details

Bioinformatics Software Engineer II/III

Job ID: req3384
Employee Type: exempt full-time
Division: Bioinformatics and Computational 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.

Accountability, Compassion, Collaboration, Dedication, Integrity and Versatility; it's the FNL way.


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 Bioinformatics and Computational Science (BACS) 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. 

The Advanced Biomedical and Computational Science (ABCS) group is a part of BACS within Leidos Biomedical Research as a technological hub of translational scientists with expertise in structural biology, biology, chemistry, imaging, and informatics. ABCS develops state-of-the-art technologies in large-scale data modeling, analysis, and integration and supports the scientific research at the Frederick National Lab by helping translate scientific questions to technical solutions for cancer and biomedical research. 


  • 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 II/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 Bachelor’s degree from an accredited college/university according to the Council for Higher Education Accreditation (CHEA) in Computer Science, Math or Biomedical Science related field or four (4) years relevant experience in lieu of degree.  Foreign degrees must be evaluated for U.S. equivalency 
  • Software Engineer II - In addition to the education requirement, a minimum of two (2) years of progressively responsible experience 
  • Software Engineer III - In addition to the education requirement, a minimum of five (5) years of progressively responsible experience  
  • Ability to obtain and maintain a security 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)



A rewarding career with global impact

Whether you’re an expert in your field or just starting out, we have a career opportunity for you. We’re always looking for people to join us in fulfilling the mission of the Frederick National Laboratory: discovery, innovation, and success in the biomedical sciences.

Our team of 2,400+ scientists, technicians, administrators, and support staff work at the forefront of basic, translational, and preclinical science, with a focus on cancer, AIDS, and other infectious diseases.

We collaborate with colleagues across the National Cancer Institute, National Institutes of Allergy and Infectious Diseases, and others throughout the National Institutes of Health. We also engage with extramural investigators in academia, government and industry.

Your path to joining our team begins with the desire to work for the only national laboratory dedicated to biomedical research. Our employees share a common desire to help make a difference in cancer research and public health concerns. As you search for a career that fits your education, skills, and abilities, explore the core values that guide us and emphasize work-life balance.

Discover why joining the Frederick National Laboratory team could be the most important career step you take



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