Senior Bioinformatics Software Engineer

E-logic is seeking a highly skilled Senior Bioinformatics Software Engineer to drive the operations, maintenance, and modernization of Secure HIV-TRACE, a secure, web-based bioinformatics application utilized by state and local health departments across the National Center for HIV, Viral Hepatitis, STD, and TB Prevention (NCHHSTP). This critical platform applies advanced molecular epidemiology and evolutionary principles to detect growing HIV transmission clusters in near real-time, guiding timely public health interventions. In this role, you will lead full-stack development, refactor legacy codebases into modern modular architectures, develop REST APIs, optimize heavy computing workflows in AWS, and collaborate closely with CDC program informatics and security teams.

Key Responsibilities

• Codebase Refactoring & Architecture: Modernize, refactor, and document the existing codebase (Python, C++, JavaScript, Node.js) into a modular, REST-based architecture separating the user interface from backend computational engines.
• Cloud & Workflow Optimization: Manage application performance within CDC's AWS cloud environment, utilizing advanced high-performance computing frameworks like AWS ParallelCluster to optimize job processing.
• System Enhancement & DME: Design and implement next-generation features, including multijurisdictional cluster visualization, time-space cluster detection methodologies, and custom data visualization exports (integrating Power BI, Tableau, and REDCap via APIs).
• Operations & Maintenance (O&M): Provide database administrator (DBA) support, patch security vulnerabilities, maintain high availability, and capture system error logs for continuous performance metrics.
• Compliance & Open Source Mandates: Ensure all developed code and documentation strictly comply with the Federal SHARE IT Act (releasing software as public open-source on GitHub), HHS Enterprise Performance Life Cycle (EPLC), and Section 508 accessibility guidelines.
• Tiered Help Desk Support: Provide technical assistance and troubleshoot processing errors for approximately 150 end-users across state and local health jurisdictions.

Required Qualifications & Technical Expertise

• Bioinformatics Expertise: Strong foundational knowledge of HIV molecular epidemiology, sequence analysis, and phylogenetic/phylodynamic methods. Experience comparing molecular tools (e.g., HIV-TRACE, BEAST, TimeTree) is highly desirable.
• Project Management Professional (PMP) certification is a strong plus (at least one key personnel member must hold this credential).
• AWS Certified Solutions Architect or DevOps Engineer.
• Core Languages: Fluency in Python, C++, and JavaScript / Node.js.
• Cloud Infrastructure: Hands-on experience deploying and monitoring applications in AWS GovCloud environments, including containerization, server administration, and infrastructure-as-code.
• Database Management: Competency with relational and non-relational database management systems (e.g., PostgreSQL, SQL Server, MongoDB).
• Modern API Development: Proven track record building secure, performant RESTful APIs.
• Tools: Expert proficiency with Git/GitHub Enterprise, Jira, and Confluence.

Important Notice:

This role is part of a proposal for National Center for HIV, Viral Hepatitis, STD, and TB Prevention (NCHHSTP). Hiring is contingent upon the selection of the consultant. Selected candidates will be included in the proposal and must authorize the use of their resume for submission.