Sr Bioinformatics Software Engineer

About the Role

The Senior Bioinformatics (BI) Software Engineer plays a critical technical role, responsible for designing, developing, and maintaining scalable and efficient software solutions for Baylor Genetics’ bioinformatic pipelines. This role involves collaborating with and supporting cross-functional teams to deliver data-driven software solutions aligning with business needs.

Responsibilities

• Design, develop, and maintain robust software solutions using various tools, databases, and technologies to meet business requirements.
• Create and optimize data models, ensuring the accuracy, integrity, and performance of computational algorithms, particularly for assembly, mapping, variant calling, and variant annotation.
• Develop and optimize ETL (Extract, Transform, Load) processes to efficiently extract data from various sources, transform it, and load it into the BI system, with an emphasis on utilizing APIs.
• Analyze and optimize SQL queries and database performance to enhance data retrieval and reporting speed; contribute to schema design and review sessions.
• Develop interactive dashboards and automated reports using BI tools (e.g., Azure Pipelines, Teams Power Automate, email, Nextflow) to provide actionable insights for stakeholders.
• Collaborate closely with stakeholders, including data analysts, business users, clinical reviewers, laboratory personnel, and software developers, to scope requirements and deliver timely integrations.
• Integrate disparate data sources and ensure consistency, accuracy, and reliability of data across the BI system, focusing on minimal code debt and high maintainability.
• Conduct rigorous testing of BI solutions to ensure data accuracy, system stability, and optimal performance, including automating testing suites (e.g., pytest, doctest, Azure Pipelines).
• Create comprehensive documentation, including in-line comments (Jira ticket references, genomic diagrams, reasoning, TODOs, docstrings), wikis, README files, and trace mappings for software organization and user implementation.
• Perform other advanced job-related duties as assigned.

Requirements

• Bachelor’s degree in Computer Science, Software Engineering, Bioinformatics, or a related field; Master’s degree preferred.
• Minimum of 5 years of experience in software development, with a proven track record of designing and implementing scalable software solutions based on diverse user feature needs.
• Proven experience implementing production-ready software solutions from scratch.
• Prior experience or domain knowledge collaborating with laboratory scientists, computational biologists, or clinical reviewers is a plus.

Skills

• Technical Skills:
  • Deep knowledge and expertise in at least two programming languages (Python, Perl, R, Bash; Java, C++, and Groovy also considered).
  • Proficient in database technologies, including SQL Server, NoSQL, MongoDB, MySQL, and ElasticSearch, with skills in database management, optimization, and query development.
  • Proficiency in Agile frameworks and CI/CD practices using Git; knowledge of Azure is a bonus.
  • Strong implementation of object-oriented programming (OOP), including building intuitive classes relevant to science, systems, or services.
  • Demonstrated ability to build performant, maintainable, and production-ready software packages from scratch.
  • Solid understanding and practice of unit and integration testing.
  • High regard for documentation and explicit object/variable naming; ability to relay scientific concepts in documentation or code.
  • Proficiency in designing and building APIs and microservices from scratch.
  • Familiarity with Linux OS and HPC clusters (SLURM, Kubernetes, GCP, Azure) is a plus.
  • Solid understanding of package management (PIP, Conda) and containerization (Docker, Singularity).
  • Proficiency or knowledge of workflow management tools (Nextflow, Airflow, Snakemake) is a plus.
• Analytical Thinking: Strong problem-solving skills with the ability to translate complex business needs into technical solutions; works independently and collaborates with stakeholders and subject-matter experts.
• Team Collaboration: Excellent interpersonal and communication skills to collaborate effectively with multidisciplinary teams; open to receiving and giving constructive feedback.
• Adaptability: Ability to adapt to evolving technologies, learn new tools, and implement best practices in BI software engineering; assesses when drop-in solutions are preferable to custom implementations and runs proof-of-concepts as needed.
• Project Management: Experience managing individual projects, adhering to timelines, and delivering high-quality solutions while communicating scope fluctuations.

Physical Demands and Work Environment

• Frequently required to sit and stand.
• Frequently required to utilize hand and finger dexterity.
• Frequently required to talk or hear.