Senior Bioinformatics Software Engineer

Baylor Genetics•,

19h

About The Position

The Senior Bioinformatics Software Engineer designs, develops, and maintains scalable, efficient software solutions for Baylor Genetics’ bioinformatics pipelines. The role collaborates with cross-functional teams to deliver data-driven solutions aligned with business needs. The position develops and optimizes data models, ETL processes, APIs, SQL queries, databases, dashboards, reports, and integrations. It emphasizes accurate and reliable data, maintainable and flexible systems with minimal code debt, rigorous automated testing, and comprehensive code and user documentation. The engineer works with data analysts, business users, clinical reviewers, laboratory personnel, and software developers to scope requirements and deliver integrations. Other advanced job-related duties may be assigned.

Requirements

Bachelor’s degree in Computer Science, Software Engineering, Bioinformatics, or a related field.
At least 5 years of software development experience.
Proven track record designing and implementing scalable software solutions based on diverse user feature needs.
Proven track record implementing production-ready software solutions from scratch.
Deep knowledge and expertise in at least two programming languages; Python, Perl, R, or Bash are cited, with Java, C++, and Groovy also considered.
Proficiency with database technologies, including SQL Server, NoSQL, MongoDB, MySQL, and Elasticsearch, and with database management, optimization, and query development.
Proficiency working in an Agile framework and implementing CI/CD practices using Git.
Ability to implement object-oriented programming and build intuitive classes relevant to the science, system, or service.
Knowledge of standard software design practices and ability to build performant, maintainable, tested, production-ready software packages from scratch.
Solid understanding and practice of unit and integration testing.
Strong documentation practices, explicit object and variable naming, and ability to explain scientific concepts in documentation or code.
Proficiency designing and building APIs and microservices from scratch.
Understanding of package management practices such as pip and Conda, and containerization such as Docker and Singularity.
Strong analytical and problem-solving skills, including translating complex business needs into technical solutions and working independently.
Good communication skills and flexibility to consult stakeholders and subject-matter experts as needed.
Interpersonal and communication skills for effective collaboration with multidisciplinary teams; openness to giving and receiving measured, problem-focused feedback.
Ability to adapt to evolving technologies, learn tools, implement best practices, assess when an existing solution is preferable to custom software, and conduct proof-of-concepts as needed.
Experience managing individual projects, meeting timelines, and communicating when project scopes fluctuate.

Nice To Haves

Master’s degree.
Prior experience or domain knowledge collaborating with laboratory scientists, computational biologists, or clinical reviewers.
Knowledge of Azure.
Familiarity with Linux operating systems and HPC clusters, including SLURM, Kubernetes, GCP, or Azure.
Proficiency or knowledge of workflow management or orchestration tools such as Nextflow, Airflow, or Snakemake.

Responsibilities

Design, develop, and maintain robust software solutions using tools, databases, and technologies to meet business requirements.
Create and optimize data models, ensuring accuracy, integrity, and performance of computational algorithms, particularly for assembly, mapping, variant calling, and variant annotation.
Develop and optimize ETL processes to extract, transform, and load data, with an emphasis on using APIs.
Analyze and optimize SQL queries and database performance; contribute to schema design and review sessions.
Develop interactive dashboards and automated reports using business intelligence tools and technologies, including Azure Pipelines, Teams Power Automate, email, and Nextflow.
Collaborate with data analysts, business users, clinical reviewers, laboratory personnel, and software developers to scope requirements and deliver software integrations.
Integrate disparate data sources and ensure data consistency, accuracy, and reliability while creating maintainable and flexible systems with minimal code debt.
Test business intelligence solutions for data accuracy, system stability, and performance, and automate test suites where appropriate.
Document developed solutions, including code comments, genomic diagrams, docstrings, wikis, README files, installation and implementation instructions, and trace mappings.
Provide support and maintenance for developed solutions.
Manage individual projects and adhere to timelines while communicating when project scopes fluctuate.
Perform other advanced job-related duties as assigned.