Senior Bioinformatics Software Engineer

Big Rio is a remote-based, technology consulting firm with headquarters in Boston, MA. We deliver software solutions ranging from custom development and software implementation to data analytics and machine learning/AI integrations. As a one-stop shop, we attract clients from a variety of industries due to our proven ability to deliver cutting‑edge, cost‑effective software solutions.

The Senior Bioinformatics (BI) Software Engineer plays a critical technical role in the design, development, and maintenance of scalable and efficient software solutions for bioinformatics pipelines. This position requires close collaboration with cross‑functional teams to deliver data‑driven software solutions that align with business objectives.

• BI Development: Build and maintain reliable software solutions using diverse technologies and databases to meet business requirements.
• Data Modeling: Develop and refine data models to ensure computational algorithm performance and integrity, particularly in areas like genome assembly, mapping, variant calling, and annotation.
• ETL Processes: Design and enhance ETL processes to extract, transform, and load data efficiently, often through API‑based integrations.
• Query Optimization: Optimize SQL queries and database performance. Participate in schema design and review processes to maintain high performance and scalability.
• Dashboard & Report Creation: Create interactive dashboards and automated reports using tools like Azure Pipelines, Power Automate, and Nextflow to support data‑driven decision‑making.
• Collaboration: Work closely with stakeholders, such as analysts, clinicians, lab staff, and developers, to understand needs and deliver timely software solutions.
• Data Integration: Integrate diverse data sources, ensuring accuracy and reliability while minimizing code debt and maintaining system flexibility.
• Quality Assurance: Perform rigorous testing and automate test suites (e.g., with pytest, doctest, Azure Pipelines) to ensure software quality and stability.
• Documentation & Maintenance: Produce clear, comprehensive documentation including inline code comments, wikis, READMEs, and trace mappings to ensure ease of use and maintainability.
• Education: Bachelor’s degree in Computer Science, Software Engineering, Bioinformatics, or related field (Master’s preferred).
• Experience: Minimum of 5 years in software development, with experience designing and implementing scalable, production‑ready software solutions. Experience working with lab scientists, computational biologists, or clinical professionals is a plus.

• Proficient in at least two programming languages (Python, Perl, R, or Bash preferred; Java, C++, Groovy also acceptable).
• Strong background in database systems such as SQL Server, No
  
  SQL, Mongo
  
  DB, MySQL, or Elastic Search.
• Agile development experience with Git and CI/CD implementation. Knowledge of Azure is a plus.
• Comfortable with object‑oriented programming and software architecture design best practices.
• Skilled in writing well‑tested, maintainable, production‑ready code with a strong focus on unit and integration testing.
• Exceptional at writing documentation and translating scientific concepts into accessible code annotations or supporting documentation.
• Experience designing and building APIs and microservices from scratch.
• Familiarity with Linux and HPC environments (e.g., SLURM, Kubernetes, GCP, Azure) is beneficial.
• Knowledge of package managers (PIP, Conda) and containerization tools (Docker, Singularity).
• Exposure to workflow management/orchestration tools (e.g., Nextflow, Airflow, Snakemake) is a plus.
• Excellent analytical thinking with the ability to translate complex problems into clear technical solutions and communicate them effectively.
• Strong team player with excellent communication skills, open to feedback, and focused on collaborative problem‑solving.
• Flexible and adaptable, with a proactive approach to learning new technologies and implementing best practices in software development.
• Capable of independently managing project timelines and communicating effectively through changing project scopes.