Sr Bioinformatics Software Engineer

JOB SUMMARY: The Senior Bioinformatics (BI) Software Engineer holds 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.

KEY RESPONSIBILITIES BI Development:

Design, develop, and maintain robust software solutions using various tools, databases, and technologies to meet business requirements. Data Modeling:

Create and optimize data models, ensuring the accuracy, integrity, and performance of the underling computational algorithms, especially as pertains to assembly, mapping, variant calling and variant annotation. ETL Processes:

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 Query Optimization:

Analyze and optimize SQL queries and database performance to enhance data retrieval and reporting speed. Contribute to schema design and review sessions to ensure high performance and maintainable databases. Dashboard & Report Creation:

Develop interactive dashboards and automated reports using BI tools (e.g., Azure Pipelines, Teams Power Automate, email, Nextflow) to provide actionable insights for stakeholders.

Collaboration:

Work and align closely with stakeholders, including data analysts, business users, clinical reviewers, laboratory personnel and software developers, to scope their requirements and deliver timely integrations of new software. Data Integration:

Integrate disparate data sources and ensure consistency, accuracy, and reliability of data across the BI system, with a focus on devising systems that have minimal to no code debt and are highly maintainable and flexible. Quality Assurance:

Conduct rigorous testing of BI solutions to ensure data accuracy, system stability, and optimal performance, with the ability to automate testing suites using packages (e.g. pytest, doctest, Azure Pipelines) Documentation & Maintenance:

Create comprehensive documentation for developed solutions and provide support and maintenance as necessary. This generally includes: (1) detailed in-line commenting noting Jira ticket request numbers, genomic diagrams, reasoning and personal thoughts, TODO comments, docstrings, BG headers, etc.; (2) wikis and README files instructing users on how to install and implement the software along with trace mappings detailing how the software is generally organized.

QUALIFICATIONS Required

Education:

Bachelor’s degree in Computer Science, Software Engineering, Bioinformatics or a related field;
Master’s degree preferred.

Experience:

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. Must have a proven track record of implementing production ready software solutions from scratch. Prior experience or domain knowledge from collaborating with laboratory scientists, computational biologists, or clinical reviewers is a nice-to-have.

COMPETENCIES Technical

Skills:

Deep knowledge and expertise in at least two programming languages (Python, Perl, R, or Bash, will also consider Java, C++, and Groovy).  Proficient in a range of database technologies, including SQL Server, No

SQL, MongoDB, MySQL, and Elastic Search, demonstrating comprehensive skills in database management, optimization, and query development. Proficiency in working in an Agile framework and implementing CI/CD practices using Git. Knowledge of Azure is a bonus.

Implementation of object orientated…