Sr Bioinformatics Software Engineer
HybridHouston, Texas, United States
Job Summary
Design, develop, and maintain scalable bioinformatics software solutions using Python, SQL, and Azure while optimizing ETL processes and database performance for assembly, mapping, and variant calling pipelines. Create interactive dashboards and automated reports using Nextflow and Power Automate to deliver actionable insights, and conduct rigorous testing to ensure system stability and data accuracy. Collaborate closely with data analysts, clinical reviewers, and laboratory personnel to scope requirements, integrate disparate data sources, and deliver maintainable software with minimal code debt. Document solutions comprehensively with inline comments and wikis, manage Jira tickets, and support cross-functional teams in aligning technical outputs with business needs.
Required Qualifications
- Bachelor's degree in Computer Science, Software Engineering, Bioinformatics or a related field
- Minimum of 5 years of experience in software development
- Proven track record of designing and implementing scalable software solutions based on diverse user feature needs
- Proven track record of implementing production ready software solutions from scratch
- Deep knowledge and expertise in at least two programming languages (Python, Perl, R, or Bash)
- Proficient in a range of database technologies, including SQL Server, NoSQL, MongoDB, MySQL, and ElasticSearch
- Demonstrating comprehensive skills in database management, optimization, and query development
- Proficiency in working in an Agile framework
- Implementing CI/CD practices using Git
- Implementation of object orientated programming (OOP)
- Building intuitive classes relevant to the science, system, or service
- Standard software design practices relevant to that language
- Demonstrated ability to build entire software packages from scratch that are performant and highly maintainable
- Ensuring they are tested and are production ready
- Solid understanding and habitual practice of unit and integration testing of software
- High regard for documentation and object/variable naming that is explicit
- Ability to relay or distill scientific concepts within supplemental documentation or inline code itself
- Proficiency or knowledge of workflow management or orchestration tools (Nextflow, Airflow, Snakemake, etc.)
- Solid understanding of package management practices (PIP, Conda, etc.)
- Containerization (Docker, Singularity, etc.)
- Proficiency or knowledge of workflow management or orchestration tools (Nextflow, Airflow, Snakemake, etc.)
- Strong analytical and problem-solving skills
- Ability to translate complex business needs into technical solutions
- Work independently to solve problems
- Good communication skills
- Flexibility to reach out to stakeholders and SMEs as necessary
- Excellent interpersonal and communication skills
- Collaborate effectively with multidisciplinary teams
- Open and willing to receive and give criticism and feedback in a measured manner
- Ability to adapt to evolving technologies
- Learn new tools
- Implement best practices in BI software engineering and development
- Assess situations when a drop-in solution would be preferable to a custom software implementation
- Run proof-of-concepts as needed
- Highly familiar with best practices in software development
- Advocate of best practices, even under pressure
- Experience in managing individual projects
- Adhering to timelines
- Delivering high-quality solutions
- Ensuring good communication in situations where project scopes may fluctuate
Desired Qualifications
- Master's degree
- Prior experience or domain knowledge from collaborating with laboratory scientists, computational biologists, or clinical reviewers
- Knowledge of Azure
- Familiarity with Linux OS and HPC clusters (SLURM, Kubernetes, GCP, Azure, etc.)
- Solid understanding of package management practices (PIP, Conda, etc.)
- Containerization (Docker, Singularity, etc.)
- Proficiency or knowledge of workflow management or orchestration tools (Nextflow, Airflow, Snakemake, etc.)
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