Bioinformatics Software Engineer II

Full-time - Mid Level

Remote - Aliso Viejo, CA

Ambulatory Health Care Services

About the position

The Bioinformatics Software Engineer II position at Ambry involves engineering, deploying, and maintaining bioinformatics pipelines while collaborating with a cross-functional team. The role focuses on developing technical solutions, writing code, and participating in scrum ceremonies to enhance product offerings and improve workflows.

Responsibilities

• Drive technical solutions to problems, including end-to-end process flow from ideation to release, and estimating time and complexity
• Design and develop custom software according to ticket specifications
• Act as a role model for the team, setting standards for excellence and mentoring junior engineers
• Provide clear and consistent feedback on code reviews
• Meet with clients, partners, product owners, or other stakeholders to understand and clarify workflows and requirements
• Highlight blockers or issues arising during development to resolve in a timely manner
• Monitor process and log information, troubleshooting issues as needed
• Other duties as assigned.

Requirements

• Bachelor's degree (5+ years work experience), Master's degree (2+ years' work experience), or PhD degree in Bioinformatics, Computer Science, or a related field or equivalent work experience
• Proficient in Python coding
• Intermediate-to-advanced experience working in Linux environments (e.g. compiling programs from source, performing text manipulations with pipes)
• Intermediate-to-advanced experience in relational databases (e.g., MySQL, PostgreSQL, Microsoft SQL Server)
• Proficiency with software engineering best practices, including git version control, unit testing, and documentation
• Knowledge of next-generation sequencing technologies and standard bioinformatics data formats (e.g., FASTQ, BAM, VCF, GTF)
• Excellent communication and interpersonal skills.

Nice-to-haves

• Experience with cloud computing environment (AWS, Azure, Google Cloud)
• Knowledge of PHP (e.g. Symfony framework), Javascript, React, or Perl
• Familiarity with Atlassian suite applications (Jira, Confluence, BitBucket)
• Knowledge of clinical genetics databases (e.g., Clinvar, HGMD) and HGVS sequence variant nomenclatures
• Prior experience in biology and/or an understanding of mutation analysis
• Creating and developing Docker containers
• Experience developing APIs
• Experience with CI/CD (e.g. Bamboo, Jenkins, AWS Code Pipeline)

Benefits

• Compensation range of $111,000-$140,000 per year
• Eligibility for a Short-Term Incentive Plan with a target at 7.5% of annual earnings