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Systems Engineer, Scientific Computing Platforms

Location San Rafael, California Workstyle Hybrid
Who We Are

It takes a village, and at BioMarin our corporate groups are the people behind our success. Groups such as IT, Finance, Legal, Global Compliance & Ethics, and our People Team provide foundational support of all areas of operation at BioMarin.


The BioMarin R&D IT team seeks a highly talented and motivated Systems Engineer, Scientific Computing Platforms to support BioMarin’s Research and Data Sciences teams. The successful candidate will have the opportunity to partner closely with both IT professionals and scientists from multiple groups across the organization. They will play a key role in evaluating, designing, developing, and maintaining computational platforms used for analytics pipelines for scientific projects and clinical data analysis. A strong candidate will have a successful track record implementing, maintaining, and/or working with shared data science or bioinformatics platforms using DevOps processes in cloud Linux ecosystems. Experience with pharmaceutical/biopharmaceutical fields would be a plus.

BioMarin is a high-performing, team-based organization, where colleagues are flexible, multi-skilled and empowered to make decisions.  Applicants must bring a high level of initiative, energy and motivation to the role and have excellent communication and organizational skills.


  • Facilitate the delivery of computation platform resources to a diverse R&D department by leveraging modern DevOps processes, promoting collaboration among users, and empowering user autonomy.
  • Develop, implement, and document flexible, user-centric solutions within the data science, bioinformatics and computational science space, that encourage user freedom while still adhering to corporate security, governance, and compliance requirements.
  • Proactively identify and mitigate existing technical debt while minimizing further accumulation, fostering a culture of effective resource management and sustainable engineering practices.
  • Closely manage and own the complete system development lifecycle for data science and bioinformatics applications, ensuring seamless design, development, testing, deployment, and ongoing maintenance, while adhering to industry best practices and regulatory guidelines.
  • Proactively engage with scientists and researchers to facilitate the adoption and deployment of future bioinformatics tools, fostering a cutting-edge environment and optimizing research efforts through continuous exploration and evaluation of innovative solutions.

Required Qualifications:

  • 5+ years of experience implementing and managing Linux-based systems and solutions.
  • 5+ years of experience designing, deploying, and maintaining cloud IaaS and PaaS services in AWS and/or Azure.
  • 5+ years of experience using languages such as Bash, Python, or PowerShell, developing scripts and automation, writing unit/integration tests, and following test-driven development processes.
  • Strong knowledge of cloud-based compute, storage, and database workloads – services, architectures, resourcing, monitoring, and data flows.
  • Demonstrated experience designing and implementing CI/CD pipelines for testing and deploying infrastructure and applications through tools such as CircleCI, GitLab CI, GitHub Actions, or Azure Pipelines.
  • Experience developing infrastructure-as-code solutions using tools such as Terraform, AWS CDK/CloudFormation, and Azure ARM/Bicep templates.
  • Expert in job schedulers like SLURM, AWS Batch, and Azure Batch.
  • Effective communication skills for engaging with scientific, technical, and non-technical stakeholders, and the ability to interface between them.
  • Strong emphasis on prioritization, delivering results with high quality, technical rigor, and attention to detail.

Preferred Experience:

  • Relevant professional certifications in AWS (e.g., AWS Certified DevOps Engineer, AWS Certified Developer Associate, AWS Certified Solutions Architect…) or Azure (e.g., Microsoft Certified: DevOps Engineer Expert, Microsoft Certified: Azure Developer Associate, Microsoft Certified: Solutions Architect Expert…).
  • Experience working with and supporting informatics and data science SaaS solutions, specifically in a scientific domain, such as DNAnexus and Pumas-AI.
  • Familiarity with broad software libraries and applications in bioinformatics or data sciences domains (i.e. conda, CRAN R packages, Bioconductor).
  • Experience working in an Agile Scrum environment for project and task management.
  • Experience using source control management tools, such as GitHub, GitLab, Bitbucket, or Azure Repos.
  • Proficient in supporting and maintaining interactive data science platforms like RStudio or Jupyter in a shared environment.
  • Experience in software testing, performance profiling, or workflow optimization.
  • Prior experience in a validated/qualified GxP environment.
  • Data pipeline engineering experience using a workflow management system such as Snakemake a plus.
  • Experience with next generation sequencing platforms such as PacBio or Illumina a plus.


  • Bachelor's degree in computer science, bioinformatics, or other engineering discipline (or equivalent experience), plus five years of relevant professional experience.

We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, gender, gender identity, sexual orientation, national origin, disability status, protected veteran status, or any other characteristic protected by law.

In the U.S., the salary range for this position is $ 108,800 to $ 163,200 per year, which factors in various geographic regions. The base pay actually offered will take into account internal equity and also may vary depending on the candidate's geographic region, job-related knowledge, skills, and experience among other factors. A discretionary bonus and/or long-term incentive units may be provided as part of the compensation package, in addition to the full range of medical, financial, and/or other benefits, dependent on the level and position offered.

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San Rafael


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