Job Description

Overview The Stanford Center for Genomics and Personalized Medicine (SCGPM) has an exciting opportunity available for a motivated Biomedical Cloud Engineer to create innovative data architectures that will automate the process of turning big genomic data into biomedical insights. The ideal candidate can listen, interpret biological questions, assess the value and relevance of technologies and methods, and deliver actionable technical solutions. Background The Department of Veterans Affairs (VA) has commissioned the sequencing of hundreds of thousands of whole genomes from participants in the Million Veteran Program (MVP). This data is delivered to the SCGPM’s cloud computing environment and constitutes one of the largest repositories of whole-genome sequencing data in the world. The scale and richness of this data make it an incredible resource for biomedical research. Our goal is to turn this data lake into a data commons: a dynamic computing environment where researchers bring questions and get answers, all without having to go through manually collecting, cleaning, massaging, scrubbing, sorting, transforming, and filtering data. As an example of a publication from this group, see: Ross, P.B., Song, J., Tsao, P.S. et al. Trellis for efficient data and task management in the VA Million Veteran Program. Scientific Reports 11, 23229 (2021). Position In this position, you would be the system developer of the cloud-based MVP data management system called Trellis. Trellis stores petabytes of sequence data contributed by veterans and orchestrates its processing while keeping track of what programs were used and maintaining detailed data provenance. To manage the enormous volumes of biomedical research data that the MVP generates, Trellis is built on the Google Cloud Platform. The architecture uses serverless cloud services (Cloud Functions, Dataproc, Cloud SQL, Pub/Sub) to trigger pipelines automatically and at scale as new data arrives. A production version has already processed the whole genomic sequences of over 150,000 veterans and we plan to process at least as many more in the coming year. You would lead in keeping this production system running and optimized and would interface with our SecOps team in a FedRAMP-secure environment. Our Team Our SCGPM bioinformatics team is a multi-disciplinary group of about a dozen scientists, engineers, and software developers with complementary backgrounds, contributing expertise in managing and analyzing complex biomedical data. Other projects supported by this team include the NCI Human Tumor Atlas Network, Human BioMolecular Atlas Program, and the Stanford Metabolic Health Center. This position can be on-site in Palo Alto, fully remote, or hybrid. Duties Include Maintaining the smooth execution of our production Trellis system Working with our Security Operations team to respond to security incidents Constructing queries to our graph database to gain insights from pipeline run data Implementing population-level genomic analyses (GWAS, PCA) to verify data integrity Designing and integrating novel bioinformatics pipelines into our Trellis system Troubleshooting data flow in our state-driven Trellis architecture Building containers for bioinformatics tools and integrating them with our internal data management system to automate workflows Collaborating with researchers to explore solutions to relevant biological questions and maximize the value of our whole-genome sequencing dataset to the public Other duties may also be assigned Desired Qualifications Four-year degree in Genetics, Computer Science, Bioinformatics, Computational Physics, or a related field Experience with biomedical data formats (FASTQ, FASTA, BAM, CRAM, Hail MatrixTable, et al.) Comfortable in programming with Python Experience with cloud computing, especially Google Cloud Experience with databases, especially graph databases Experience with big data technologies (e.g., BigQuery, Spark, Hail, Terra) Familiarity with issues in computer data security Familiarity with FedRAMP cloud security Familiarity with FAIR principles of data management Excellent verbal and written communication skills An ability to independently grasp the objectives of research projects and assemble solutions from a range of technologies, standards, and approaches A desire to learn new methods and technologies and to adapt to demands of fast-paced research Education & Experience (REQUIRED) Bachelor's degree and five years of relevant experience, or a combination of education and relevant experience. Knowledge, Skills And Abilities (required) Expertise in designing, developing, testing, and deploying applications. Proficiency with application design and data modeling. Ability to define and solve logical problems for highly technical applications. Strong communication skills with both technical and non-technical clients. Ability to lead activities on structured team development projects. Ability to select, adapt, and effectively use a variety of programming methods. Knowledge of application domain. Certifications & Licenses None Physical Requirements Constantly perform desk-based computer tasks. Frequently sit, grasp lightly/fine manipulation. Occasionally stand/walk, writing by hand. Rarely use a telephone, lift/carry/push/pull objects that weigh up to 10 pounds. Consistent with its obligations under the law, the University will provide reasonable accommodations to any employee with a disability who requires accommodation to perform the essential functions of his or her job. Working Conditions May work extended hours, evening and weekends. Work Standards (from JDL) Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations. Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned. Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University\'s Administrative Guide, The job duties listed are typical examples of work performed by positions in this job classification and are not designed to contain or be interpreted as a comprehensive inventory of all duties, tasks, and responsibilities. Specific duties and responsibilities may vary depending on department or program needs without changing the general nature and scope of the job or level of responsibility. Employees may also perform other duties as assigned. Consistent with its obligations under the law, the University will provide reasonable accommodations to applicants and employees with disabilities. Applicants requiring a reasonable accommodation for any part of the application or hiring process should contact Stanford University Human Resources at stanfordelr@stanford.edu. For all other inquiries, please submit a contact form. Stanford is an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law. Additional Information Schedule: Full-time Job Code: 4822 Employee Status: Regular Grade: J Requisition ID: 107025 Work Arrangement: On Site #J-18808-Ljbffr Inside Higher Ed

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