Senior HPC Engineer

Senior HPC Engineer

Location: Remote

Skills: HPC, Python, Linux

Job Description:

Key responsibilities will include being single point of contact for design, deployment, maintenance, and optimization of on prem Linux / High-Performance Computing (HPC) environments for processing large-scale biological data. The role involves a mix of system administration, software engineering, and scientific collaboration. The immediate responsibility will be setting up new systems as a cluster and development environment to replicate our current production environments. The current bioinformatics pipelines will need to be made functional in the dev environment. Experience working with bcbio pipelines and Cebtos7 and Crnyos10 migration will be important.

• Pipeline Development & Automation: Support integration of existing pipelines on new cluster and help design, develop, and maintain robust, automated bioinformatics pipelines for next-generation sequencing.
• Software Development: Collaborate with software developers to create or modify custom bioinformatics software and tools, ensuring they are scalable and efficient on the cluster compute environment.
• Database Management: Create, maintain, and manage databases to store, organize, and track large volumes of biological data and metadata, ensuring data integrity and security.
• Troubleshooting and Support: Diagnose and resolve technical problems in system configuration, job schedulers, and scientific applications; train and support researchers in the use of tools and infrastructure.
• Collaboration and Communication: Work effectively within interdisciplinary teams of scientists, bioinformaticians, and IT staff to determine data needs, gather requirements, and present analysis results and reports.
• Innovation and Evaluation: Research and evaluate new technologies, tools, and algorithms, to improve operations and analytical capabilities.

Requirements:

• Programming Languages: Proficiency in relevant languages such as Python, R, and Linux bash scripting is essential.
• HPC & Cloud Experience: Proven track record of managing data and infrastructure in High-Performance Computing (HPC) clusters is required. Knowledge of cloud computing environments is nice to have.
• Workflow Systems & Containers: Experience with workflow management systems (e.g., Nextflow, Snakemake, WDL) and containerization technologies (e.g., Docker, Singularity).
• Version Control: Knowledge and experience using code management tools, such as Git/GitHub.
• Ideally but not required Biological Knowledge: A solid understanding of molecular biology, genomics, and relevant biological domain knowledge (e.g., oncology, rare diseases) is often necessary for context-specific problem-solving.
• Problem-Solving: Strong analytical, problem-solving, and conceptual skills to address complex data challenges.