Director, Scientific Cloud Engineering

ABOUT FLAGSHIP PIONEERING Flagship Pioneering is a life sciences innovation enterprise that invents and builds transformative companies. Since its founding in 2000, Flagship has originated more than 100 ventures, including Moderna, and has deployed over $4 billion toward scientific discovery. Our Scientific Cloud team is the connective tissue that powers data and technology infrastructure across Flagship's growing portfolio of companies.

About Scientific Cloud:
Scientific Cloud is Flagship Pioneering's portfolio-facing IT organization, responsible for the cloud engineering, data and informatics engineering, research systems, lab systems, and vendor management capabilities that power Flagship's emerging companies. The team operates with a portfolio-first orientation — building durable, shared infrastructure that individual ventures can rely on at every stage of company formation and growth.

THE POSITION The Director, Scientific Cloud Engineering is a senior technical organizational leader responsible for engineering the cloud and computational infrastructure that underpins scientific discovery across the Flagship portfolio. Reporting to the Senior Director of Scientific Cloud, this individual will manage and lead a growing team of engineers — including Cloud Dev Ops and Bioinformatics— and serve as the primary technical authority for scientific , and scientific computing platforms.

This role sits at the intersection of cloud engineering and life sciences. The Director will bring both the technical depth of an experienced cloud architect and a meaningful understanding of the computational demands of biotech research — including genomics workflows, high-performance computing, containerized pipelines, and AI/ML infrastructure. They will partner closely with Data Architecture & Engineering, Lab Systems, and Research Systems teams to ensure that what gets built is scalable, reproducible, and grounded in the realities of scientific work.

CORE RESPONSIBILITIES Team Leadership & Engineering Management Lead, mentor, and grow , including external contractors and consultants; set a high technical bar and foster a culture of rigor, collaboration, and continuous improvement.

Serve as a player-coach — providing direct technical contributions while managing team capacity, priorities, and professional development.

Partner with the Senior Director of Scientific Cloud to define team roadmap, resource allocation, and hiring strategy as the portfolio scales.

Establish engineering best practices, code review standards, and documentation norms across their Scientific Cloud Engineering team.

Cloud Architecture & Infrastructure Own and evolve the cloud architecture strategy for Scientific Cloud, designing scalable, secure, and cost-efficient infrastructure across AWS and/or Azure environments.

Architect and deliver reusable infrastructure-as-code (IaC) solutions — including Terraform modules, CDK constructs, and containerized service templates — that portfolio companies can adopt without custom engineering.

Partner with Infrastructure, Operations, and Architecture (IO&A) to define and enforce cloud governance guardrails: identity and access management (IAM), networking, secrets management, cost tagging, and security posture.

Design and maintain HPC and compute environments — including Nextflow/Cromwell execution layers, Kubernetes clusters, and GPU-enabled instances — optimized for scientific workloads.

Evaluate and adopt emerging cloud capabilities, including serverless orchestration, data lakehouse patterns, and managed ML platforms (e.g., AWS Sage Maker, Azure ML).Scientific Computing & Bioinformatics Platformsand data scientists to architect robust, reproducible pipeline infrastructure for genomics, proteomics, and…