What if…you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

Flagship Pioneering’s venture creation engine, Flagship Labs, is where companies such as Moderna Therapeutics (NASDAQ: MRNA), Rubius Therapeutics (NASDAQ: RUBY), and Editas Medicines (NASDAQ: EDIT) were conceived and created.  Since Flagship’s founding in 2000, the firm has originated and fostered the development of more than 100 scientific ventures, resulting in over $34 billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents.

Flagship Pioneering’s Digital Ecosystem: 

Flagship Pioneering is driving innovations in how it manages and supports its growing portfolio of companies, including the development of a cross-portfolio Digital and Data team. We believe that the sophisticated use of modern digital and data technologies is a strategic differentiator for companies, with the potential to significantly advance their productivity, market position and long-term success. 

The Mission:

The Flagship Ecosystem presents a compelling opportunity for impact-focused technology professionals for a number of reasons:

  • Flagship’s companies create medicines that save and improve the lives of patients.  Moreover, the companies in the Flagship network have the potential to dramatically change disease treatment, healthcare, and sustainable agriculture on a global scale. 
  • The Flagship portfolio is composed of new and growing companies with widely varying needs that span all aspects of technology, presenting incredible opportunities for making lasting impact, learning and development. 
  • Flagship creates new, cloud-centric companies that operate without the burden of legacy systems or technical debt.  Individuals that understand the technical opportunities and challenges in company growth will have the opportunity to influence and shape the trajectory of dozens of companies. 

To deliver on this mission, Flagship Pioneering seeks individuals who have a proven track record of solving enterprise-scale challenges while thriving in a dynamic startup culture.   

Position Summary:

What you’ll do: In this key role, you’ll play a major part in shaping the digital and data cultures of the next generation of biotech companies; interface directly with scientific and company leadership in a consultative and advisory capacity; own the engagement and ultimate success around specific projects; develop deep expertise in the challenges faced by biotech startups and how to address them with cloud-based solutions; design architectural standards for how data lands, moves, morphs and is accessed to ensure appreciating value. In any given week you may find yourself deploying a data lake, advising on container orchestration, designing launch templates, or helping ML teams design a data versioning system.

How you’ll succeed: You will have a “go see for yourself” mentality to ensure that advice and solutions meet the particular needs of our companies. You’ll develop deep relationships with various stakeholders and become a respected partner in both strategic thinking and execution. Your mindset will be focused on creating generalized and extensible tools that make an impact at individual companies as well as the portfolio in aggregate.

The ideal candidate will have a strong background in AWS architecture, data modeling, DevOps and automation. A history of delivering impactful solutions in an agile manner with strong attention to diverse customer needs is necessary for success in this role. Experience in the biopharma industry with familiarity of various data types (e.g. NGS, *omics, imaging) is highly valued.

We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort working in and contributing to a dynamic and cross-functional team environment.  The level of the role will align with education and experience. This position will be part of the Flagship Digital team, reporting to the Vice President of Data & Systems Engineering.

Key Responsibilities:

  • Design reference implementations, guidelines, platform tools and trainings to support Flagship companies
  • Educate and assist companies on the pragmatic application of FAIR principles
  • Lead the implementation of data lakes and supporting components (e.g., pipelines, crawlers, transformations, catalogs, CI/CD, etc) for portfolio companies
  • Provide expert guidance on the appropriate use of various database models, technologies and methods (e.g. normalized vs denormalized, document vs key/value, RDS vs Athena, etc)
  • Design integration patterns for common biotech research scenarios
  • Consult with data scientists and engineers around best practices for DevOps and MLOps
  • Develop strong relationships with our companies as well as Flagship Digital and operations colleagues
  • Stay current with relevant tools and methods and advise on how they can help our companies
  • Help to build and nurture our cross-portfolio engineering community by organizing meetups and focus-groups
  • May lead small teams of consultants for larger projects

Minimum Qualifications:

  • 6+ years data engineering and systems integration experience
  • 3+ years experience building AWS solutions using various technologies (e.g. S3, Lake Formation, Glue, DataSync, Athena, etc)
  • Expertise with a variety of data technologies, including RDBMS, NoSQL, warehouses and data lakes
  • Proficiency with python, SQL, IaC and DevOps best practices
  • Expertise with containers, orchestration and cost-effective scaling practices
  • Goal-oriented and organized with excellent project management skills
  • Outstanding communication skills, particularly as they relate to collaborations across the boundaries of science, technology and business
  • A people person with an exceptional ability to collaborate with scientists of different backgrounds

Preferred Qualifications:

  • AWS Solutions Architect or DevOps Engineer professional level certification
  • Familiarity with bioinformatics, computational biology/chemistry
  • Knowledge of public life science datasets (e.g. dbGaP, UKBB, etc) and best practices for their use
  • Experience using, modeling and integrating modern research-support systems, including ELN, LIMS, registration & inventory systems etc. Benchling experience preferred
  • Familiarity with the specialized needs of data science and ML teams


More About Flagship Pioneering

We are creative optimists and we would love for you to consider joining our team!  See all our open opportunities across Flagship Pioneering’s Ecosystem!

We believe pioneering is best done by teams, and that it is a process that can be taught, learned, and replicated.  Learn more about our Company Creation Model.

Can Breakthrough Innovations Be Made Systematically? A Conversation With Noubar Afeyan, Flagship Pioneering’s CEO.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

Recruitment & Staffing Agencies:  Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates.  The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team.   Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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