Senior Systems Engineer - Cloud HPC

Who We Are 
Generate Biomedicines, Inc. is a Flagship backed, privately held biotechnology company on a mission to reimagine the drug discovery process to one of dynamic, data-driven generation. We pursue this audacious vision because we believe in the unique and revolutionary power of generative biology to radically transform the lives of billions, with an outsized opportunity for patients in need. Generate will be successful by constantly turning innovative ideas into methods, technologies, and products that solve some of the most difficult challenges with developing medicines. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us! 

Generate was founded by Flagship Pioneering. Flagship Pioneering conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. Since its launch in 2000, the firm has applied a unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures, resulting in over $30 billion in aggregate value. The current Flagship ecosystem comprises 37 transformative companies, including: Moderna Therapeutics (NASDAQ: MRNA), Rubius Therapeutics (NASDAQ: RUBY), Indigo Agriculture, and Sana Biotechnology. 
Position Summary 
Machine learning-powered protein generation is at the core of Generate’s platform. We aim to upend the traditional approach to drug development towards one characterized by intentionality, surgical precision, and speed by developing methods for protein generation that can reliably generalize across biological functions, disease areas, and therapeutic modalities. 

We are seeking a creative and motivated Systems Engineer to build the advanced computational platform required to achieve our goals. The successful candidate will join the Informatics/IT team at Generate and work closely with Machine Learning Scientists, Structural Biologists, and Computational Biologists to implement a scalable platform that rapidly advances our scientific programs. This role is deeply technical, spanning linux system administration, cloud infrastructure, software development and everything between. 

Key responsibilities: 

  • Design, implement and maintain Generate’s scientific compute platform, including: 
    • Customized workstations optimized for machine learning research 
    • Fast, scalable data storage 
    • Elastic and highly parallel infrastructure for pipeline execution 
    • Python SDK for development of parallel tasks and workflows 
    • Automation of key workflows 
  • Maintain awareness with commercial tools & industry best practice, and champion new solutions internally 
  • Deploy and maintain systems on AWS 

Qualifications, Knowledge & Skills: 

  • Strong experience in scientific/distributed computing 
    • Understanding of scientific tools like numpy, scipy, pytorch, keras, etc. 
    • Experience with Prefect and Dask is a plus 
  • Strong experience deploying, configuring, and maintaining Kubernetes/EKS 
  • Strong experience developing software in Python 
  • Strong understanding of containerization & environment deployment (Docker, Conda, etc) 
  • Experience with Linux system administration 
  • Experience with shell scripting (Bash, Python) 
  • Experience with file traditional share infrastructure (SMB/CIFS, NFS) and cloud file storage (S3, EFS, etc) 
  • Understanding of GPU technologies 
  • Understanding of AWS infrastructure, cloud architecture, and networking 
  • Strong collaborator with excellent communication skills and history of success in fast and dynamic teams 
  • Experience with Terraform, Ansible, and Version Control/CI/CD tools (Gitlab) 
  • Demonstrated understanding of IT and Cloud Security best practices 
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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