Senior Software Engineer I, DevOps

About Generate:Biomedicines

Generate:Biomedicines is a new kind of therapeutics company – existing at the intersection of machine learning, biological engineering, and medicine – pioneering Generative Biology™ to create breakthrough medicines where novel therapeutics are computationally generated, instead of being discovered. The Company has built a machine learning-powered biomedicines platform with the potential to generate new drugs across a wide range of biologic modalities. This platform represents a potentially fundamental shift in what is possible in the field of biotherapeutic development.

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. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us!

Generate:Biomedicines was founded in 2018 by Flagship Pioneering and has received over $750 million in funding, providing the resources to rapidly scale the organization. The Company has offices in Somerville and Andover, Massachusetts with 325+ employees.

The Role: 

Generate:Biomedicines is leading a revolutionary approach to therapeutic development, pioneering Generative Biology to create breakthrough medicines. We are seeking a Senior Software Engineer to drive infrastructure and workflow optimization for machine learning (ML) and protein design. This role sets the standard for technical excellence, scaling our tools and platforms to meet G:B's ambitious goals. 

As a senior team member, you will define and enforce best practices in containerization, CI/CD automation, and Infrastructure as Code (IaC). Familiarity with Kubernetes management tools (e.g., kubectl, Argo CD) is preferred, and a deep understanding of Python deployment and development dependencies is essential. You will collaborate with teams across data science, ML engineering, and bioinformatics, optimizing and securing workflows to ensure scalable, robust systems. This position will be onsite in Somerville, MA with flexibility to work a hybrid schedule. 

Here's how you will contribute:

• Python Environment & Packaging Standards: Define best practices for Python virtual environments, package creation, and dependency management, supporting a streamlined, digital-first approach. 

• Docker & Remote Development: Design and maintain Docker containers, including production-grade base images and remote VSCode development environments, empowering the team with efficient dependency management and prototyping. 

• Monitoring & Reliability: Implement performance monitoring and alerting systems for internal model serving, enhancing reliability. Collaborate with cross-functional teams to integrate security best practices. 

• CI/CD & Automation: Establish CI/CD standards for testing, image building, and deployment automation, driving operational efficiency. 

• Infrastructure & Dependency Standardization: Develop and uphold standards for dependency management, containerization, and workflow design, supporting scalable, resilient ML and biomedicine workflows. 

• AWS Services: Leverage AWS resources (e.g., EC2, S3, Lambda) to support infrastructure and workflow optimization in partnership with our Cloud team, driving scalable, secure, and cost-effective solutions. 

• IaC Standards: Use Terraform to define IaC standards, ensuring infrastructure consistency and adaptability. 

The Ideal Candidate will have:

• Proven experience in designing and managing Docker environments for ML or bioinformatics workflows. 

• Expertise in Python environments and package management, including pip-installable packages and Artifactory integration. 

• Proficiency in GitLab CI/CD with a strong understanding of automated testing, deployment, and monitoring. 

• Strong skills in Git and UNIX, with the ability to establish and mentor best practices in version control and shell scripting. 

Preferred Qualifications 

• Experience in setting and enforcing engineering best practices. 

• Adaptability in a dynamic environment, demonstrating a resilient, science-first approach. 

• Familiarity with bioinformatics or ML model deployment in a high-impact, patient-centered environment. 

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Generate:Biomedicines is 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.

COVID Safety:

Generate:Biomedicines enforces a mandatory vaccination policy for COVID-19. All employees must be fully vaccinated and have received a booster.  The purpose of this policy is to safeguard the health of our employees, their families, and the community at large from infectious disease that may be reduced by vaccinations.  The Company will make exceptions to this policy if required by applicable law and will consider requests for an exemption from this policy due to a medical reason, or because of a sincerely held religious belief, or any other exemptions that may be recognized by applicable.

Recruitment & Staffing Agencies: Generate:Biomedicines does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Generate:Biomedicines or its employees is strictly prohibited unless contacted directly by the Company’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Generate:Biomedicines and the Company will not owe any referral or other fees with respect thereto.