Director, Software / Informatics Engineering

Company overview:

Flagship Labs 109, Inc. (FL109) is a privately held, early-stage technology company pioneering the use of artificial intelligence, physics and hardware to transform the way we see biology. FL109 was conceived by Flagship Pioneering, which brings the courage, long-term vision, and resources needed to realize unreasonable results. Become part of our mission-driven team and help envision the future of science.

About Us

FL109 is a brand-new structural biology company pushing the boundaries of molecular discovery. By merging cutting-edge AI, experimental biology, new hardware, and software engineering, we aim to unlock transformative insights into the molecular world.

As our first Software Informatics Lead, you will play a pivotal role in shaping the technical backbone of our company. You will own the end-to-end development of scalable software solutions that empower our platform, ensuring it is robust, innovative, and ready to scale.

The Role

We are seeking a hands-on technical leader who thrives in an early-stage environment. This role will involve building data infrastructure, managing petabytes of data, scaling ML pipelines, and leading the development of a production-ready platform. You’ll also manage contractors for front-end development and oversee metadata/schema creation for our in-house database. You’ll set the tone for engineering excellence by actively coding and mentoring a small but growing team.

How You Will Contribute

• Technical Leadership: Build and lead the software engineering function, defining technical roadmaps, best practices, and scalable architecture.
• Hands-On Development: Code alongside your team to establish standards and demonstrate engineering excellence. Build systems that support end-to-end solutions, from prototype to production.
• Infrastructure and Scaling: Design and deploy scalable, cloud-based infrastructure for managing petabytes of public and proprietary data.
• ML Pipeline Integration: Collaborate closely with the ML team to scale AI pipelines into production-ready systems.
• Database Design: Create and manage metadata tracking, schemas, and the architecture of our in-house database to ensure seamless data access and tracking.
• Team Collaboration: Work cross-functionally with the ML and experimental teams to align technical needs with company goals. Oversee and manage contractors as needed.
• Culture Building: Set a high standard of operational excellence and mentor direct reports (including a software engineer and computational structural biology scientist). Foster a “builder” mindset in the team.

The Ideal Candidate Will Have:

• Hands-On Technical Expertise: Proven ability to build and deploy software solutions at scale (cloud infrastructure, databases, front-end interfaces). Experience with Python, Linux, AWS, Docker, and modern frameworks.
• End-to-End Builder: Demonstrated experience in developing products from ideation to production in resource-constrained environments.
• Data & Infrastructure Expertise: Deep understanding of designing and scaling data systems for large, heterogeneous datasets. Familiarity with metadata and schema management.
• Leadership Experience: Successful track record of leading small teams and mentoring early-career engineers. Ability to manage contractors effectively.
• AI Pipeline Experience: Proven ability to work with ML pipelines, ensuring scalability and smooth integration into production systems.
• Early-Stage Mentality: A resourceful, startup-oriented mindset with a focus on building systems that deliver immediate impact and scale over time.
• Collaboration Skills: Strong communication and interpersonal skills to work effectively across teams, especially with ML scientists and experimentalists.

Preferred Qualifications:

• Experience in structural biology, computational biology, or life sciences.
• Experience designing user-friendly front-end interfaces for complex systems.
• Experience working with high-dimensional datasets, including 2D image data and 3D volumetric data.
• Knowledge of modern data visualization tools and practices.

About Flagship

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in generation of over 500 patents, initiation of over 50 clinical trials for novel therapeutic agents and an aggregate value of more than $90 billion. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

Flagship Pioneering 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.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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.