Principal Software Engineer - Agentic Platform at Flagship Pioneering, Inc.

About the role

At Flagship Pioneering, the Pioneering Intelligence team is dedicated to creating advanced software systems that integrate agentic artificial intelligence with scientific reasoning to improve discovery and decision-making processes. This position focuses on an autonomous research platform designed to empower AI systems in addressing intricate biological problems. We are seeking a Principal Software Engineer to spearhead the development of the core agentic platform, which acts as the orchestration layer for extensive scientific workflows.

Key facts

Location: Cambridge, MA USA

Engagement: Full-time

Team: Agentic AI

What you’ll do

- Assume complete responsibility for the agentic platform, overseeing its evolution from a research prototype to a fully operational production system, while building a dependable orchestration layer for complex scientific workflows.
- Design and implement systems for workflow orchestration, evaluation frameworks, and event-driven distributed architectures that guarantee both scalability and reliability.
- Create software development kit (SDK) abstractions and application programming interface (API) contracts to ensure seamless integration between model outputs and downstream systems, reducing friction during model iterations.
- Develop infrastructure-as-code reference implementations utilizing AWS CDK, Terraform, and containerized services, transforming exploratory AI concepts into robust, reusable solutions.
- Oversee the platform’s cost-effectiveness and scalability while ensuring optimal performance and accuracy for both experiments and end users.




- Establish and standardize agent design and deployment methodologies, setting the technical standards for the platform.
- Collaborate with diverse teams, including modeling and product groups, to align integration points and timelines, while also providing mentorship to engineers and scientists.
- Engage in continuous improvement of the platform by implementing feedback loops and iterating on design based on user experience and performance metrics.

Requirements

- A Bachelor's or Master's degree in Computer Science, Engineering, or a related field, coupled with over 10 years of professional experience in software development.
- Demonstrated expertise in designing and maintaining large-scale distributed systems within a production workplace, particularly in technology companies.
- In-depth knowledge of workflow orchestration and event-driven architecture, including principles of stateful execution, idempotency, and durable retries.
- Strong experience in cloud-native engineering on AWS, with a focus on infrastructure-as-code, containerization, and autoscaling techniques.
- Proven ability to transition systems from prototype to reliable, observable, and operational production environments.
- Experience in designing SDKs, APIs, and data contracts that cater to multiple downstream teams.




- Exceptional communication skills with a history of building consensus around platform-related decisions.
- A collaborative mindset, capable of understanding the needs of both scientists and engineers, and leading through influence.
- Experience in establishing technical strategy and mentoring engineers in a fast-paced environment.

Nice to have

- Practical experience with agentic AI and orchestration frameworks such as Pydantic AI, LangGraph, LangChain, CrewAI, or AutoGen.
- Familiarity with integrating large language models (LLMs) and model platforms like Anthropic, OpenAI, Vertex AI, and Amazon Bedrock, including the development of evaluation frameworks for agentic systems.
- Knowledge of sandboxed code execution and the development of agent harnesses.
- Experience with observability and monitoring tools for LLMs, as well as cost-governance practices for AI infrastructure.
- A background in scientific disciplines such as biology, chemistry, or complex systems is beneficial but not mandatory.

Skills & tools

- Proficient in programming languages such as Python, Java, or Go.
- Familiar with cloud services and infrastructure management tools, particularly AWS.
- Experienced in using containerization technologies like Docker and orchestration tools such as Kubernetes.
- Knowledgeable in CI/CD practices and tools for continuous integration and deployment.
- Familiar with Agile methodologies and best practices in software development.

Practical notes

This role is open to candidates who may require visa sponsorship. We provide competitive benefits and foster a supportive work environment.

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📌 Principal Software Engineer - Agentic Platform (Cambridge)
🏢 Flagship Pioneering
📍 Cambridge