{"id":36367,"url":"https://alion.io/job/flagshippioneering-principal-software-engineer-agentic-platform","title":"Principal Software Engineer - Agentic Platform","company":{"id":8393,"name":"Flagship Pioneering","domain":"flagshippioneering.com","url":"https://alion.io/company/flagshippioneering","size_band":"1001-5000","is_staffing_agency":false,"employer_type":"direct","is_intermediary":true,"listed_via":null,"ats_vendor":"Greenhouse","truth_index":{"grade":"A","score":85,"open_postings":10,"ghost_share":0,"stale_share":0.4,"repost_share":0,"time_to_fill_p50_days":62,"computed_at":"2026-10-17T05:46:00Z"}},"role":"Backend","role_family":"Backend","seniority":"lead","employment_type":null,"work_mode":"on_site","remote_scope":null,"remote_scope_basis":null,"remote_working_hours":null,"hiring_geo_confidence":"explicit","locations":["Cambridge, United States"],"countries":["US"],"hiring_countries":[],"hiring_countries_total":0,"salary":{"min":188000,"max":257500,"currency":"USD","period":"year","gross":null,"usd_annual":257500},"salary_estimate":null,"experience_years_min":10,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"AI Agents","optional":false},{"name":"AWS","optional":false},{"name":"AWS CDK","optional":false},{"name":"Machine Learning","optional":false},{"name":"Terraform","optional":false},{"name":"Anthropic","optional":true},{"name":"AutoGen","optional":true},{"name":"AWS Bedrock","optional":true},{"name":"CrewAI","optional":true},{"name":"FinOps","optional":true},{"name":"GDPR","optional":true},{"name":"LangChain","optional":true},{"name":"LangGraph","optional":true},{"name":"LLM","optional":true},{"name":"OpenAI","optional":true},{"name":"Vertex AI","optional":true}],"status":"live","first_seen_at":"2026-06-11T22:37:48Z","employer_posted_date":"2026-10-05","last_verified_at":"2026-10-18T03:25:36Z","board_verified":true,"closed_at":null,"days_open":128,"trust":{"level":"ok","repost_count":null,"flags":[],"days_open":128},"description":"ABOUT PIONEERING INTELLIGENCE\nPioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.\nThe Role \nThe Pioneering Intelligence group at Flagship Pioneering is building intelligent software systems that integrate agentic AI with scientific reasoning to accelerate discovery and decision-making. At the center of this effort is a new autonomous research platform. It supports autonomous AI systems that reason over complex biological problems. \nWe are seeking a Principal Software Engineer to own the underlying agentic platform: the durable orchestration layer on which long-running, multi-agent, multi-model scientific workflows run reliably. \nThis is a hands-on architect role for a senior engineer who has built and operated distributed systems at scale and wants to take agentic AI from research to production. You will set the technical foundation and standards for the platform, work shoulder-to-shoulder with AI scientists, engineers, and domain experts, and turn frontier agent patterns into reusable, dependable infrastructure. \nKey Responsibilities \nOwn the agentic platform end to end, from research prototype to production, building the durable orchestration layer for long-running, multi-stage scientific workflows. Architect workflow orchestration, evaluation frameworks, and event-driven distributed systems that deliver scale, resilience, and reliability. \nDefine SDK abstractions and API contracts between model and agent outputs and downstream consumers, decoupling rapid model iteration from product stability and reducing integration friction across teams. \nDeliver infrastructure-as-code reference implementations (AWS CDK, Terraform, containerized services) and transform exploratory AI proof-of-concepts into hardened, reusable patterns adopted across product domains. \nOwn platform cost-efficiency and scalability while preserving the performance and accuracy that our experiments and end users require. \nExplore and template agent design and deployment patterns, and set technical standards, code quality, and architectural direction for the platform. \nPartner across teams (modeling and agent teams, product) to align on integration points, dependency timelines, and delivery, and mentor engineers and scientists. \nProfessional Experience & Qualifications \nB.S. or M.S. in Computer Science, Engineering, or a related field, with 10+ years of professional software development experience. \nDemonstrated track record architecting and maintaining large-scale distributed systems in production at technology companies. \nDeep expertise in workflow orchestration and event-driven architecture, including stateful execution, idempotency, durable retries, and replay. \nStrong cloud-native engineering on AWS with infrastructure-as-code, containerization, and autoscaling. \nProven ability to take systems from prototype to hardened, observable, operationally excellent production. \nExperience designing SDKs, APIs, and data contracts that serve multiple downstream teams. \nExcellent communication skills and the ability to build organizational consensus around platform decisions. \nCollaborative and empathetic working style: listens to understand the needs of scientists, engineers, and downstream teams, and leads through influence. \nProven track record setting technical strategy and direction for a growing engineering organization, and mentoring engineers in a fast-moving environment. \nPreferred Qualifications \nHands-on experience with agentic AI and orchestration frameworks (e.g., Pydantic AI, LangGraph, LangChain, CrewAI, AutoGen). \nExperience integrating LLMs and model platforms, including Anthropic, OpenAI, Vertex AI, and Amazon Bedrock, and building evaluation and feedback-loop frameworks for agentic systems. \nFamiliarity with sandboxed code execution and agent harness development. \nExperience with LLM observability and monitoring tooling and cost-governance / FinOps for AI infrastructure. \nBackground in scientific domains such as biology, chemistry, or complex systems (a plus, not required). \nWhy Join Us \nBy joining the Agentic AI team within Flagship’s Pioneering Intelligence group, you will: \nOwn the platform foundation for a category-defining autonomous scientific reasoning engine. \nTake frontier agentic AI from research to dependable production at scale. \nCollaborate with visionary thinkers and top-tier researchers across Flagship’s ecosystem. \nSet the technical standards that the broader platform and product teams build on. \nShape the future of AI-powered discovery in a role that combines deep engineering excellence with direct human-health impact. \nABOUT FLAGSHIP PIONEERING\nFlagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies 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. \nFlagship 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.\nAt Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.\nWe are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.\nWe recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your backgroundand interest in Flagship.\nRecruitment & 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.\nThe salary range for this role is $188,000 - $257,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.\nPrivacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. 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