Sr. Research Systems Analyst

ABOUT FLAGSHIP PIONEERING Flagship Pioneering is a life sciences innovation enterprise that invents and builds transformative companies. Since its founding in 2000, Flagship has originated more than 100 ventures, including Moderna, and has deployed over $4 billion toward scientific discovery. Our Scientific Cloud team is the connective tissue that powers data and technology infrastructure across Flagship's growing portfolio of companies. About Scientific Cloud: Scientific Cloud is Flagship Pioneering's portfolio-facing IT organization, responsible for the cloud engineering, data and informatics engineering, research systems, lab systems, and vendor management capabilities that power Flagship's emerging companies. The team operates with a portfolio-first orientation — building durable, shared infrastructure that individual ventures can rely on at every stage of company formation and growth. THE POSITION The Senior Research Systems Analyst is a key member of the Scientific Cloud team, managing and optimizing the digital platforms that power scientific research and data management across Pioneering Medicines and Flagship Labs companies. This role is primarily responsible for administering and configuring core research platforms such as Benchling, CDD Vault, Quilt, AWS, Code Ocean, Seqera, etc., translating stakeholder requirements into system configurations, troubleshooting issues, and standing up these systems for Flagship's emerging companies. A meaningful part of the role involves staying current on the AI features available within these platforms and providing researchers with practical use cases and recommendations for using them well. The successful candidate brings hands-on platform expertise, structured thinking, and the ability to translate complex capabilities into practical enablement resources for bench scientists and data consumers alike. CORE RESPONSIBILITIES Research Systems Administration & Support Administer and optimize core research systems including ELN, LIMS, data management platforms, and other scientific tools including Benchling, CDD Vault, Quilt, AWS, Code Ocean, and Seqera, ensuring reliability, performance, and user satisfaction. Collaborate with stakeholders to gather, document, and translate requirements for R&D applications into actionable system configurations and enhancements.Provide Tier 2/3 technical support and troubleshooting for research, scientific, and data management systems, serving as an escalation point for complex issues. Monitor system performance, coordinate with IT infrastructure teams on uptime and capacity, and manage vendor relationships for supported platforms. Implementation & Portfolio Company Onboarding Partner directly with Flagship Labs and Pioneering Medicines startups to stand up and configure core research systems, ensuring new companies are up and running quickly on platforms suited to their research needs.Implement system configurations, data structures, and integrations tailored to each company's stage and scientific priorities.Train startup teams on platform best practices and workflows so they can operate independently from day one.Proactively identify opportunities for future integrations and platform enhancements as portfolio companies grow and their needs evolve. AI Features & Usage Maintain working knowledge of the AI features available within core research platforms, and stay current as new capabilities are released.Develop practical use cases and recommendations that help researchers and portfolio companies get the most value out of each platform's AI features. Advise on when a platform's native AI features are sufficient versus when a deeper integration may be worth pursuing. Training, Documentation & User Enablement Create high-quality user documentation, training materials, and quick-reference guides for research systems. Design and deliver training sessions and onboarding programs that drive system adoption and empower researchers to work effectively with digital tools. Develop and maintain a knowledge base that captures best practices, FAQs, and enablement resources for research systems across Pioneering Medicines and Flagship Labs companies. Continuous Improvement & Innovation Stay current with developments in laboratory informatics and cloud-native data management relevant to life sciences research platforms. Proactively identify opportunities to improve system usability, data quality, and researcher productivity, and contribute to roadmap planning discussions. Support process improvement initiatives and contribute to IT project delivery across the Research Systems team. Cross-Functional Collaboration Work closely with laboratory researchers, bioinformatics engineers, data architects, and IT colleagues to deliver integrated solutions that align with scientific priorities. Act as a liaison between research end users and IT, translating scientific needs into system requirements and ensuring technology investments deliver measurable value. REQUIRED QUALIFICATIONS Bachelor's degree in Information Technology, Computer Science, Bioinformatics, or a life sciences-related field; equivalent experience considered. At least 5 years of experience supporting, configuring, or administering laboratory or data management systems within the life sciences industry. Hands-on experience with one or more core research platforms (e.g., Benchling, CDD Vault, Quilt, AWS, Code Ocean, Seqera, or similar ELN/LIMS/data management tools). Familiarity with AI/ML concepts and an interest in how AI features are being embedded into enterprise research platforms. Demonstrated ability to create clear technical documentation, training materials, and user-facing guidance for diverse audiences. Strong analytical and problem-solving skills, with the ability to assess platform capabilities and translate them into actionable recommendations. Excellent communication skills with the ability to convey complex technical concepts to non-technical stakeholders effectively. Proven ability to manage multiple concurrent priorities in a fast-paced, science-driven environment. PREFERRED QUALIFICATIONS Familiarity with prompt engineering, LLM integration patterns, or AI feature evaluation for enterprise tools. Experience with scientific programming languages (e.g., Python, SQL) for data integration, reporting, or automation. Knowledge of cloud-based data management platforms (AWS S3, Glue, Athena) and FAIR data principles. Experience in a biotech, pharmaceutical, or academic research environment with cross-functional team engagement. ABOUT FLAGSHIP PIONEERING:Flagship 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. 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 .At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.We 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.We 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 background and interest in Flagship.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.Privacy 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. To exercise your rights or for questions, contact View email address on click.appcast.io. The salary range for this role is $108,000 - $148,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Flagship Pioneering currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Flagship Pioneering's good faith estimate as of the date of publication and may be modified in the future.Privacy 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. To exercise your rights or for questions, contact View email address on click.appcast.io.