Senior Software Engineer II, Trial Engine

Formation; Town of Boston (NY); Hybrid; USD 214,000 - 267,000; Full time

Benefits offered by this job

Equity

Comprehensive benefits

Hybrid work model

Job summary

Formation Bio in New York City and Boston seeks a Senior Software Engineer II to own production software for active clinical trials, integrating with EDC and other clinical systems and shaping the technical approach.

You will collaborate with Clinical Operations, Data Management, Regulatory, QA, Data Engineering, and Infrastructure to deliver auditable, compliant software in a regulated space, focusing on AI-native pipelines and end-to-end trial support.

Qualifications

• 7+ years of experience building production software for clinical trials or regulated environments.
• Familiarity with GxP/GCP concepts, electronic signatures, and validation practices.
• Experience with cloud platforms (AWS, GCP, Azure) and modern distributed systems.
• Experience embedding AI-like tools and agentic pipelines into regulated software.
• Strong communication skills and ability to work with non-engineers and cross-functional teams.

Responsibilities

• Drive design, delivery, and operation of production software used in live clinical trials from site startup to data collection and close-out.
• Coordinate cross-functional dependencies with clinical, regulatory, data, and infrastructure teams.
• Translate validation requirements into testable software and improve engineering workflows for compliant delivery.
• Design and ship AI-native trial execution capabilities with provenance and audit trails for regulated contexts.
• Build integrations across clinical systems (EDC, CTMS, eTMF, CRO data feeds) to form a coherent trial picture.
• Own the trial-specific domain logic and collaborate with data engineering on ingestion, orchestration, and governance.

Skills

Production software

Regulated environment

Cloud fundamentals

AI tooling in regulated context

Mentoring & leadership

Effective communicator

Tools

AWS

GCP

Azure

Job description

Senior Software Engineer II, Trial Engine

New York, NY; Boston, MA; San Francisco, CA

About Formation Bio

Formation Bio is a tech and AI driven pharma company differentiated by radically more efficient drug development.

Advancements in AI and drug discovery are creating more candidate drugs than the industry can progress because of the high cost and time of clinical trials. Recognizing that this development bottleneck may ultimately limit the number of new medicines that can reach patients, Formation Bio, founded in 2016 as TrialSpark Inc., has built technology platforms, processes, and capabilities to accelerate all aspects of drug development and clinical trials. Formation Bio partners, acquires, or in-licenses drugs from pharma companies, research organizations, and biotechs to develop programs past clinical proof of concept and beyond, ultimately helping to bring new medicines to patients. The company is backed by investors across pharma and tech, including a16z, Sequoia, Sanofi, Thrive Capital, John Doerr, Spark Capital, SV Angel Growth, and others.

You can read more at the following links:

At Formation Bio, our values are the driving force behind our mission to revolutionize the pharma industry. Every team and individual at the company shares these same values, and every team and individual plays a key part in our mission to bring new treatments to patients faster and more efficiently.

About the Position

Clinical trials are where drug development actually gets slow and expensive. Sites take months to activate. Data arrives late, in fragments, from a dozen systems and vendors that don't talk to each other. People spend their weeks reconciling spreadsheets instead of making decisions. The Trial Execution team exists to fix that, and this role is a senior seat on it.

The constraint that makes this interesting: our trials run in a regulated space. Systems that touch patient safety or trial integrity are GxP-relevant, which means computer system validation, 21 CFR Part 11, audit trails, traceability, and a real burden of proof that the software does what it claims. Most engineers treat that as a wall. We think it's a design problem — and we think the companies that figure out how to run AI inside those constraints, rather than around them, will develop drugs faster than anyone else. We're looking for someone who finds that genuinely exciting rather than merely tolerable.

You’ll build the systems that run active trials: integrations with EDC and other clinical systems, site selection and activation, clinical data flows, monitoring and signal detection, timeline reconciliation across CROs and vendors. Increasingly that work is agentic — agents reading source data directly to surface discrepancies, signals, and tasks that a human would otherwise have hunted for by hand. Designing that so it's auditable, provenance-tracked, and appropriately human-in-the-loop is the hard and interesting part of the job.

As a Senior Software Engineer II, you’ll be a senior individual contributor and the technical owner of a meaningful slice of our Trial Execution platform. You’ll drive work across multiple quarters, from identifying the opportunity and shaping the technical approach through shipping and operating differentiated software used in active trials. You will partner directly with Clinical Operations, Data Management, Regulatory, QA, Data Engineering, and Infrastructure to develop the systems, integrations, data flows, and controls required to put that software into production. You will bring enough familiarity with regulated delivery to identify potential GxP implications early and engage the right QA and validation experts.

Responsibilities

• Drive and own the design, delivery, and operation of differentiated production software used in live clinical trials, from site startup and activation through data collection, monitoring, and close-out.
• Bring together clinical, regulatory, data, and infrastructure partners to resolve cross-functional dependencies and take software from technical design through validated use in active trials.
• Build within a validated SDLC: partner with QA and CSV experts to translate validation requirements into traceable, testable software, and improve the engineering workflows that make compliant delivery efficient and predictable.
• Design and ship AI-native trial execution capabilities — agents and pipelines that read clinical and operational source data to surface signals, discrepancies, and tasks — with the provenance, audit trails, and human review that a regulated context requires.
• Build integrations across the clinical systems and vendor landscape (EDC, CTMS, eTMF, CRO and lab data feeds, safety systems), and turn fragmented inputs into a coherent, queryable picture of a trial.
• Own the trial-specific domain logic and software built on clinical data, partnering with Data Engineering on shared ingestion, orchestration, warehouse, quality, and governance capabilities that clinical teams can trust and that stand up to inspection.
• Shift work left. Find the trial activities that traditionally happen sequentially and build the tooling that lets them start earlier or run in parallel.
• Develop strong working fluency in the team's regulated context. Recognize when GxP considerations apply, bring QA and validation partners into decisions early, and help translate their requirements into practical engineering approaches.
• Set technical direction and raise the bar: review designs, mentor engineers and other builders, and build the guardrails and automation that let the whole organization move fast safely.

About You

• 7+ years of experience building production software, including hands-on experience shipping software for use in a clinical trial. You are familiar with clinical systems and data flows and understand the operational realities of delivering software into an active trial environment.
• Familiarity with software delivery in a regulated or controlled environment, including concepts such as GxP/GCP, computer system validation, requirements traceability, audit trails, electronic signatures, and change control. You do not need to be the organization's regulatory expert, but you should know when these considerations matter and how to work effectively with QA and validation partners.
• You see regulation as a design constraint to work within, not a reason systems cannot improve. You can help translate regulatory requirements into software that is both compliant and well engineered.
• A strong builder: clean, maintainable code, solid distributed systems and cloud fundamentals (AWS, GCP, or Azure), and the judgment to know when to build for the next five years and when to build for next week.
• You build with AI tools daily — LLMs, agentic workflows, retrieval pipelines — and you're actively interested in how to bring them into regulated clinical work responsibly. This is a core part of the role, not a side interest.
• Track record of technical ownership at senior scope: multi-quarter efforts, cross-functional dependencies, and designs that other engineers built on.
• Excellent communicator with non-engineers. You can sit with a clinical operations lead or a QA director, understand their world, and align on an approach.
• Comfortable with ambiguity. Our trial portfolio and our approach both change; the roadmap you inherit will not be the one you finish.

Total Compensation Range: $213,500 - $267,000

CompensationIndividual compensation is determined by several factors, including role scope, geographic location, and skills & experience. Your offer will reflect where you fall within the range based on these considerations. In addition to base salary, we offer equity, comprehensive benefits, and generous perks.

Where We Hire Formation Bio is prioritizing hiring in key hubs, primarily the New York City and Boston metro areas, with a hybrid model requiring 3 days per week in office. Applicants from the Research Triangle (NC) and San Francisco Bay Area may also be considered.

Equal Opportunity Formation Bio is committed to building a diverse and inclusive team. We are an equal opportunity employer and welcome candidates from all backgrounds. All qualified applicants will receive consideration for employment without regard to race, color, creed, religion, national origin, ancestry, sex (including pregnancy, childbirth, breastfeeding, and related medical conditions), gender identity or expression, sexual orientation, age, disability, genetic information, marital status, military or veteran status, or any other characteristic protected by federal, state, or local law.