Senior Software Engineer II, Trial Engine

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

Job summary

Formation Bio is seeking a Senior Software Engineer II to join the Trial Execution team in New York/Boston area. You will own critical software that runs active clinical trials, ensuring regulatory compliance and data provenance while enabling AI‑driven insights.

In this hybrid role, you will collaborate with Clinical Operations, Data Management, Regulatory, QA, and Infrastructure to ship robust software, integrate clinical systems, and drive software quality in a regulated environment.

Qualifications

• 7+ years of production software experience in regulated environments.
• Familiar with GxP/GCP, validation, and audit trails.
• Strong cloud fundamentals and modern software delivery practices.

Responsibilities

• Drive design, delivery, and operation of production software for active trials.
• Coordinate with cross‑functional teams to align on functional and regulatory needs.
• Translate validation requirements into traceable, testable software and improve workflows.
• Design and ship AI‑native trial execution capabilities with provenance and human review.
• Build integrations across clinical systems and vendor data feeds.
• Own trial‑specific domain logic and data governance with data engineering.
• Shift work left to enable earlier and parallel activities.
• Engage QA and validation partners early and ensure compliance in decisions.
• Set technical direction, mentor others, and establish safe fast delivery practices.

Skills

Production software

GxP/GCP

Cloud fundamentals

Cross‑functional communication

Regulatory awareness

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're going to 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. If the posted range doesn't match your expectations, we still encourage you to apply!

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. Please apply only if you reside in these locations or are willing to relocate

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.

Voluntary Self-Identification

For government reporting purposes, we ask candidates to respond to the below self-identification survey. Completion of the form is entirely voluntary. Whatever your decision, it will not be considered in the hiring process or thereafter. Any information that you do provide will be recorded and maintained in a confidential file.

As set forth in Formation Bio’s Equal Employment Opportunity policy, we do not discriminate on the basis of any protected group status under any applicable law.

If you believe you belong to any of the categories of protected veterans listed below, please indicate by making the appropriate selection. As a government contractor subject to the Vietnam Era Veterans Readjustment Assistance Act (VEVRAA), we request this information in order to measure the effectiveness of the outreach and positive recruitment efforts we undertake pursuant to VEVRAA. Classification of protected categories is as follows:

A "disabled veteran" is one of the following: a veteran of the U.S. military, ground, naval or air service who is entitled to compensation (or who but for the receipt of military retired pay would be entitled to compensation) under laws administered by the Secretary of Veterans Affairs; or a person who was discharged or released from active duty because of a service‑connected disability.

A "recently separated veteran" means any veteran during the three‑year period beginning on the date of such veteran's discharge or release from active duty in the U.S. military, ground, naval, or air service.

An "active duty wartime or campaign badge veteran" means a veteran who served on active duty in the U.S. military, ground, naval or air service during a war, or in a campaign or expedition for which a campaign badge has been authorized under the laws administered by the Department of Defense.

An "Armed forces service medal veteran" means a veteran who, while serving on active duty in the U.S. military, ground, naval or air service, participated in a United States military operation for which an Armed Forces service medal was awarded pursuant to Executive Order 12985.

Select...

Voluntary Self-Identification of Disability

Form CC‑305

Page 1 of 1

OMB Control Number 1250-0005

Expires 07/31/2029

Why are you being asked to complete this form?

We are a federal contractor or subcontractor. The law requires us to provide equal employment opportunity to qualified people with disabilities. We have a goal of having at least 7% of our workers as people with disabilities. The law says we must measure our progress towards this goal. To do this, we must ask applicants and employees if they have a disability or have ever had one. People can become disabled, so we need to ask this question at least every five years.

Completing this form is voluntary, and we hope that you will choose to do so. Your answer is confidential. No one who makes hiring decisions will see it. Your decision to complete the form and your answer will not harm you in any way. If you want to learn more about the law or this form, visit the U.S. Department of Labor’s Office of Federal Contract Compliance Programs (OFCCP) website at www.dol.gov/ofccp.

How do you know if you have a disability?

A disability is a condition that substantially limits one or more of your “major life activities.” If you have or have ever had such a condition, you are a person with a disability. Disabilities include, but are not limited to:

• Alcohol or other substance use disorder (not currently using drugs illegally)
• Autoimmune disorder, for example, lupus, fibromyalgia, rheumatoid arthritis, HIV/AIDS
• Blind or low vision
• Cancer (past or present)
• Cardiovascular or heart disease
• Celiac disease
• Cerebral palsy
• Deaf or serious difficulty hearing
• Diabetes
• Disfigurement, for example, disfigurement caused by burns, wounds, accidents, or congenital disorders
• Epilepsy or other seizure disorder
• Gastrointestinal disorders, for example, Crohn's Disease, irritable bowel syndrome
• Intellectual or developmental disability
• Mental health conditions, for example, depression, bipolar disorder, anxiety disorder, schizophrenia, PTSD
• Missing limbs or partially missing limbs
• Mobility impairment, benefiting from the use of a wheelchair, scooter, walker, leg brace(s) and/or other supports
• Nervous system condition, for example, migraine headaches, Parkinson’s disease, multiple sclerosis (MS)
• Neurodivergence, for example, attention‑deficit/hyperactivity disorder (ADHD), autism spectrum disorder, dyslexia, dyspraxia, other learning disabilities
• Partial or complete paralysis (any cause)
• Pulmonary or respiratory conditions, for example, tuberculosis, asthma, emphysema
• Short stature (dwarfism)
• Traumatic brain injury

Disability Status Select...

PUBLIC BURDEN STATEMENT: According to the Paperwork Reduction Act of 1995 no persons are required to respond to a collection of information unless such collection displays a valid OMB control number. This survey should take about 5 minutes to complete.