Principal Software Engineer

Neomorph•San Diego, CA

About The Position

The Principal Software Engineer is a senior individual contributor responsible for designing, building, and improving the internal systems that power Neomorph’s scientific operations, data workflows, lab-facing software, and data-driven decision-making. This is a hands-on role focused on delivering scalable, reliable systems that people depend on every day. Working closely with Data Sciences, Biology, Chemistry, Molecular Sciences, and Operations, you’ll turn complex requirements into practical, well-designed systems. You’ll extend and improve a sophisticated internal platform of interconnected applications, including compound management, data visualization, and program management. You’ll build new capabilities, improve existing integrations, and diagnose production issues, working directly with scientific users to turn real-world needs into software they can depend on. The role includes ownership and evolution of systems and integrations within the broader platform. The ideal candidate is comfortable working in large codebases, takes ownership of data correctness, and ships pragmatic solutions in a fast-paced, collaborative environment.

Requirements

BS/MS in Computer Science, Engineering, or related field (or equivalent experience)
10+ years of software engineering experience, including work in complex, established codebases
Strong proficiency in Java. The core platform is built on Java 25 and Jakarta EE (Servlets, Hibernate/JPA); this is not a Spring Boot environment.
Strong SQL skills, including relational data modeling, schema design, and query optimization across databases such as PostgreSQL, MySQL, and Snowflake
Proven experience operating at a senior or principal-level
Experience designing and operating production APIs and integration-heavy, data-pipeline systems
Experience debugging cross-system data issues and building reliable operational workflows
Experience with AWS or similar cloud environments
Comfortable working directly with scientists, executives, and non-technical stakeholders to define and deliver practical solutions

Nice To Haves

Experience in biotech, data-intensive, or scientific environments
Familiarity with scientific platforms such as ELN, LIMS, inventory management, compound registration or assay/screening systems
Exposure to machine learning or data science workflows
Experience building internal tools or lightweight user-facing applications
Startup experience and comfort balancing speed with long-term maintainability

Responsibilities

Application & Systems Development Design, build, and maintain backend services, internal applications, automation jobs, and APIs within a Java-based platform Architect and implement new features and capabilities within an existing application framework. Build lightweight React frontends where needed, integrated with Java backends
Systems Integration Build and maintain integrations with external scientific platforms Develop and maintain import/export pipelines, event-driven workflows, and API-based data synchronization Debug and resolve failures at the boundaries between internal and external systems
Engineering Excellence Maintain high standards for code quality, testing, and documentation Improve system reliability, performance, and observability over time Contribute to CI/CD pipelines and development workflows
Cross-Functional Collaboration Work directly with scientific and operational teams to develop solutions that meet user needs Identify opportunities to simplify and automate manual workflows, including evaluation and adoption of emerging technologies (e.g., AI agents, workflow orchestration, lab automation)
Platform Evaluation Contribute to the evaluation of third-party scientific platforms (ELN, LIMS, inventory systems) as potential replacements for or complements to internal systems Assess vendor APIs, data integration feasibility, and instrumentation compatibility
Technical Leadership Provide technical guidance and mentorship Contribute to planning and prioritization discussions Lead by example as a hands-on builder

Benefits

Industry-competitive compensation
Annual target bonus
Stock options
401K plan
Career advancement opportunities
Monthly town halls to share business and scientific updates
Comprehensive medical, dental, and vision plans for employees and their dependents
Health and Dependent Care FSA and HSA Plan with monthly Neomorph contribution
Employee Assistance Program
10 holidays + Winter Shutdown + 3 weeks of vacation time with additional accruals after 2nd year of employment, separate sick leave.
Supplemental pay for Pregnancy Disability Leave
Paid Parental Leave for employees with a newborn child or a child placed with them for adoption or foster care
Casual work environment
Volunteer days off each year to spend time contributing to causes you care about
Flexible work schedule
Access to onsite gym
Onsite space to store your bicycle (or surfboard)
We believe in work/life balance and Fun is at the core of our Core Values. In addition to department and company happy hours, we have regular company-wide and department lunches and social events (ie Padres games, summer picnic, holiday party, bring your kids to work day).