Principal Software Engineer
Neomorph, Inc., San Diego, CA, United States
**** Overview
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.
Responsibilities
**1. ******
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
**
2.
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
**
3.
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
4.
**
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)
5.
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
6.
Technical Leadership
Provide technical guidance and mentorship
Contribute to planning and prioritization discussions
Lead by example as a hands-on builder
Qualifications
Required
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
Preferred
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
**
**
**
**
**
**
What we offer:
Industry-competitive compensation
Annual target bonus
Stock options
401K plan
Career advancement opportunities
Monthly town halls to share business and scientific updates
Work Hard, Stay Well
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
Lifestyle
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)
**
**
Have Fun!
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).
About Us:
Neomorph is a venture backed biotechnology company solving critical problems in human health through the discovery and development of innovative new medicines against ‘undruggable targets’. Our team is comprised of industry leading experts in protein degradation and molecular glues who have a track record of ground-breaking discoveries in the field. We are committed to leadership in advancing the science and technology of molecular glue drug discovery, while prosecuting a pipeline of projects through clinical development. Our patient-first, science-driven approach is complemented by our dedication to a supportive and collaborative work environment.
Neomorph is headquartered in San Diego, California.
Neomorph is committed to pursuing and hiring a diverse workforce and is proud to be an equal opportunity employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of any characteristic protected by applicable federal, state or local law.
**
Notice to agencies: **
Neomorph will not accept unsolicited assistance from recruiting/search agencies for this employment opportunity. Please, no phone calls or emails. All resumes submitted by recruiting or search agencies to any employee at Neomorph via email, the Internet or in any form and/or method without a valid written search/recruitment agreement in place for this position will be deemed the sole property of Neomorph. No fee will be paid in the event the candidate is hired by Neomorph as a result of the referral or through other means.
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.
Responsibilities
**1. ******
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
**
2.
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
**
3.
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
4.
**
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)
5.
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
6.
Technical Leadership
Provide technical guidance and mentorship
Contribute to planning and prioritization discussions
Lead by example as a hands-on builder
Qualifications
Required
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
Preferred
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
**
**
**
**
**
**
What we offer:
Industry-competitive compensation
Annual target bonus
Stock options
401K plan
Career advancement opportunities
Monthly town halls to share business and scientific updates
Work Hard, Stay Well
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
Lifestyle
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)
**
**
Have Fun!
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).
About Us:
Neomorph is a venture backed biotechnology company solving critical problems in human health through the discovery and development of innovative new medicines against ‘undruggable targets’. Our team is comprised of industry leading experts in protein degradation and molecular glues who have a track record of ground-breaking discoveries in the field. We are committed to leadership in advancing the science and technology of molecular glue drug discovery, while prosecuting a pipeline of projects through clinical development. Our patient-first, science-driven approach is complemented by our dedication to a supportive and collaborative work environment.
Neomorph is headquartered in San Diego, California.
Neomorph is committed to pursuing and hiring a diverse workforce and is proud to be an equal opportunity employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of any characteristic protected by applicable federal, state or local law.
**
Notice to agencies: **
Neomorph will not accept unsolicited assistance from recruiting/search agencies for this employment opportunity. Please, no phone calls or emails. All resumes submitted by recruiting or search agencies to any employee at Neomorph via email, the Internet or in any form and/or method without a valid written search/recruitment agreement in place for this position will be deemed the sole property of Neomorph. No fee will be paid in the event the candidate is hired by Neomorph as a result of the referral or through other means.