PRINCIPAL SOFTWARE ENGINEER

Socket.dev; San Diego (CA); On-site; USD 181,000 - 245,000; Full time

Job summary

Sanford Burnham Prebys Medical Discovery Institute is seeking a senior software engineer to lead biotech software efforts. The role focuses on architecting scalable, multi-language software for cancer data science, spanning Python, C++, R, and more, with HPC and containerization at its core.

You will guide design, implement robust dev practices, mentor staff, and collaborate with bioinformaticians and cloud operations to deliver impactful research software while contributing to open-source

Qualifications

• BSc or higher degree in software engineering, computer science, or a related discipline.
• Ten years of progressive software engineering roles, with at least 2 years in biomedical computing.
• Fluency in at least three of python, C#, C++, R, Nextflow and bash.
• Experience administering complex software source-code control environments.
• At least two years of HPC experience in a containerized environment.
• Experience working with SQL and database technology.

Responsibilities

• Architect, design and implement robust software development practices.
• Architect and develop complex software for cancer data science in C++, python, perl, R and other programming languages as best suit project needs.
• Optimize software for high-performance computing environments, including containerization, dev/ops, test-driven development and other techniques.
• Assist with systems administration, liaising closely with Dev/Ops, Sys/Ops and Cloud/Ops.
• Write high-quality, user-facing and developer-facing documentation.
• Mentor junior staff, fostering improved software development and technical growth.
• Implement and optimize AI-based software development tools.
• Present results and ideas related to assigned projects both verbally and in writing.
• Performs other related tasks, duties and responsibilities as required.

Skills

Python

C++

C#

R

Nextflow

bash

Education

BSc or higher in software engineering or computer science

Tools

Git

Docker

SQL

Job description

Sanford Burnham Prebys is much more than a research facility and hub for innovation; it’s a vibrant global community of talented scientists and researchers from over 30 countries. This worldwide representation enriches our perspectives and enhances our creative approach to solving complex scientific challenges.

We strive to be leaders not only in biomedical research but also in creating an environment where excellence thrives through collaboration across cultures and backgrounds. Our mission is to advance the biomedical sciences by cultivating the next generation of scientific leaders, providing meaningful opportunities for researchers of all backgrounds to learn, innovate, and make breakthrough discoveries that improve human health.

Together, we translate science into health.

The duties and responsibilities contained in the job description are intended to be examples of the accountabilities for which the person in the position will demonstrate competency through performance. The job description is not intended to be an all-inclusive list. Duties and responsibilities are subject to change and other duties may be assigned as necessary.

Position Summary:

This senior technology role in the institute’s NCI-designated Cancer Center will be responsible for technical leadership in applying software engineering techniques to the processing and management of complex biomedical data. They will be responsible for architecting and implementing sophisticated, multi-language, modular software that works scalably with very large datasets. Software tasks will support aspects ranging from SDLC (including dev/ops and overall software development practices), data ingestion, quality-control, feature-extraction, data-visualization, scalable analyses including parallelization and concurrency, full-stack interfaces, containerization and load-sensitive software design. This will require a very strong background in both theoretical and applied computer science, with particular benefit to previous software engineering experience dealing with complex scientific or other datasets. The successful candidate will have experience in designing and implementing software solutions in a wide range of programming languages and computing environments. They will have a particular emphasis on deploying design, analysis and programming skills to create systems that improve code-quality and boost productivity of large development teams of mixed skillsets. In particular, they will work closely with bioinformaticians, cloud ops and other related positions. They will provide technical guidance and mentorship to junior staff, including software engineers and trainees. They will be responsible for identifying technical opportunities, including recognition of new algorithms and software development opportunities. They may be involved in assembling and submitting funding applications. They may have external-facing roles, including interactions with collaborating research groups, commercial entities and other partner organizations. They will provide technical support to other researchers. They will also serve as a point of expertise throughout the organization in computer science and software engineering. They will be expected to generate peer-reviewed scientific research, both as a lead and as a collaborator. They will work in a variety of statistical and programming environments including python, Nextflow and R. They will be expected to contribute actively to open-source software development. They will set project milestones collaboratively with the PI, then manage themselves and other technical staff to meet them.

Amongst their key early roles will be standing up a robust software-development infrastructure for the rapidly-growing Institute cancer data science group. This will involve close collaborations across the Institute, particularly with the Center for Data Science.

Duties and Responsibilities:

• Architect, design and implement robust software development practices
• Architect and develop complex software for cancer data science in C++, python, perl, R and other programming languages as best suit project needs
• Optimize software for high-performance computing environments, including use of containerization, dev/ops, test-driven development and other software- and cloud-engineering techniques
• Assist with systems administration, liaising closely with Dev/Ops, Sys/Ops and Cloud/Ops
• Write high-quality, user-facing and developer-facing documentation
• Mentor junior staff, fostering improved software development and technical growth
• Implement and optimize AI-based software development tools
• To effectively present results and ideas related to assigned projects both verbally and in writing
• Performs other related tasks, duties and responsibilities as required, assigned, or directed.

Minimum Qualifications:

Education:

BSc or higher degree in software engineerng, computer science, or a related discipline

Experience:

• Ten (10) years of progressive software engineering roles, with at least 2 years working in a biomedical computing environment
• Fluency in at least three of python, C#, C++, R, Nextflow and bash
• Documented ability to drive process-improvement in software development, including dev/ops
• Experience administering complex software source-code control environments
• At least two years of HPC experience in a containerized environment
• Experience working with SQL and database technology

Certifications, Licenses, etc

None

Other Knowledge, Skills and/or Abilities:

• Work independently as well as in a team environment
• Be responsible, organized, and a problem solver
• Possess strong attention to detail, analytical, time management, organizational, communication, and interpersonal skills
• Professional proficiency in Microsoft Office, statistical software and programming
• Deep understanding of good software development practices
• Fluency in working on HPC environments, particularly those that are containerized

Supervisory Responsibilities:

Direct: Yes

Indirect: No

Work Environment:

The work environment characteristics described here are representative of those an employee encounters while performing the essential functions of this job.

This is an on-site position. When working on-site, the work environment is in a standard office setting. May occasionally be exposed to low to excessive noise, various odors, temperature changes, and equipment with moving parts, including but not limited to computers, phones, printers, and other standard office equipment.

Physical Requirements:

This role may require specific physical capabilities, including:

• Standing and Walking: Ability to occasionally (up to 3 hrs) stand or walk and move between different work areas.
• Other physical activity: This role basically requires constant (6 – 8 hrs) sitting, but no bending, squatting, climbing, kneeling, crawling or twisting is necessary.
• Lifting and Carrying: Other than lifting/carrying a their laptop, the ability lift and carry equipment and materials, is not required.
• Manual Dexterity: While no pushing, pulling, grasping or reaching should be required, the main constant use of their hands will mainly be keyboarding.

Compensation:

The expected hiring rate for this position is $212,904.00/annually

We welcome talented individuals of all backgrounds regardless of gender, sex, religion, race, national origin, citizenship, age, disability, perceived disability, pregnancy, pregnancy-related condition, reproductive health decisions, sexual orientation, gender identity, gender expression, genetic information, HIV/AIDS, marital status, covered veteran status, or any other characteristic protected by local, state, or federal laws, rules, or regulations. We are proud to be an equal employment opportunity employer.

As part of this commitment, Sanford Burnham Prebys Medical Discovery Institute will ensure that persons with disabilities are provided reasonable accommodations for the hiring process. If a reasonable accommodation is needed, please contact our Benefits Team at [phone] or via e-mail at [e-mail].