Research Software Engineer I - Laboratory of Dr. Talmo Pereira

About the role

The Pereira Lab at the Salk Institute for Biological Studies is seeking a Research Software Engineer to develop and maintain the software that transforms computer vision models into biological discovery. The role involves working closely with plant biologists to turn their experimental questions into reproducible analyses.

Responsibilities

• Develop, maintain, and release open-source scientific Python packages for pose-estimation-based phenotyping.
• Maintain and extend Bloom, the lab’s web application and scientific database for plant phenotyping data.
• Maintain and release Bloom Desktop, the Electron/React application for acquiring images and uploading them to Bloom.
• Build, operate, and improve containerized, GPU-accelerated analysis pipelines.
• Train, evaluate, and deploy deep learning pose-estimation models.
• Connect analysis pipelines to Bloom through data contracts and provenance tracking.
• Support and make use of shared high-performance computing resources.
• Rapidly prototype, build, and iterate on internal applications and utilities.
• Integrate systems and services through APIs and automation.
• Work directly with biologists to translate their experimental goals into technical solutions.
• Prepare and maintain documentation and training materials.
• Contribute to the lab’s open-source software community.

Requirements

• Bachelor’s degree in computer science, engineering, quantitative science, or a related discipline.
• Demonstrated software engineering ability through internships, research projects, open-source contributions, or personal projects.
• Full-stack software engineering ability, including proficiency in Python and at least one other language (TypeScript preferred).
• Experience with the scientific Python stack, including NumPy, pandas, scikit-learn.
• Proficiency with relational databases (PostgreSQL).
• Experience with at least one deep learning framework (PyTorch).
• Fluency with modern software development tools and methodologies.
• Working familiarity with Linux/Unix environments and version control (Git).
• Experience with containerization (Docker) and GPU resource scheduling (Kubernetes, SLURM).
• Experience with web development (React, FastAPI, Django).
• Experience with desktop application development (Electron).
• Experience with computer vision/image analysis.
• Experience with scientific instrument/data acquisition hardware.
• Strong communication skills and ability to work directly with scientists.

Qualifications

• Master’s degree or post-baccalaureate certification in a computational or scientific field.
• Prior internship, research, or work experience in a scientific, laboratory, or academic environment.
• Experience with full-stack web development.
• Experience with desktop application development.
• Experience with computer vision/image analysis.
• Experience with containerization and GPU resource scheduling.
• Experience with scientific instrument/data acquisition hardware.
• Experience with open-source software development.
• Track record of shipping small tools or projects quickly and independently.

Skills

• Python
• TypeScript (preferred)
• Deep learning frameworks (PyTorch)
• Scientific Python stack (NumPy, pandas, scikit-learn)
• Relational databases (PostgreSQL)
• Containerization (Docker)
• GPU resource scheduling (Kubernetes, SLURM)
• Web development (React, FastAPI, Django)
• Desktop application development (Electron)
• Computer vision/image analysis
• Scientific instrument/data acquisition hardware
• Open-source software development

Benefits

• Competitive pay range of $33.00 to $38.00 per hour.
• Comprehensive benefits package including medical, dental, vision, retirement, paid time off, tuition reimbursement, patient advocacy services, and transit/parking program.