Senior Computational Scientist / Scientific Software Engineer for Cryo-ET Workflow Development

About the role

The St. Jude Center of Excellence for Structural Cell Biology (CoE-SCB) is seeking an innovative and highly motivated Senior Computational Scientist / Scientific Software Engineer to develop next-generation computational infrastructure for cryo-electron tomography (cryo-ET), and structural cell biology workflows.

Responsibilities

• Design, develop, and maintain scalable computational pipelines for cryo-ET workflows with a high level of automation and reproducibility.
• Architect software solutions optimized for local workstations, HPC systems, and cloud-based environments.
• Refactor existing analysis workflows into modular, maintainable, and reusable software components and libraries.
• Develop user-friendly APIs and interfaces for data analysis, workflow management, and visualization.
• Work closely with CoE-SCB scientists, faculty, and HPC engineers to identify computational bottlenecks and implement scalable, high-performance solutions for cryo-ET workflows.
• Develop and optimize workflows for large-scale cryo-ET datasets, including preprocessing, tomographic reconstruction, segmentation, template matching, subtomogram averaging, and AI/ML-assisted analysis.
• Evaluate, benchmark, and integrate emerging computational tools and technologies into existing workflows.
• Implement robust software engineering practices, including version control, testing, profiling, optimization, logging, and error handling.
• Scale local analysis workflows to distributed HPC and cloud infrastructures while ensuring efficient data handling and storage integration.
• Assist with software deployment, troubleshooting, and standardization across the CoE-SCB computational ecosystem.
• Maintain clear and comprehensive code documentation and user documentation.
• Contribute to the strategic development of computational infrastructure supporting multimodal and multiscale structural cell biology workflows.

Requirements

• Advanced proficiency in Python, Linux, and shell scripting.
• Strong software engineering and system design experience across local, HPC, and cloud computing environments.
• Experience developing scientific software pipelines and automation frameworks.
• Expertise in handling and processing large scientific datasets, including efficient storage, retrieval, and distributed processing strategies.
• Experience with SQL databases and Object-Relational Mapping (ORM) frameworks.
• Familiarity with Cryo-EM/Cryo-ET software ecosystems such as RELION, CryoSPARC, Warp, AreTomo, Dynamo, PyTom, EMAN2, SerialEM, Tomography 5, or related tools.
• Experience with workflow orchestration, containerization, or distributed computing technologies is highly desirable.
• Experience developing user interfaces and web-based tools using modern web technologies (HTML, CSS, JavaScript) is beneficial.
• Familiarity with machine learning and AI-based image analysis approaches is desirable.
• Strong commitment to reproducible research, maintainable codebases, and collaborative software development practices.
• Excellent communication and collaboration skills in multidisciplinary scientific environments.

Preferred Skills And Experience

• Experience in leading computationally focused scientific research projects.
• Proven performance in earlier role/comparable role.
• Experience in computational research techniques and processes.