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Science and Engineering Associate 2

School of Medicine, Stanford, California, United States

New

Research

Post Date 2 days ago

Requisition # 103780

Fixed-Term 1 year

The Cardiovascular Biomechanics Computation Lab at Stanford University (Dr. Marsden, PI) performs computational modeling of the cardiovascular system to support surgical planning in pediatric and adult patients, medical device design, and basic research in cardiovascular biomechanics and mechanobiology. As part of its mission, the lab leads the development of the SimVascular open-source project, the leading software package for patient-specific modeling and blood flow simulation. The lab also supports the Vascular Model Repository (VMR), which provides about 250 freely available SimVascular-compatible projects from various anatomies and diseases.

The lab is seeking a Science and Engineering Associate 2 to perform advanced computational engineering tasks in support of the VMR with the goal of expanding the database and making it compatible with research tasks in machine learning (ML) and artificial intelligence (AI). Specific tasks will include data curation and database expansion, database management, website and data server maintenance, data archiving, working with Stanford libraries, and creating computational tools such as Python scripts for data processing to support artificial intelligence and machine learning efforts in cardiovascular imaging and modeling. The candidate will collaborate with Stanford libraries to ensure data integrity and facilitate the integration of new datasets into the Vascular Model Repository (https://vascularmodel.com). Additionally, they will update and maintain comprehensive documentation (https://vascularmodel.com/documentation.html) for the repository, encompassing medical images, 3D anatomical models, meshes, and blood flow simulation results, ensuring accessibility and usability for researchers and engineers. They will also manage updates and enhancements for the SimVascular software platform, ensuring that the latest versions and features are available and usable (https://simvascular.github.io).

The ideal candidate will collaborate with Marsden lab members to collect and archive data and assist with readying the VMR database for AI and ML tasks. They should have experience with computer programming (e.g., Python), possess excellent communication skills, a collaborative attitude, and the ability to work effectively in a team environment.

Duties include:

• Support complex scientific and research programs related to computational cardiology and biomechanics; analyze data, perform data curation and data archiving tasks, and expand existing data repositories.

• Collaborate with team members (graduate students and postdocs in the Marsden lab as well as outside collaborators and users of SimVascular) to gather and archive data for public release in repositories.This will result in significant expansion of the size of the VMR (currently 250 datasets).

• Assist with source code testing and open-source project management for the VMR and SimVascular as needed, such as answering questions posted in the user forum or trouble-shooting issues encountered by users in the research community.

• Carry out independent activities to write computer code (e.g. developing custom Python scripts) for data retrieval from repositories in support of AI-readiness or validation and data curation tasks.Create databases and methods for public machine learning challenges.

• Collaborate with senior engineers and scientists to maintain and support open source and open data projects and websites.Assist with providing user support to the broader research community.

• Work with Stanford libraries to create professional data archiving methods with assigned DOIs. Create appropriate interfaces between data archives and public websites.

• Create online documentation, website resources, and educational materials related to open source (SimVascular) and open data (VMR) projects and make them available to the public via the project websites.

• Assist with project planning to ensure ongoing sustainability of open source and open data resources supported by the lab.

• Regularly communicate progress (such as number of datasets posted and archived, number of downloads of VMR data) to the PI (Dr. Marsden) and discuss goals in bi-weekly meetings.

All members of the Department of Pediatrics are engaged in continuous learning and improvement to foster a culture where diversity, equity, inclusion, and justice are central to all aspects of our work. The Department collectively and publicly commits to continuously promoting anti-racism and equity through its policies, programs, and practices at all levels.

Stanford University provides pay ranges representing its good faith estimate of what the University reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location, and external market pay for comparable jobs. The pay range for this position working in the California Bay area is $109,000 to $129,000.

DESIRED QUALIFICATIONS:

EDUCATION & EXPERIENCE (REQUIRED):

Bachelor’s degree in engineering, science, or related quantitative field with introductory computer programming skills demonstrated through research, coursework and/or industry experience.

KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED):

• Demonstrated knowledge and skills of advanced scientific or engineering principles and practices.

• Demonstrated experience applying complex scientific and engineering principles and performing special technical services involving both development and performance.

• In-depth experience with computer programming or software engineering demonstrated through coursework, research experience and / or relevant industry experience.

• Ability to independently carry out computer programming tasks such as writing Python scripts for data format conversion, extracting data from a data repository, or automating data workflows.

• Eagerness to uphold a culture of open source contributions, including proper source code version control in GitHub, posting issues on GitHub, and regularly communicating with the development team and lead software engineer.

• Ability to collaborate with senior engineering and scientific staff to design and develop custom software solutions for computational engineering research projects.

• Experience overseeing the plan, design, and implementation of major scientific or engineering initiatives and ensuring project objective are met.

• Demonstrated ability to review research proposals, evaluate research capabilities, and make recommendations.

• Demonstrated ability to establish, communicate, and enforce compliance with health and safety policies and procedures.

CERTIFICATIONS & LICENSES:

None

PHYSICAL REQUIREMENTS*:

• Frequently grasp lightly/fine manipulation, perform desk-based computer tasks, lift/carry/push/pull objects that weigh up to 10 pounds.

• Occasionally stand/walk, sit, twist/bend/stoop/squat, grasp forcefully.

• Rarely kneel/crawl, climb (ladders, scaffolds, or other), reach/work above shoulders, use a telephone, writing by hand, sort/file paperwork or parts, operate foot and/or hand controls, lift/carry/push/pull objects that weigh >40 pounds.

* - Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job.

Additional PHYSICAL REQUIREMENTS: (remove if none)

WORKING CONDITIONS:

• May be exposed to high voltage electricity, radiation or electromagnetic fields, lasers, noise > 80dB TWA, Allergens/Biohazards/Chemicals /Asbestos, confined spaces, working at heights ?10 feet, temperature extremes, heavy metals, unusual work hours or routine overtime and/or inclement weather.

• May require travel.

Additional Information

• Schedule: Full-time

• Job Code: 4992

• Employee Status: Regular

• Grade: J

• Department URL: http://pediatrics.stanford.edu/

• Requisition ID: 103780

• Work Arrangement : On Site