CryoEM Center Computational & Data Management Specialist

94749 Requisition #

Main work location: Stanford, CA

Sponsorship will not be provided for this position.

Stanford wants you! Come join the Stanford Research Computing team to provide critical expertise and consultation for Stanford’s growing cryoEM research community. You will spend most of your time working with the Stanford cryoEM center (cEMc), a state-of-the-art cryoEM imaging facility. The facility currently includes 2 Titan Krios and a Glacios, but more equipment will be installed in the near future. The cEMc’s goals are to facilitate single-particle and cellular cryo-electron tomography studies and also train Stanford users in these technologies. Come be part of the cEMc and Research Computing teams as a cryoEM computational specialist, building the foundational pieces needed to fulfill cEMc’s training mission of supporting all users and labs in managing and processing their cryoEM data. The successful candidate will be responsible for procuring, configuring and maintaining the center’s local data management and computational processing systems, developing efficient pipelines for users to pre-process and transfer data to their own resources, and provide consultation to labs to optimize cryoEM related workflows. In addition, this individual will provide essential bridging and collaboration with the Research Computing engineers and consultants who manage shared campus infrastructure used by cEMc researchers to ensure friction-free pathways to research success.


Specifically related to the Stanford cryoEM center (cEMc), provide highly specialized technical research and support, expert instruction, and consultation; identify and design solutions to a wide range of unique problems and other research and development activities. Work in collaboration with senior research staff members as well as campus computational and storage system engineers and administrators to ensure optimal use of resources within shared compute and storage environments.


  • Design and develop complex and specialized systems and workflows for data processing associated with cryoEM research
  • Develop advanced technological ideas, and guide their development into a final product or new approaches to achieving desired research productivity
  • Coordinate detailed phases of work related to responsibility for parts of the overall suite of cEMc research projects and programs
  • Develop technical and methodological solutions to complex engineering/scientific problems requiring independent analytical thinking and advanced knowledge, specifically related to cryoEM-based storage and data management requirements
  • Develop creative new or improved processes and methods associated with data management and image processing workflows that are important to the advancement of the field.
  • Contribute technical expertise to cEMc research data and computational solutions and systems

Specifically, this position will:

  • Support all computational needs of researchers engaged in cryoEM-based research
  • Serve as a computational liaison between Research Computing engineers and systems, and the cEMc community of researchers
  • Design, implement and finetune workflows for data processing
  • Assist researchers with installing/administering domain-specific software and workflows operated locally or on central shared infrastructure
  • Assist researchers with data storage and archiving strategies and planning
  • Provide consultation around the design of processes and workflows dedicated to computational cryoEM data processing
  • Design and implement just-in-time data processing pipelines during data collection and other workflows as needed by researchers
  • Design and administer solutions for data storage
  • Support cryoEM image processing workflow training
  • Interface with SLAC cryoEM IT personnel to optimize data flows between SLAC and Stanford



Education & Experience:

Bachelor's degree and five years of relevant experience, or a combination of education and relevant experience for the R&D Scientist & Engineer level 2 classification.  

(Note: We will also consider candidates with a Bachelor’s degree and 3 years of relevant experience, or combination of education and relevant experience for R&D Scientist & Engineer level 1 classification.)

Knowledge, Skills and Abilities:

  • Technical knowledge of and advanced operational experience using Linux
  • Experience setting up, configuring and supporting scientific workstation hardware and software
  • Experience with basic scripting
  • Demonstrated proficiency using python
  • Experience with Linux environment modules, especially lmod, and Anaconda
  • Experience using shared high performance computing clusters, including parallel file systems, managing complex NFS3 and NFS4 permissions
  • Excellent oral and written communication skills

Desired skills:

  • Experience with cryoEM image processing for single-particle or tomography reconstructions

Certifications and Licenses:



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


  • Occasional evening and weekend work as required
  • Participation in winter break staff rotation as needed


  • Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations.
  • Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned.
  • Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University's Administrative Guide,


The job duties listed are typical examples of work performed by positions in this job classification and are not designed to contain or be interpreted as a comprehensive inventory of all duties, tasks, and responsibilities. Specific duties and responsibilities may vary depending on department or program needs without changing the general nature and scope of the job or level of responsibility. Employees may also perform other duties as assigned.

Stanford is an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

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