Encode Data Submission Engineer

California, United States
20 Jun 2019
End of advertisement period
20 Aug 2019
Contract Type
Full Time

The Stanford Center for Genomics and Personalized Medicine (SCGPM) has an excellent opportunity available for a motivated ENCODE Data Submission Engineer.

A worldwide effort involving over 30 research groups and hundreds of scientists starting in 2003, the ENCODE Project was launched as a follow-up to the Human Genome Project; the HGP sequenced the DNA that makes up the human genome, the ENCODE Project seeks to interpret this sequence.  The approximately 20,000 genes that provide instructions for making proteins account for only about 1 percent of the human genome; researchers embarked on the ENCODE Project to figure out the purpose of the remaining 99 percent of the genome. Scientists discovered that more than 80 percent of this non-gene component of the genome, which was once considered “junk DNA,” actually has a role in regulating the activity of particular genes (gene expression).

This person will own the management of the flow of SCGPM sequencing data into the data repository for the ENCODE Project.  This ownership includes the maintenance and continued development of our in-house Pulsar Laboratory Informatics Management System (LIMS) web app, written in Rails, used to store the JSON-structured metadata associated with the ENCODE sequencing data and experiments (ChIP-seq, ATAC-seq, single cell ATAC-seq, CUT&RUN).  You will be responsible for submitting sequencing results files and their associated experiment metadata files to the ENCODE Consortium repository.  You will work closely with the ENCODE Project Manager to tailor the Pulsar LIMS to their needs and to assist with overall data management.  You will also interface with the ENCODE data wranglers and sequencing technicians to ensure that all the proper metadata associated with dataset input is captured and recorded.  Occasionally, you will be asked to write and maintain apps in bioinformatics-processing cloud platforms (e.g., DNAnexus, Seven Bridges) to assist in the analysis and quality control of sequencing results.  In all of your work, you will follow software development best-practices, such as source control, regression testing, and code reviews.

For a brief description of the process which this position will execute, please look at https://en.wikipedia.org/wiki/ENCODE#Data_Management_and_Analysis . In that description, you would be fulfilling the role of “the lab” which submits the data.

The successful candidate will have knowledge of high-throughput sequencing technologies and experience with genomic data and analysis. Excellent communication skills are also critical:  a significant part of your work will involve interacting with people of different scientific backgrounds, creating documentation, and contributing to wikis and FAQs.

Experience with web development, particularly using Rails, will be necessary for developing and maintaining the Pulsar LIMS application.

The successful candidate must be able to learn to work independently and collaborate effectively with co-workers. The work will take place in a dynamic environment where the workload often changes rapidly in response to data flow demand, so the candidate needs to be good at multi-tasking and managing the expectations of multiple stakeholders.

Previous experience working in an academic environment is a plus.

The successful candidate will comply with university and government health and safety regulations and policies.

Stanford University, located between San Francisco and San Jose in the heart of California's Silicon Valley, is one of the world's leading teaching and research universities. Since its opening in 1891, Stanford has been dedicated to finding solutions to big challenges and to preparing students for leadership in a complex world.

Supporting that mission is a staff of more than 10,000, rooted in a culture of excellence and valuing innovation, collaboration, and life-long learning.  To foster the talents and aspirations of our staff, Stanford offers career development programs, competitive pay that reflects market trends, and benefits that increase financial stability and promote healthy, fulfilling lives.  An award-winning employer, Stanford offers an exceptional setting for professionals looking to advance their careers.


  • An advanced degree in Biology, Computational Biology, Bioinformatics, Computer Science, or a related field is preferred
  • Technical expertise in genetics, molecular biology, or bioinformatics.
  • Experience with web application technologies, particularly Rails.
  • Experience with relational databases.
  • Some experience with genomics laboratory techniques.
  • Some experience with user support.
  • Experience working in academic environments is preferred.


  • Bachelor's degree and five years of relevant experience, or a combination of education and relevant experience.


  • Expertise in designing, developing, testing, and deploying applications.
  • Proficiency with application design and data modeling.
  • Ability to define and solve logical problems for highly technical applications.
  • Strong communication skills with both technical and non-technical clients.
  • Ability to lead activities on structured team development projects.
  • Ability to select, adapt, and effectively use a variety of programming methods.
  • Knowledge of application domain.


  • Constantly perform desk-based computer tasks.
  • Frequently sit, grasp lightly/fine manipulation.
  • Occasionally stand/walk, writing by hand.
  • Rarely use a telephone, lift/carry/push/pull objects that weigh up to 10 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


May work extended hours, evening and weekends.


  • 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, http://adminguide.stanford.edu.

Additional Information

Schedule: Full-time
Job Code: 4822
Employee Status: Regular
Grade: J
Department URL: http://genetics.stanford.edu/
Requisition ID: 83561