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.
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.
EDUCATION & EXPERIENCE (REQUIRED): Bachelor's degree and five years of relevant experience, or a combination of education and relevant experience.
KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED):
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.
Location: School of Medicine, Stanford, California, United States Schedule: Classification Level:
Stanford is an equal opportunity employer and all qualified applicants will receive consideration without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, veteran status, or any other characteristic protected by law.
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Located between San Francisco and San Jose in the heart of Silicon Valley, Stanford University is recognized as one of the world's leading research and teaching institutions. Leland and Jane Stanford founded the University to "promote the public welfare by exercising an influence on behalf of humanity and civilization." Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing students for leadership in a complex world. The University's thriving diverse community is comprised of nearly 7000 undergraduate students, 9000 graduate students, 2000 faculty members, 1900 postdoctoral scholars, and over 11,000 academic and administrative staff in seven schools including several interdisciplinary research centers and institutes. The campus spreads over 8000 contiguous acres and nearly all undergraduates live on campus. Stanford offers bachelor's and master's degrees in addition to doctoral degrees (PhD, MD, DMA and JD) plus a number of professional and continuing education programs and certifications. More at http://facts.stanford.edu and http://www.stanford.edu. Stanford University is an ...equal opportunity employer and is committed to increasing the diversity of its faculty. It welcomes nominations of and applications from women, members of minority groups, protected veterans and individuals with disabilities, as well as from others who would bring additional dimensions to the university’s research, teaching and clinical missions.