Job Description:
As a member of SCGS, you will be joining a large team of Clinical Lab Scientists, BioInformaticians, Clinical Data Scientists, Curators, Genetic Counselors and Physicians working together to help provide genomics driven Precision/Personalized Medicine to patients. SCGS provides a unique opportunity to do both Clinical Genomics and research in Translational Genomics through collaborations with research labs within Stanford School of Medicine. SCGS is fully funded and is not dependent on NIH or other Grants for its operations. We offer competitive salaries (even by Bay Area industry standards), generous benefits and a collaborative work culture with mutual respect. Essential Functions: -Develop cost-effective pipelines that appropriately balance the cost of analysis against turnaround times. -Develop and maintain an appropriate framework that allows for development, testing and release cycles. -Partner with Algorithms team to ensure that the algorithms are high scalable. -Develop and maintain a knowledge database of variants and annotations discovered in processing of samples. -Develop and maintain a database of public annotation sources such as ClinVar, Exome Variant Server, 1000 Genomes, TCGA and DGV. -Develop efficient protocols and tools to upload WGS/WES data from internal servers to Cloud Storage (AWS S3/GoogleStorage). -Develop web interface used for sample tracking. -Develop and maintain a backend MySQL database used in genomics information management system. -Develop the interface for message passing between the genomics system and EPIC Interface engine such as Ensemble. -Implement automated and exploratory testing processes that provide continuous feedback on quality issues; find ways to break our web application before their public release -All qualified applicants will receive consideration for employment without regard to race, sex, color, religion, national origin, protected veteran status or on the basis of disability. Qualifications: Any combination of education and experience that would likely provide the required knowledge, skills and abilities as well as possession of any required licenses or certifications is qualifying. Education: Graduate Degree (Ph.D/M.S) in a work-related field/discipline from an accredited college or university. Experience: Ph.D plus Two (2) or M.S Plus Six (6) years of experience developing genomics analysis pipelines (preferably in a Clinical setting). Knowledge, Skills, and Abilities: -Experience developing genomics analysis pipeline on the Cloud - preferably in a Clinical setting. -Experience automating the provisioning, administering, monitoring, and testing of distributed systems on the cloud. -Demonstrated experience with Cloud architecture and familiarity with Cloud based dev-ops tools. -Experience with SQL databases such as MySQL and/or non-SQL databases such as MongoDB. -Must demonstrate strong understanding of scientific workflow manager such as Kepler, Galaxy etc. -Experience with fine or course-grained parallel program development preferred. -Preferred programming language is Python. Proficiency in C++, Java, or Scala may be considered for competency evaluation. -Experience with code versioning and issue tracking tools such as Github and JIRA -Strong analytical abilities and communication skills.
Additional Info:
Stanford Clinical Genomics Service (SCGS) is a joint effort between Stanford Health Care (Stanford Hospital & Lucile Packard Children's Hospital) and Stanford School of Medicine to provide best-in-class clinical genomics sequencing service for patients with unexplained heritable diseases and inherited cancer predisposition. [Click Here to Access the Original Job Post]
As a member of SCGS, you will be joining a large team of Clinical Lab Scientists, BioInformaticians, Clinical Data Scientists, Curators, Genetic Counselors and Physicians working together to help provide genomics driven Precision/Personalized Medicine to patients. SCGS provides a unique opportunity to do both Clinical Genomics and research in Translational Genomics through collaborations with research labs within Stanford School of Medicine. SCGS is fully funded and is not dependent on NIH or other Grants for its operations. We offer competitive salaries (even by Bay Area industry standards), generous benefits and a collaborative work culture with mutual respect. Essential Functions: -Develop cost-effective pipelines that appropriately balance the cost of analysis against turnaround times. -Develop and maintain an appropriate framework that allows for development, testing and release cycles. -Partner with Algorithms team to ensure that the algorithms are high scalable. -Develop and maintain a knowledge database of variants and annotations discovered in processing of samples. -Develop and maintain a database of public annotation sources such as ClinVar, Exome Variant Server, 1000 Genomes, TCGA and DGV. -Develop efficient protocols and tools to upload WGS/WES data from internal servers to Cloud Storage (AWS S3/GoogleStorage). -Develop web interface used for sample tracking. -Develop and maintain a backend MySQL database used in genomics information management system. -Develop the interface for message passing between the genomics system and EPIC Interface engine such as Ensemble. -Implement automated and exploratory testing processes that provide continuous feedback on quality issues; find ways to break our web application before their public release -All qualified applicants will receive consideration for employment without regard to race, sex, color, religion, national origin, protected veteran status or on the basis of disability. Qualifications: Any combination of education and experience that would likely provide the required knowledge, skills and abilities as well as possession of any required licenses or certifications is qualifying. Education: Graduate Degree (Ph.D/M.S) in a work-related field/discipline from an accredited college or university. Experience: Ph.D plus Two (2) or M.S Plus Six (6) years of experience developing genomics analysis pipelines (preferably in a Clinical setting). Knowledge, Skills, and Abilities: -Experience developing genomics analysis pipeline on the Cloud - preferably in a Clinical setting. -Experience automating the provisioning, administering, monitoring, and testing of distributed systems on the cloud. -Demonstrated experience with Cloud architecture and familiarity with Cloud based dev-ops tools. -Experience with SQL databases such as MySQL and/or non-SQL databases such as MongoDB. -Must demonstrate strong understanding of scientific workflow manager such as Kepler, Galaxy etc. -Experience with fine or course-grained parallel program development preferred. -Preferred programming language is Python. Proficiency in C++, Java, or Scala may be considered for competency evaluation. -Experience with code versioning and issue tracking tools such as Github and JIRA -Strong analytical abilities and communication skills.
Requeriments :
Skills :
- Cloud Computing
- Database design
- MongoDB
- MySQL
- NoSQL
- Programing in C++
- Programing in Python
- Programming in Java
- SQL
Areas :
Additional Info:
Stanford Clinical Genomics Service (SCGS) is a joint effort between Stanford Health Care (Stanford Hospital & Lucile Packard Children's Hospital) and Stanford School of Medicine to provide best-in-class clinical genomics sequencing service for patients with unexplained heritable diseases and inherited cancer predisposition. [Click Here to Access the Original Job Post]