Genetics Bioinformatics Service Center
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Services Offered

GBSC is set up to facilitate massive scale Genomics at Stanford and supports omics, microbiome, sensor and phenotypic data types:

State-of-the-art computational infrastructure with 1000+ cores and 3.5+ Petabytes of high performance storage

  • Architecture specifically suited to genomics data analysis
  • 250+ bioinformatics software installed and ready to use
  • Specialized data analysis solutions, Bina & Galaxy, available
  • dbGAP (NIH) complaint for data security since 2013. Regular Stanford IT audits to keep up with compliance requirements
  • Office hours, wiki, bioinformatics training sessions, and seminars
  • Integrated with iLab services for billing management. Granular billing with details of use so project specific PTAs can be used
  • High performance computing system administration services via Stanford Research Computing Team
  • Cluster is hosted at Stanford Data Center that offers >99% uptime SLA

NGS "Informatics-as-a-Service"

  • Best practice data analysis along with Quality Control (QC) and visualization (plots/charts) for common NGS data types for:
  • RNA­Seq
  • Single cell RNA­Seq
  • RNA­Seq with synthetic spike­ins
  • ChIP­Seq
  • DNA­Seq
  • Whole Genome Seq
  • Whole Exome Sequencing
  • Deep Sequencing (Gene panels)
  • Cancer Seq (Germline and somatic)
  • Microbiome Seq
  • Custom/novel development for RNA­Seq, DNA­Seq, ChIP­Seq and microbiome data type

Integrated with Google Cloud and made dbGAP compliant

  • Specifically suited to large scale computational bursts requiring 10,000s-100,000s of compute nodes for short periods of time
  • Use Big Query for data analysis like GWAS style annotated variant analysis or sensor data analytics. In a study, >25M annotated variants were queried in near real time. Typical query latency was 5-10s at a cost of $0.30-$0.40 per query
Utility to Stanford researchers
  • Best-in-class facility available to all Stanford University researchers
  • Many technology and genomics solutions are routinely tried. Winning solutions are made available to the community for in-depth exploration. If a technology is adopted by the community, GBSC brokers Master Service Agreement, negotiates rates and enables procurement so community can access these solutions
  • Highly competitive pay-as-you-go cost model to accommodate both small and large labs
  • A genomics community that allows otherwise siloed researchers to ramp up faster and increase contribution to this fast-evolving field of research
    • 500+ researchers supported
    • Many departments represented: Biochemistry, Biology, Chemical Engineering, Computer Science, Developmental Biology, Genetics, Health Research & Policy, Medicine, Cardiovascular, Hematology, Oncology, Neurosurgery, Orthopedic Surgery, Pathology, Pediatrics, Psychiatry & Behavioral Sciences, Radiology, Statistics, Stem Cell Biology

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