Genetics Bioinformatics Service Center

Services Offered

GBSC is set up to facilitate massive scale Genomics at Stanford and supports omics, microbiome, sensor, and phenotypic data types. Our facilities are available to any Stanford University Faculty member or Principal Investigator. We offer:

On-premise computational cluster: specially suited to NGS analysis

  • 2800+ cores and 4+ Petabytes of high performance storage
  • Architecture specifically suited to large scale genomics data analysis but also supports general scientific computing
  • 350+ bioinformatics software packages installed and ready to use
  • Specialized data analysis solutions, Bina & Galaxy, are available. Inquire for ongoing pilot programs.

"Bioinformatics-as-a-Service": consulting for hands-on help

  • Payable on an hourly basis
  • We support analysis for common NGS data types such as RNA­Seq, ChIP­Seq, MethylSeq, Whole Genome/Whole Exome Seq, CancerSeq, Microbiome.
  • Custom/novel development for other data types is available
  • Along with Secondary analysis, we provide consulting in Quality Control, downstream tertiary analysis, data interpretation and visualization. 
  • Consulting services leverages best-practices and cutting-edge methodologies developed by Stanford Center for Genomics and Personalized Medicine core bioinformatics team's work with various large scale projects such as ENCODE, CIRM Center for Excellence in Stem Cell Genomics, Clinical Genomics Service and VA Million Veteran Program.

Google Cloud Gateway: for scale out computing supporting HPC and Hadoop stacks

  • Cloud services backed by SU agreements 
  • Security compliance set up by GBSC system admins
  • Deep discounts available on certain Cloud services

System Security: supports biomedical research compliance needs

  • Services support SU mandated security requirements e.g. two-factor authentication
  • On-premise and Cloud gateway support NIH dbGaP security best-practices
  • Regular Stanford IT audits to keep up with security compliance requirements

User Support: for bioinformatics and distributed computing

  • Large user community, over 700 users currently supported on the system
  • Regular office hours for hands-on training 
  • Email based troubleshooting and support offered during regular work hours
  • Detailed wiki 
  • Monthly bioinformatics seminars
  • Bioinformatics software package installation service is currently offered pro bono by Stanford Center for Genomics and Personalized Medicine core bioinformatics team

IT System Administration: for user and system management

  • On-premise infrastructure is hosted at Stanford Data Centers that offers >99% uptime
  • High performance computing system administration services via Stanford Research Computing Center team. This team has in-depth expertise across the spectrum of HPC services including storage, networking, schedulers, monitoring, operating systems, system security, vendor management, inventory and user management.

Financial Administration: University oversight for robustness and continuity

  • Stanford Department of Genetics provides financial backing and organizational support at no operational cost to GBSC
  • Oversight by Office of Research Deans
  • Services offered at deeply discounted rates due to various SU subsidies and scale of operation
  • On-premise computing, Cloud computing and consulting bills rolled into a single comprehensive invoice
  • Granular billing with details of services used, allowing project-specific funds to be used
  • Integrated with Stanford's iLabSolutions for billing management and ease of payment

 

Utility to Stanford Researchers

  • Best-in-class facility available to all Stanford University researchers. A large number of labs are supported. 
  • Leverages expertise of professional research groups at Stanford such as Stanford Research Computing Center and Stanford Center for Genomics and Personalized Medicine core bioinformatics team.
  • Many technologies and solutions are routinely evaluated. Winning solutions are made available to the community for in-depth exploration. If a technology is adopted by the community, GBSC brokers a Master Service Agreement, negotiates competitive rates, and enables procurement so the Stanford community can access these solutions easily.
  • Highly competitive pay-as-you-go cost model to accommodate both small and large labs.
  • A genomics community that allows researchers to ramp up faster and increase contribution to this fast-evolving field of research.
    • 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

Announcements

Past announcements...

For more information

  • Stanford affiliates can click here to access the wiki for the GBSC.
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