Genetics Bioinformatics Service Center

Services Offered

Genetics Bioinformatics Service Center (GBSC) is a School of Medicine service center operated by Department of Genetics. 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 researcher and Stanford affiliates unless noted otherwise. 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 solution, Galaxy, available to users. Inquire for ongoing pilot programs.

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

  • Payable on an hourly basis
  • We not only support analysis for popular NGS data types such as RNA­Seq, ChIP­Seq, MethylSeq, Whole Genome/Whole Exome Seq, CancerSeq, and Microbiome, we also support new data types like Hi-C, and ATAC-Seq.
  • Along with Secondary analysis, we provide consulting in quality control, downstream tertiary analysis, data interpretation and visualization. Custom/novel development is available.
  • Consulting services leverages best-practices and cutting-edge methodologies developed by Stanford Center for Genomics and Personalized Medicine core bioinformatics team.
  • Our bioinformatics services are avaliable (in limited quantity) to other academic institutes and industry. Please inquire for availability, rates and process.
  • For use cases and more information about the team, click here.

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

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. See the announcements on right hand side column.
  • Bioinformatics software package installation service is currently offered pro bono by Stanford Center for Genomics and Personalized Medicine core bioinformatics team
  • Further community resources can be found here.

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 Administration, Policy and Compliance (RAPC)
  • 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

 

2016 Events and Announcements

 

2015 Events and Announcements

 

2014 Events and Announcements

  • SCGPM Bioinformatics team is hiring a Sr Bioinformatician (Req 65923) for a new microbiome initiative.
  • Join us for Spiral Genetics workshop on Oct 3, 2014.
  • Please join us for annual SCG3 User Meeting on Dec 5, 2014.
  • We have a Galaxy workshop coming up on Tue, Sept 23, 2014.
  • SCGPM Bioinformatics team has two new positions open with our bioinformatics team. Please look at requisitions 63768 and 63762 on Stanford career site.
  • Bina seminar and hands on workshop on June 5, 2014.
  • SCGPM Bioinformatics team has a position open, Req 62907, for Bioinformatics Developer (Req 62907) for our new CIRM initiative, Center of Excellence in Stem Cell Genomics.
  • SCGPM Bioinformatics team has a position open for bioinformatics software developer (Req 62060) for our newly minted clinical service.
  • Join us for a workshop on Ingenuity Variant Analysis on March 6, 2014.
  • SCGPM bioinformatics staff are participating in an exciting new clinical genomics program.
  • Stanford's HugeSeq variant calling pipeline is available to Genomics community on Seven Bridges platform. Slide deck of this event is available here
  • GIAB workshop on Jan 27-28 at Stanford.
  • Hands-on training to start prototyping and developing on SAP HANA, massively parallel, in-memory database and application server platform, on Jan 31 and Feb 7th
  • Computational Services and Bioinformatics Resources is hosting a hands onGolden Helix workshop on Monday, Feb 10, for DNA-Seq variant interpretation.
  • Virginia Bioinformatics Institute at Virginia Tech is hosting the third annual "High Performance Computing in the Life/Medical Sciences" 2-week summer institute sponsored by the NSF. 
  • SCGPM Bioinformatics team will be present at the upcoming PMWC2014 conference
  • Stanford Center for Genomics and Personalized Medicine (SCGPM) is hiring a Bioinformatics Data Analyst (Req 60513).

 

2013 Events and Announcements

2017 Events and Announcements

  • SCGPM team is hiring an expert bioinformatician to support our Bioinformatics-as-a-Service (BaaS) program (Stanford careers website link).
  • SCGPM Seminar: "ADAM: Fast, Scalable Genome Analysis", Frank Nothalf of UC Berkeley on Feb 17th at noon in Clark S361.
  • GBSC is hosting user group meeting on Feb 01. Get latest updates on our infrastructure (new Isilon storage, and container technologies). Our guest speaker, Jessilyn Dunn, PhD, will present on wearable biosensors. - Jan 20, 2017
  • SCGPM bioinformatician, Vandhana Krishnan, MS, will be presenting on "Assessment of Variant Calling Pipelines for Clinical Diagnosis" at Precision Medicine World Conference Session "Learnings from Precision Medicine Centers" (more) - Jan 20, 2017
  • SCGPM Bioinformatics team member, Denis Salins, is co-author of "Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information". (Link) - Jan 12, 2017