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
- SCGPM hosted Cloud workshop videos are now available. Learn more about DNAnexus command line interface, GUI and how to buid a new app. And learn a whole lot more about RNA-Seq
- SCGPM Seminar: Jun Ye, Sentieon and Dangna Li, Stanford - Aug 22nd, 2016
- SCGPM hosted an interactive training workshop on Cloud Bioinformatics on July 15th. Read more about the event on DNAnexus blog (link)
- SCGPM bioinformatics core team has a new opening for Biomedical Systems Engineer. Job number 71608 (link). Apply via Stanford career site
- SCGPM Seminar: Paul Billing-Ross, Stanford University - June 14th, 2016
- SCGPM bioinformatics core team has two new openings for Data Scientists. Job number 71032 (link). Apply via Stanford career site
- Join SCGPM at our Microbiome Bioinformatics Symposium on Fri, May 27th, 2016, an all-day event where new computational technologies addressing metagenomics challenges will be discussed
- SCGPM Seminar: Jason Chin, and Luke Hickey, PacBio - May 10th, 2016
- The Sequencing Service offered by Stanford Center for Genomics and Personalized Medicine has moved processing, storage, and distribution of all sequencing data generated from our core facility to DNAnexus. Our core facility serves multitude of labs at Stanford and other academic centers. This move enables our customers to utilize ENCODE data analysis pipelines more easily. - May 1, 2016
- SCGPM Seminar: Jian Li, and Mohammed Sahraeian, Bina Roche - April 19th, 2016
- SCGPM builds mega-scale variant analysis pipeline on Google Genomics - April 6th, 2016
- SCGPM researcher, Gregory McInnes, presented at "Genomics on the Fronline with Google Cloud Platform", on Interactive Cloud Analytics: XL Scale Genomics Data. - March 30, 2016
- SCGPM Seminar: George Asimenos, DNAnexus - March 23rd, 2016
- Come to SCGPM hosted Genomics and Patient Privacy Conference, March 11th, 2016
- SCGPM Seminar: Sasha Zaranek, and Jonathan Sheffi, Curoverse - March 10th, 2016
- SCGPM Seminar: Gaurav Kaushik, Seven Bridges Genomics - March 9th, 2016
- SCGPM Seminar: Deanna Church, 10X Genomics - February 16th, 2016
- SCGPM researcher, Somalee Datta, hosted a session at Personalized Medicine World Conference (PMWC 2016) titled Genome: Silos, Hacking Privacy, Collaboration. (more) - Jan 26, 2016
- SCGPM hosted annual SCG Cluster user group meeting - Dec 2nd, 2015