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-premises computational cluster: specially suited to NGS analysis
- 2800+ cores and 7+ Petabytes of high performance storage
- Architecture specifically suited to large scale genomics data analysis but also supports general scientific computing
- 500+ bioinformatics software packages installed and ready to use
- A graphical data analysis platform, Galaxy, is made available to users.
"Bioinformatics-as-a-Service (BaaS)": consulting for hands-on help
- Payable on an hourly basis
- Billable to Stanford PTAs
- We support analysis for popular NGS data types such as RNASeq, ChIPSeq, MethylSeq, Whole Genome/Whole Exome Seq, CancerSeq, and Microbiome, and analysis for 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
- 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. Learn more about dbGaP here.
- Peer reviewed publication on Cloud security
- Regular Stanford IT audits to keep up with security compliance requirements
User Support: for bioinformatics and distributed computing
- Large user community, over 1000 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-premises infrastructure is hosted at Stanford Data Centers that offers >99% uptime
- High performance computing system administration services are provided by the 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-premises 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
2018 Events and Announcements
SCGPM Seminar: "Multi-scale Deep Tensor Factorization Learns a Latent Representation of the Human Epigenome", Jacob Schreiber, University of Washington, Monday June 11th at 12:00 - 1:00PM in Clark S361. Lunch provided: please register here.
- SCGPM Seminar: "An Introduction to the LabKey Server", Josh Eckels from Labkey, Monday, April 2nd at 3:30-4:45PM in Munzer Auditorium. LabKey is an open-source software platform designed to help organizations integrate, analyze, and share complex biomedical data.