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 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
- 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
- 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 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
2017 Events and Announcements
- SCGPM Seminar: "Summing the Parts: How Invitae Created a Best-in-Class Variant Interpretation System", Jon Sorenson of Invitae, April 19th at noon at Clark S361 [TO BE RESCHEDULED]
- SCGPM team is hiring an expert bioinformatician to support our VA Collaboration (Stanford careers website link).
- Biorxiv paper with details on 4000 sequencing issues related to Exclusion Amplification (ExAmp) clustering chemistry. (link) - Apr 9, 2017
- See post from Genome Sequencing Service Center on HiSeq 4000 sequencing issues related to Exclusion Amplification (ExAmp) clustering chemistry. (link) - March 22, 2017.
- GBSC received approval to procure a supercomputer (SGI UV 300) under Shared Instrumentation Grant (SIG) Program (S10) from National Institutes of Health (NIH) Office of Research Infrastructure Programs (ORIP). ORIP's S10 Programs support purchases of state-of-the-art commercially available instruments to enhance research of NIH–funded investigators. - March 14, 2017
- SCGPM team is hiring a Biomedical Research Engineer to support our Big Data efforts. (Stanford careers website link) - THIS POSITION IS FILLED
- SCGPM Seminar: "Accelerating genomics in the cloud", Ravi Pandya of Microsoft Research on March 15th at noon in Clark S360.
- 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 Nothaft 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