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
- 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
2016 Events and Announcements
- Stanford Sequencing Centre is expanding its Cloud footprint - SCGPM is the first organization to adopt DNAnexus on Azure. The multi-cloud availability of DNAnexus now makes for a wider collaboration network. Read the press release.
- SCGPM Seminar: Stanford Clinical Genomics Service Engineering Team presents on Genome Information Management System - Oct 24th, 2016. See event video.
- At DNAnexus user meeting, DNAnexusConnect2016, SCGPM team presented on how the Center accelerates research and collaboration - Sep 29th, 2016
- Please join Stanford Research Computing Center and Chris Dagdigian from BioTeam to discuss current state of and future directions for bio and genomic computing. - Sep 28, 2016
- SCGPM Seminar: Ramesh Nair and Wendy Zhang, SCGPM/GBSC - Sep 19th, 2016
- PrecisionFDA's inaugural app-a-thon in a Box, a joint UCSF-Stanford-CERSI effort, was held at Stanford on Aug 31, 2016. SCGPM bioinformatics team member, Isaac Liao, participated by adding Real Time Genomics software application. See event video with introduction by Russ Altman.
- 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
2015 Events and Announcements
- GBSC hosted annual SCG Cluster user group meeting - Dec 2nd, 2015
- SCGPM Bioinformatics team is hiring an Engineering Research Associate (Req 67780) for our Clinical Genomics Service.
- H2O presentation and demo on July 29th, 2015.
- Join us for a Bioinformatics Seminar on July 23, 2015.
- SCGPM Bioinformatics team is hiring a Bioinformatics Software Developer/Analyst (Req 66307) to support sequencing informatics.
- SCGPM Bioinformatics team at XLDB 2015 conference.
- SCGPM Bioinformatics team at Big Data 2015 conference
- SCGPM Bioinformatics team at PMWC 2015 Silicon Valley conference.
- Join us for a Galaxy Workshop on April 1, 2015.
- Join us for a Bina seminar on March 24, 2015.
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
- Annual SCG user meeting, Dec 2013
- 3rd NGS Bioinformatics seminar and GBSC open house, Nov 2013
- Seven Bridges Genomics Workshop for Cloud computing, Sept 2013
- GBSC officially opened to facilitate Big Data Genomics at Stanford (9/1/2013).
- 2nd NGS Bioinformatics Seminar, July 2013
- 1rst NGS Bioinformatics Seminar, April 2013
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