Conferences and Workshops by SCGPM Bioinformatics Team

Microbiome Symposium 2017

Monday September 11, 2017

8:00AM - 7:00 PM at Quadrus Conference Center

Now in its second year, the purpose of the conference is to bring together leading minds looking to catalog the human microbiome using modern genetics tools and especially those looking to apply new computational technologies to solve complicated problems in metagenomics to answer such questions such as: a) How are changes in the microbiome associated with diseases in the population, b) How can you identify novel microbes using sequence-based analysis, c) How can you improve patient outcomes by characterizing microbiome dynamics, d) How can you better understand host-microbiome symbiosis to be able to understand and target microbial vulnerabilities, e) How can you track dynamic microbiome shifts during disease, etc. While genetics tools to characterize the human microbiome is no doubt important, the goal of this conference is to focus on computational tools that help solve any or all of the above complicated metagenomics problems.

Genomics on the Cloud

Genome Sequencing Service Center (GSSC), a Stanford Center for Genomics and Personalized Medicine (SCGPM) service, delivers mapped sequencing reads and detailed quality-control metrics, on the DNAnexus cloud genome informatics platform. Sequencing data are delivered directly to a unified cloud informatics platform that provides storage, compute, and access to popular bioinformatics tools. From that platform, data can be shared with collaborators around the world or plugged directly into downstream analyses. Many shared resources for processing sequencing data, such as ENCODE Consortium workflows for analyzing Methyl-seq, ChIP-seq, and RNA-seq data are publicly available on DNAnexus, as well as tools for generating custom workflows. All of these tools for managing, sharing, and analyzing data are accessible through an easy-to-use web interface or command-line console. By delivering sequencing data on an intuitive cloud informatics platform, we are breaking down barriers between data generators and analysts, and making bioinformatics accessible to novices and experts alike. 

Stanford Center for Genomics and Personalized Medicine (SCGPM) and DNAnexus hosted an interactive workshop demonstrating how to use the DNAnexus cloud genomics platform to easily perform an array of common bioinformatics tasks. 

Microbiome Symposium 2016

With the growing interest in the microbiome, the pace of microbiome-related data generation has increased substantially in the last five to ten years. On the heels of the announcement of the National Microbiome Initiative, it is anticipated that the pace of data generation will accelerate dramatically. Making sense of this ever growing body of information is critical, and will require a coming together of biologists, computer scientists, physicians, ecologists, statisticians and beyond. We hope that this conference, which aims to encourage creative exchange and sharing of ideas in the data analysis space, will be exciting, inspiring and productive for you all. 

Genomics and Patient Privacy Conference 2016

Purpose of this conference is to gather experts in genomics and privacy and investigate the role of privacy-preserving technologies in genomics data collaboration.

Research using genomics data is fraught with concerns around patient re-identification using de-identified sequence data. This has resulted in complex data sharing agreements and patient consent process. We believe that the current genomics research bottleneck is no longer within a data silo but being able to share insights across silos. 

At this conference, we will focus on the technological approaches to genomics privacy protection. Are there classes of relevant genomics algorithms or queries that can benefit from privacy protecting analytical methods, and be applied to real world data sharing scenarios? 

Even if these methods have limited genomic applications in the beginning, over time these methods will be able to deliver more. With availability of flexible Cloud computing resources, it has now become possible to harness computationally intensive methods at a reasonable cost e.g. boot up 1000 machines simultaneously for a brief instance. 

Our ultimate goal is to develop a set of genomics research and collaboration tools, in coordination with our industry partners, that will not only allow patients and institutes to feel more confident about privacy protection, but will also bring sophisticated risk assessment and risk management approaches to genomics.