UVA School of Medicine

Research Computing

Enabling scientific breakthroughs at scale with advanced computing


  • Infrastructure & Code

    Code & Resources SOMRC on GitHub AWS Snippets Cloud Templates Courses / Workshops Project: epihet Project: simpleCache Containers SOMRC Docker Hub Learn how to use Docker Project: LOLAweb Bots & Artificial Intelligence Alexa Skills (in development) Twitter Chatbot (in development) DC/OS Mesos Launching in late 2018, this platform will orchestrate container deployments for both on-demand, short-lived workflows and long-running services. Some example workloads:
  • Cloud Solutions

    var aText = new Array( “serverless website”, “pipelines”, “containers”, “jobs more efficiently” ); Run your Cloud computing is ideal for running flexible, scalable applications on demand, in periodic bursts, or for fixed periods of time. UVA SOMRC works alongside researchers to design and run research applications and datasets into Amazon Web Services, the leader among public cloud vendors. This means that server, storage, and database needs do not have to be estimated or purchased beforehand – they can be scaled larger and smaller with your needs, or programmed to scale dynamically with your application.
  • Quick Start

    User Support School of Medicine Research Computing (SOMRC) is committed to providing individualized support for researchers who are engaged in computationally intensive projects. We offer support in a variety of contexts: Support tickets in ZenDesk Documentation & FAQs Weekly Office Hours Hands-On Workshops In-person Consultations Learn more
    Services SOMRC has expertise in the following service areas. Click on an area for more information: Bioinformatics & Genomics Cloud Solutions Data Analysis Image Processing Scientific Computing Request a Consultation

  • User Support

    School of Medicine Research Computing (SOMRC) is committed to providing individualized support for researchers who are engaged in computationally intensive projects. With expertise in high-performance computing, SOMRC provides support in the following areas: Bioinformatics & Genomics Cloud Solutions Data Analysis Scientific Computing Image Processing SOMRC delivers the services above in the context of system support (web-based ticketing) and consultations (in-person meetings). In either scenario, we seek long-term scientific collaborations.
  • Courses

    In addition to providing free, in-person workshop training, School of Medicine Research Computing staff teach for-credit courses. Below is a selection of courses that SOMRC has taught, co-taught or provided guest lectures: BIMS 8382: Introduction to Biomedical Data Science Spring 2017, Spring 2018 This course introduces methods, tools, and software for reproducibly managing, manipulating, analyzing, and visualizing large-scale biomedical data. Specifically, the course introduces the R statistical computing environment and packages for manipulating and visualizing high-dimensional data, covers strategies for reproducible research, and culminates with analysis of data from a real RNA-seq experiment using R and Bioconductor packages.
  • Workshops

    School of Medicine Research Computing provides training opportunities covering a variety of data analysis, basic programming and computational topics. All of the classes listed below are taught by SOMRC experts and are freely available to UVa faculty, staff and students. Beginning in Spring 2018, SOMRC will be offering workshop registration through CADRE Academy, a new portal that presents workshops sequentially in tracks of particular topics. Users can register for upcoming sessions, follow their progress, and find out about related classes on the site.
  • What is Research Computing?

    UVA School of Medicine Research Computing (SOMRC) is a new program that aims to support computational biomedical research by providing advanced cyberinfrastructure and expertise in data analysis at scale. Our mission is to foster a culture of computational thinking and promote interdisciplinary collaboration in various data-driven research domains. We offer services related to high performance computing, cloud architecture, scientific programming and big data solutions. We also aim to promote computationally intensive research at UVA through collaborative efforts such as UVA’s own CADRE (Computation And Data Resource Exchange) and XSEDE (Extreme Science and Engineering Discovery Environment).
  • Computing Systems

    UVA Research Computing can help you find the right system for your computational workloads. From supercomputers to HIPAA secure systems to cloud-based deployments with advanced infrastructure, various systems are available to researchers. Rivanna HPC A traditional high performance cluster with job scheduler, large file system, modules, and MPI processing. Please see the ARCS page for how to begin working in Rivanna. Get Started on Rivanna
    Ivy Secure Platform A multi-platform, HIPAA-compliant system for secure data that includes dedicated virtual machines (Linux and Windows), Domino Data Lab, and Hadoop/Spark.

  • Why use the Cloud?

    “Cloud computing” has come to mean a lot of things in recent years: web-based email services, or SaaS (software-as-a-service), or cloud-based storage like UVA’s use of Box. But behind all of these practical, useful tools is another cloud, made up of impossibly large, global-scale hardware farms that the above examples live and run on. These farms make up “cloud infrastructure,” and are now sold to consumers by Google, Rackspace, Microsoft, and Amazon.
  • Cloud Storage Solutions

    Amazon Web Services Tiered object storage Amazon S3 and Glacier offer cloud-based, affordable, unlimited capacity for storage from anywhere. Advanced features include scalability, lifecycle management, encryption, and sharing. S3 is ideal for static files that need to be retrieved from any location (PDFs, images, video, etc.). Glacier is archival storage, perfect for grant compliance that reqires data retention. How SOMRC can help: Lower pricing - UVA has an Internet2 discount available for educational use.
  • Bioinformatics User Guides

    Bioinformatics on Rivanna UVA’s High-performance Computing Cluster All faculty, research staff and graduate students of UVA have access to Rivanna, university’s high-performance computing system with 290+ compute nodes (6500+ cores) for high-throughput multithreaded jobs, parallel jobs as well as memmory intensive large-scale data analyses. The architecture is specifically suited for large scale distributed genomic data analysis, with 100+ bioinformatics software packages installed and ready to use. Learn more Bioinformatics using FireCloud FireCloud Home
  • User Guides

    High Performance Computing Standard and high security HPC to run your code, generally written in R, Python or shell scripts. Get Started › Learn More › – Storage Need large, or extremely large storage offsite or on grounds? Can you count in GB, TB, or PB? Learn more about storage options and pricing. Get Started › Cloud Have an idea you’d like to test?