Microservice architecture is an approach to designing and running applications. Such applications are typically run within containers, made popular in the last few years by Docker. Containers are portable, efficient, and disposable, and contain code and any dependencies in a single package. Containerized microservices typically run a single process, rather than an entire stack within the same computing environment. This allows portions of your application to be easily replaced or scaled as needed. Research Computing runs microservices in an orchestration environment named DCOS (Distributed Cloud Operating System), based on Apache Mesos and Apache Marathon. DCOS makes the deployment and management of many containers easy and scalable.
OMERO is a database for management of imaging data. UVA is is hosting a centralized OMERO database instance backed by centralized storage that facilitates sharing, processing and annotating images for your research group and invited collaborators.
Overview With the advent of high-throughput screening, the need for efficient image management tools is greater than ever. From the microscope to publication, OMERO is a database solution that handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. Work with your images from a desktop app (Windows, Mac or Linux), on UVA’s high performance computing platform (Rivanna), from the web, or through 3rd party software like Fiji and ImageJ, Python, and MATLAB.
Ivy Ivy is a secure computing environment for researchers consisting of virtual machines (Linux and Windows). Researchers can use Ivy to process and store sensitive data with the confidence that the environment is secure and meets HIPAA or CUI requirements.
Overview Ivy consists of both virtual computing environments and secure storage. In order to obtain access to either system, users must 1. Submit an account request, 2. Complete the Information Security Awareness Training, and 3. Ensure their personal computer meets all High Security VPN requirements.
Requesting Access Training High Security VPN Virtual Machines JupyterLab Notebooks Data Transfer In/Out of Ivy HIPAA Compliance Requesting Access University of Virginia tenure stream and academic general faculty, research faculty, research scientists, and postdoctoral associates may request an account on Ivy.
Globus Data Transfer Globus is a simple, reliable, and fast way to access and move your research data between systems. Globus allows you to transfer data to and from systems such as:
Laptops HPC clusters (Rivanna) Lab / departmental storage Tape archives Cloud storage Off-campus resources (XSEDE, National Labs) Globus can help you share research data with colleagues and co-investigators, or to move data back and forth between a lab workstation and Rivanna or your personal computer.
Are your data stored at a different institution? At a supercomputing facility? All you need is your campus login.
Getting Started A Globus “collection” (also called an “endpoint”) is any computer running the Globus Connect software.
Rivanna is the University of Virginia’s High-Performance Computing (HPC) system. As a centralized resource it has hundreds of pre-installed software packages available for computational research across many disciplines. Currently the Rivanna supercomputer has over 8,000 cores and 8PB of various storage.
All UVA faculty, staff, and postdoctoral associates are eligible to use Rivanna, or students when part of faculty research.
The sections below contain important information for new and existing Rivanna users. Please read each carefully. New users are invited to attend one of our free orientation sessions (“Introduction to the HPC System”) held throughout the year during office hours or by appointment.