UVA Research Computing

Research Computing

Creating innovative solutions for researchers

/category/userinfo

  • Ivy Secure Environment

    Ivy Ivy is a secure computing environment for researchers consisting of virtual machines (Linux and Windows) and Jupyter Notebooks. Researchers can use Ivy to process and store sensitive data with the confidence that the environment is secure and meets HIPAA requirements. Overview Ivy consists of two separate computing environments. Access to one environment does not automatically grant access to the others: Virtual Machines JupyterLab Notebooks - Coming Soon! Data Transfer In/Out of Ivy HIPAA Compliance Coming Soon - Secure HPC 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 Data Transfer Is a simplified way to access and move your research data, across all systems, using any existing identity. Transfer data to and from systems such as: Laptops HPC clusters (Rivanna) Secure computing (Ivy) Lab / departmental storage Tape archives Cloud storage Off-campus resources (XSEDE, National Labs) Access them all using just a web browser. This can help you share research data with colleagues, co-investigators, or to move data back and forth between a lab workstation and Rivanna or your personal computer. Data stored at a different institution? At a supercomputing facility? All you need is your campus login.
  • Research Value Storage

    Overview Research Computing offers several budget options for storing non-sensitive research data. The Research Value Storage provides users with a solution for research data storage and collaboration. Members in the same group have access to a shared directory created by the team lead or PI. Group membership can be defined and managed through ITS MyGroups system. Value storage is mounted on the Rivanna HPC cluster and can also be accessed on a personal computer with an SMB mount, allowing for point-and-click file manipulation. If you are not a researcher, UVA ITS offers Academic Value storage for long-term storage of large scale data.
  • Non-Sensitive Data Storage

    /home /home is a free 50GB space provided to users of the Rivanna HPC system and is visible from the Rivanna login and compute nodes. /home is the default working directory when logging on to Rivanna. Users can also access their home directory at /home/$USER, where $USER is an individual’s UVa computing ID. /scratch /scratch is a Lustre high performance parallel filesystem accessible via the Rivanna login and compute nodes. All Rivanna HPC users are granted 10TB for free and can access this space within Rivanna at /scratch/$USER, where $USER is an individual’s UVa computing ID. The /scratch directory is not intended for long-term data storage.
  • Microservices

    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.
  • Computing Environments at UVA

    Rivanna The primary vehicle for high-performance computing since 2014 has been the Rivanna cluster. Rivanna is a heterogenous system consisting of approximately 186 x 20-core nodes with 128GB of RAM each, 25 x 28-core nodes with 256 GB of RAM, and 152 x 40-core nodes with 384GB each. Five “big memory” nodes offer 1TB of RAM with 16 cores each. All nodes are supported by a high-performance FDR Infiniband network using Mellanox hardware and some have EDR Infiniband. A number of nodes supporting specialty hardware are included; there are 8 nodes with NVIDIA K80 GPGPUs, 4 nodes with NVIDIA V100 GPGPUs, 1 node with NVIDIA V100, and 2 nodes with NVIDIA RTX2080TI boards.
  • 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. Are you submitting a grant proposal and need standard information about UVA research computing environments? Get it here. High Performance Computing - Rivanna A traditional high performance cluster with job scheduler, large file system, modules, and MPI processing. Get Started on Rivanna
    Secure Computing for Sensitive Data - Ivy A multi-platform, HIPAA-compliant system for secure data that includes dedicated virtual machines (Linux and Windows), JupyterLab Notebooks, and Apache Spark.

  • HPC Storage

    There are a variety of options for storing large-scale research data at UVa. Non-sensitive data storage systems can be accessed from the Rivanna high performance computing system. .tg {border-collapse:collapse;border-spacing:0;border-color:#ccc;} .tg td{font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:0px;overflow:hidden;word-break:normal;border-color:#ccc;color:#333;background-color:#fff;} .tg th{font-family:Arial, sans-serif;font-size:14px;font-weight:normal;padding:10px 5px;border-style:solid;border-width:0px;overflow:hidden;word-break:normal;border-color:#ccc;color:#333;background-color:#f0f0f0;} .tg .tg-hy9w{background-color:#eceeef;border-color:inherit;vertical-align:top} .tg .tg-dc35{background-color:#f9f9f9;border-color:inherit;vertical-align:top} .tg .tg-0qmj{font-weight:bold;background-color:#eceeef;border-color:inherit;vertical-align:top} Non-Sensitive Data Storage Name Quota Price Data Protection Accessible from Best Practices /home 50GB Free 3-week snapshot Rivanna login and compute nodes /home is best used as a working directory when using Rivanna interactively. SLURM jobs run against /home will be slower than those run against /scratch. /scratch 10TB Free Data removed 90 days after last file modification timestamp Rivanna login and compute nodes /scratch is a high performance parallel filesystem that is suitable for large scale computational work.
  • Rivanna FAQs

    General Usage Allocations Applications Job Management Storage Management Data Transfer Other Questions General Usage How do I gain access to Rivanna? A faculty or research staff member must first request an allocation on Rivanna. Full details can be found here. How do I log on to Rivanna? Use an SSH client from a campus-connected machine and connect to rivanna.hpc.virginia.edu. Instructions for using ssh and other login tools, as well as recommended clients for different operating systems, are here. You can also use FastX. If you are off Grounds you must use the UVA Anywhere VPN. How do I reset my current password / obtain a new password?
  • Rivanna

    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.
  • FastX Web Portal

    Overview FastX is a commercial solution that enables users to start an X11 desktop environment on a remote system. It is available on the Rivanna frontends. Using it is equivalent to logging in at the console of the frontend. Using FastX for the Web We recommend that most users access FastX through its Web interface. To connect, point a browser to: https://rivanna-desktop.hpc.virginia.edu Login Screen After entering your computing ID and Netbadge password, you will see a launch screen. Launch In this example, we have no pre-existing sessions so we must create one. Click the Launch Session button. This will bring up a screen showing the options.
  • Open OnDemand

    Overview Open OnDemand is a graphical user interface that allows access to Rivanna via a web browser. Within the Open OnDemand environment users have access to a file explorer; interactive applications like JupyterLab, RStudio Server & FastX Web; a command line interface; and a job composer and job monitor. Logging in to Rivanna Rivanna is accessible through the Open OnDemand web client at https://rivanna-portal.hpc.virginia.edu. Your login is your UVA computing ID and your password is your Netbadge password. Some services, such as FastX Web, require the Eservices password. If you do not know your Eservices password you must change it through ITS by changing your Netbadge password.
  • Open OnDemand: File Explorer

    Open OnDemand provides an integrated file explorer to browse and manage small files. Rivanna has multiple locations to store your files with different limits and policies. Specifically, each user has a relatively small amount of permanent storage in his/her home directory and a large amount of temporary storage (/scratch) where large data sets can be staged for job processing. Researchers can also lease storage that is accessible on Rivanna. Contact Research Computing or visit the storage website for more information. The file explorer provides these basic functions: Renaming of files Viewing of text and small image files Editing text files Downloading & uploading small files To see the storage locations that you have access to from within Open OnDemand, click on the Files menu.
  • Open OnDemand: Job Composer

    Open OnDemand allows you to submit SLURM jobs to the cluster without using shell commands. The job composer simplifies the process of: Creating a script Submitting a job Downloading results Submitting Jobs We will describe creating a job from a template provided by the system. Open the Job Composer tab from the Open OnDemand Dashboard. Go to the New Job tab and from the dropdown, select From Template. You can choose the default template or you can select from the list. Click on Create New Job. You will need to edit the file that pops up, so click the light blue Open Editor button at the bottom.
  • Rivanna Queues

    Several queues (or “partitions”) are availble to users for different types of jobs. One queue is restricted to single-node (serial or threaded) jobs; another for multinode parallel programs, and others are for access to specialty hardware such as large-memory nodes or nodes offering GPUs. Partition Max time per job Max nodes per job Max cores per job Max memory per core Max memory per node per job SU Charge Rate standard 7 days 1 40 12GB 375GB 1.00 parallel 3 days 45 900 6GB 120GB 1.00 largemem 4 days 1 16 62GB 975GB 1.
  • Rivanna HPC Software

    Overview Research Computing at UVA offers a variety of standard software packages for all Rivanna users. We also install requested software based on the needs of the high-performance computing (HPC) community as a whole. Software used by a single group should be installed by that group’s members, ideally on leased storage controlled by the group. Departments with a set of widely-used software packages may install them to the lsp_apps space. The Research Computing group also provides limited assistance for individual installations. For help installing research software on your PC, please contact Research Software Support at res-consult@virginia.edu. Software Modules and Containers Software on Rivanna is accessed via environment modules or containers.
  • Pricing

    Below is a schedule of prices for Research Computing resources. Rivanna Allocations Type SU Limits Cost SU Lifetime Standard 100,000 per application; renewable up to 3x per year (400,000 total SUs) Free 12 months Deans’ Allocations None Free 12 months by default, negotiable Purchased None $0.015 (<1M SUs); $0.01 (=1M SUs) Forever Instructional 25,000 Free 2 weeks after last teaching session * GPU node charge rate is 2.0 SUs instead of 1.0. ** Non-UVA personnel are charged at a rate of $0.07/SU About Allocations
  • Allocations

    Time on Rivanna is allocated as Service Units (SUs). One SU corresponds to one core-hour. Multiple SUs make up what is called an allocation (e.g., a new allocation = 100K SUs). Allocations are managed through MyGroups groups that are automatically created for Principal Investigators (PIs) when they submit an allocation request. All UVA faculty, staff, and postdoctoral associates are considered PIs and therefore eligible for an allocation on Rivanna. Students—both graduate and undergraduate—cannot request allocations, but they are allowed to use Rivanna as members of a MyGroups group controlled by a PI. Eligibility and Account Creation University of Virginia tenure stream and academic general faculty, research faculty, research scientists, and postdoctoral associates may request any type of allocation.
  • Logging In

    Rivanna is accessible through a web portal, secure shell terminals, or a remote desktop environment. For of all of these access points, your login is your UVA computing ID and your password is your Eservices password. If you do not know your Eservices password you must change it through ITS. Off Campus? All users who wish to access Rivanna while off Grounds must use the UVA Anywhere VPN client. Only Windows and Mac OSX operating systems are supported. Linux users should refer to these unsupported instructions to install and configure a VPN. Web-based Access Open OnDemand is a graphical user interface that allows access to Rivanna via a web browser.
  • MobaXterm

    MobaXterm is the recommended login tool for Windows users. It bundles a tabbed ssh client, a graphical drag-and-drop sftp client, and an X11 window server for Windows, all in one easy-to-use package. Some other tools included are a simple text editor with syntax coloring and several useful Unix utlities such as cd, ls, grep, and others, so that you can run a lightweight Linux environment on your local machine as well as use it to log in to a remote system. Download To download MobaXterm, click the link below. Select the “Home” version, “Installer” edition, Download MobaXterm Run the installer as directed.
  • SLURM Job Manager

    Overview Rivanna is a multi-user, managed environment. It is divided into frontends, which are directly accessible by users, and compute nodes, which must be accessed through the resource manager. We use the Simple Linux Utility for Resource Management (SLURM), an open-source tool that performs cluster management and job scheduling for Linux clusters. Jobs are submitted to the resource manager, which queues them until the system is ready to run them. SLURM selects which jobs to run, when to run them, and how to place them on the compute node, according to a predetermined site policy meant to balance competing user needs and to maximize efficient use of cluster resources.
  • Research Data Storage

    There are a variety of options for storing large-scale research data at UVA. Non-sensitive data storage systems can be accessed from the Rivanna high performance computing system. Sensitive data can be stored and accessed within the Ivy secure computing environment. Information Technology Services (ITS) also provides multiple tiers of data storage for personal and non-research storage needs. .tg {border-collapse:collapse;border-spacing:0;border-color:#ccc;} .tg td{font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:0px;overflow:hidden;word-break:normal;border-color:#ccc;color:#333;background-color:#fff;} .tg th{font-family:Arial, sans-serif;font-size:14px;font-weight:normal;padding:10px 5px;border-style:solid;border-width:0px;overflow:hidden;word-break:normal;border-color:#ccc;color:#333;background-color:#f0f0f0;} .tg .tg-hy9w{background-color:#eceeef;border-color:inherit;vertical-align:top} .tg .tg-dc35{background-color:#f9f9f9;border-color:inherit;vertical-align:top} .tg .tg-0qmj{font-weight:bold;background-color:#eceeef;border-color:inherit;vertical-align:top} Non-Sensitive Data Storage Name Quota Price Data Protection Accessible from Best Practices Project Storage 1TB increments $60 /TB/yr 2 week snapshots Rivanna, NFS mount /projectis ideal for long-term storage of data to be accessed from Rivanna.
  • Rivanna Software List

    function searchFunction() { var input, filter, table, tr, td, i, txtValue; input = document.getElementById(“searchInput”); filter = input.value.toUpperCase(); table = document.getElementById(“moduleTable”); tr = table.getElementsByTagName(“tr”); for (i = 0; i -1) { tr[i].style.display = “”; } else { tr[i].style.display = “none”; } } } } Module Category Description R R is a free software environment for statistical computing and graphics. abinit chem ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
  • Software Containers

    Overview Containers bundle an application, the libraries and other executables it may need, and even the data used with the application into portable, self-contained files called images. Containers simplify installation and management of software with complex dependencies and can also be used to package workflows. Singularity is a container application targeted to multi-user, high-performance computing systems. It interoperates well with SLURM and with the Lmod modules system. Singularity can be used to create and run its own containers, or it can import Docker containers. Creating Singularity Containers To create your own image from scratch, you must have root privileges on some computer running Linux (any version).
  • Software Modules

    The lmod modules system on Rivanna enables users to easily set their environments for selected software and to choose versions if appropriate. The lmod system is hierarchical; not every module is available in every environment. We provide a core environment which contains most of the software installed by Research Computing staff, but software that requires a compiler or MPI is not in that environment and a compiler must first be loaded. View All Modules   Basic Commands List all available software in the core environment: module avail Use “module spider” to find all possible modules. module spider module spider hdf5 If a version is specified to spider, it will indicate how to load that version.
  • Acknowledgement in Publications

    Recognition and documentation of the contribution that Research Computing’s systems and support play in breakthrough research is essential to ensuring continued support for and availability of cutting-edge computing resources at The University of Virginia. Please cite UVA Research Computing in any research report, journal article, or other publication that requires citation of an author’s contributions. Suggested format: The authors acknowledge Research Computing at The University of Virginia for providing computational resources and technical support that have contributed to the results reported within this publication. URL: https://rc.virginia.edu
  • Tools for Research

    Tools and software projects that UVA Research Computing has collaborated on:

    LOLAweb LOLAweb is a web server and interactive results viewer for enrichment of overlap between a user-provided query region set (a bed file) and a database of region sets. It provides an interactive result explorer to visualize the highest ranked enrichments from the database. LOLAweb is a web interface to the LOLA R package. Launch LOLAweb
    BARTweb There are a number of commercially licensed tools available to UVa researchers for free. These products, including UVa Box, Dropbox (Health System) and CrashPlan, are most suitable for small-scale storage needs.


  • Data Transfer

    Efficient and reliable data transfer is a critical component of scientific research computing. There are a variety of useful tools available for expedient data transfer, whether you are transferring data from an external site or within different computing environments at UVa. Use Cases The data transfer method you choose heavily relies on where the data are currently located and to where you want to transfer the data. Click on a row in the table below to learn more about the data transfer methods available for a specific use case. Source Destination Example Use Cases Lab Workstation Non-Sensitive Data Storage A research scientist wants to copy data from her lab workstation to her lab’s /project storage share.
  • Sensitive Data Storage - Ivy

    Overview The Ivy secure computing environment meets both HIPAA- and CUI-compliance standards and is ideal for storing sensitive research data. Ivy offers several storage options to fit your research computing needs. Ivy Central Storage Ivy Central Storage (ICS) is a sensitive data parking zone and central storage pool with a capacity greater than 1PB. This storage space is available for researchers with highly sensitive data and can be mounted on an Ivy virtual machine (VM). For added security, files stored on ICS are read & write only. Executable files can be moved from ICS to VM storage. Researchers can request space on ICS by first requesting an Ivy account using the form on the CADRE website.
  • /project Storage

    Overview The /project file system provides users with a collaborative space for data storage and sharing. Members in the same group have access to a shared directory created by the team lead or PI. Group membership can be defined and managed through ITS MyGroups system. /project storage is mounted on the Rivanna HPC cluster and runs on a new scale-out NAS file system. How to request space in /project /project storage is available by request (via CADRE User Support page) for $90/TB/YR. When filling out the form, the PI can specify the size of the /project directory and the name of an existing or new MyGroup that can access this space.
  • Bioinformatics Packages on Ivy Linux VM

    Available Packages The following bioinformatics packages are available on the Ivy Linux Virtual Machines Bowtie2 Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes. For bowtie2 usage information, please click here HISAT2 HISAT2 is a fast and sensitive tool for aligning short reads against the general human population (as well as single reference genome) * Requires approval before installation For HISAT2 usage information, please click here
  • Bioinformatics Packages on Windows VM

    Available Packages The following bioinformatics packages are available on the Windows Virtual Machines Bowtie2 For more information on bowtie2, please click here HISAT2 Requires approval before installation. For more information on HISAT2, please click here
  • Bowtie2 on Ivy Linux VM

    Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes. It indexes the genome using FM Index, which is based on Burrows-Wheeler Transform algorithm, to keep its memory footprint small. Bowtie2 supports gapped, local and paired-end alignment modes. Alignment to a known reference using Bowtie2 is often an essential first step in a myriad of NGS analyses workflows. Bowtie2 Usage Alignment using bowtie2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data. Create indexes of your reference genome of interest stored in reference.fasta file: bowtie2-build [option(s)] <reference.fasta> <bt2-index-basename> This will create new files with the provided basename and extensions .
  • Bowtie2 on Ivy Windows VM

    Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes. It indexes the genome using FM Index, which is based on Burrows-Wheeler Transform algorithm, to keep its memory footprint small. Bowtie2 supports gapped, local and paired-end alignment modes. Alignment to a known reference using Bowtie2 is often an essential first step in a myriad of NGS analyses workflows. Bowtie2 Usage Alignment using bowtie2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data. Create indexes of your reference genome of interest stored in reference.fasta file: bowtie2-build [option(s)] <reference.fasta> <bt2-index-basename> This will create new files with the provided basename and extensions .
  • Data Analysis Packages on Ivy Linux VM

    Available Packages The following Data Analysis packages are available on the Ivy Linux Virtual Machines MATLAB MATrix LABoratory (MATLAB for short) is a software designed for quick scientific calculations, such as matrix manipulation, plotting, and others. It has hundreds of built-in functions for a wide variety of computations and several tools designed for specific research disciplines, including statistics and partial differential equations. * Limited licenses available, for more information on MATLAB and licensing, please click here SAS SAS is large platform independent software with multiple components, and is used for statistical analysis, data ETL operations, as well as several other reporting problems.
  • Data Analysis Packages on Ivy Windows VM

    Available Packages The following Data Analysis packages are available on the Ivy Windows Virtual Machines MATLAB MATrix LABoratory (MATLAB for short) is a software designed for quick scientific calculations, such as matrix manipulation, plotting, and others. It has hundreds of built-in functions for a wide variety of computations and several tools designed for specific research disciplines, including statistics and partial differential equations. * Limited licenses available, for more information on MATLAB and licensing, please click here SAS SAS is large platform independent software with multiple components, and is used for statistical analysis, data ETL operations, as well as several other reporting problems.
  • Database Software on Ivy Linux VM

    The following database software are available on the Ivy Linux Virtual Machines MySQL Is the most popular open-source relational database, used in academia and industry worldwide. It has been in use for over 20 years and is backed by a large developer community. It is available in both free and proprietary versions. MariaDB MariaDB is a community developed version of MySQL, and is highly compatible with MySQL and other relational databases. Existing databases can be easily migrated between MySQL and MariaDB, and vice versa. PostgreSQL Unlike MariaDB and MySQL, PostgreSQL is an object relational database, and can be used in a manner similar to other relational databases.
  • HISAT2 on Ivy Linux VM

    * Please note that HISAT2 requires approval prior to installation on the VM HISAT2 is a fast and sensitive tool for aligning short reads against the general human population (as well as single reference genome). It indexes the genome using a Hierarchical Graph FM Index (HGFM) strategy, i.e. a large set of small indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp). HISAT2 Usage: Alignment using HISAT2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data. Create indexes of your reference genome of interest stored in reference.
  • HISAT2 on Ivy Windows VM

    * Please note that HISAT2 requires approval prior to installation on the VM HISAT2 is a fast and sensitive tool for aligning short reads against the general human population (as well as single reference genome). It indexes the genome using a Hierarchical Graph FM Index (HGFM) strategy, i.e. a large set of small indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp). HISAT2 Usage: Alignment using HISAT2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data. Create indexes of your reference genome of interest stored in reference.
  • UVa Licensed SPSS on Ivy Windows VM

    SPSS Overview SPSS (or Statistical Package for Social Sciences), was initially developed as a social survey project but later on has grown to encompass statistical applications in almost all disciplines. Different industries use SPSS for their data analysis work. Its features include database management, reporting, graphing, among many others. SPSS Usage SPSS is available only on the Windows VM at the moment. To run SPSS go to: Start Menu > All Programs > IBM SPSS Statistics Licensing We have a limited number of SPSS licenses available, which are provided on a first-come-first-serve basis. As a consequence, availability of SPSS on your VM is not always guaranteed once a VM request is submitted.
  • cTAKES on Ivy Linux VMs

    cTAKES Overview cTAKES or The clinical Text Analysis and Knowledge Extraction System, is a Mayo Clinic developed Natural Language Processing (NLP) tool used to extract information out of clinical records. It is open-source, and built on the Apache Unstructured Information Management Architecture. cTAKES is modular, expandable, for a number of generic use cases, and contains excellent best practice notes. cTAKES Usage cTAKES components Some of cTAKES components are listed below: Sentence boundary detection (OpenNLP technology) *Tokenization (rule-based) Morphologic normalization (NLM’s LVG) POS tagging (OpenNLP technology) Shallow parsing (OpenNLP technology) Named Entity Recognition Negation and context identification (both based on NegEx) cTAKES Named Entities cTAKES contains the following Named Entities:
  • cTAKES on Ivy Windows VMs

    cTAKES Overview cTAKES or The clinical Text Analysis and Knowledge Extraction System, is a Mayo Clinic developed Natural Language Processing (NLP) tool used to extract information out of clinical records. It is open-source, and built on the Apache Unstructured Information Management Architecture. cTAKES is modular, expandable, for a number of generic use cases, and contains excellent best practice notes. cTAKES Usage cTAKES components Some of cTAKES components are listed below: Sentence boundary detection (OpenNLP technology) *Tokenization (rule-based) Morphologic normalization (NLM’s LVG) POS tagging (OpenNLP technology) Shallow parsing (OpenNLP technology) Named Entity Recognition Negation and context identification (both based on NegEx) cTAKES Named Entities cTAKES contains the following Named Entities:
  • User Licensed Stata on Ivy Linux VMs

    Stata Overview Stata is a graphical data analysis tool developed by StataCorp, and is short for Statiscs and Data. It is used in various disciplines, including biomedicine, economics, epidemiology, among others. It is capable of performing statistical analysis, simulations, regression, and data management. Besides the standard version Stata also ships with the MP version (multi=processing), and SE for large databases. NB Users requesting an installation of Stata would be required to bring their own license. Please consult with us before requesting an installation. You may also request a Stata license from the UVa Software Gateway
  • User Licensed Stata on Ivy Windows VMs

    Stata Overview Stata is a graphical data analysis tool developed by StataCorp, and is short for Statiscs and Data. It is used in various disciplines, including biomedicine, economics, epidemiology, among others. It is capable of performing statistical analysis, simulations, regression, and data management. Besides the standard version Stata also ships with the MP version (multi=processing), and SE for large databases. NB Users requesting an installation of Stata would be required to bring their own license. Please consult with us before requesting an installation. You may also request a Stata license from the UVa Software Gateway
  • UVa Licensed IDL on Ivy Linux VMs

    IDL Overview IDL, short for Interactive Data Language, is an interactive shell based data analysis programming language. Used vastly in medical imaging, it can quickly create visualizations and graphs of large data sets in a few easy steps due to its vector nature. FORTRAN users would be familiar with the IDL syntax. IDL is not to be confused with Java IDL or Microsoft IDL. Basic IDL Usage To start IDL, open a terminal window and type idl. This will start the interactive shell. Variables in IDL To initialize variables in IDL, type: <variable_name> = <variable_value> e.g. x = 3 and hit Enter/Return
  • UVa Licensed IDL on Ivy Windows VMs

    IDL Overview IDL, short for Interactive Data Language, is an interactive shell based data analysis programming language. Used vastly in medical imaging, it can quickly create visualizations and graphs of large data sets in a few easy steps due to its vector nature. FORTRAN users would be familiar with the IDL syntax. IDL is not to be confused with Java IDL or Microsoft IDL. Licensing We have a limited number of IDL Licenses available, which are provided on a first-come-first-serve basis. As a consequence, availability of IDL on your VM is not always guaranteed once a VM request is submitted.
  • UVa Licensed MATLAB on Ivy Linux Virtual Machines

    MATLAB Overview MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming environment. MATLAB stands for MATrix LABoratory. MATLAB was made to provide easy access to matrix software developed by the LINPACK (linear system package) and EISPACK (Eigen system package) projects. MATLAB includes a programming language environment with built-in editing and debugging tools, and supports object-oriented programming. Programming in MATLAB MATLAB has many advantages compared to conventional computer languages (e.g., C, FORTRAN) for solving technical problems. MATLAB is an interactive system whose basic data element is an array, and almost all problems can be solved in MATLAB using that one data element.
  • UVa Licensed MATLAB on Ivy Windows Virtual Machines

    MATLAB Overview MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming environment. MATLAB stands for MATrix LABoratory. MATLAB was made to provide easy access to matrix software developed by the LINPACK (linear system package) and EISPACK (Eigen system package) projects. MATLAB includes a programming language environment with built-in editing and debugging tools, and supports object-oriented programming. Programming in MATLAB MATLAB has many advantages compared to conventional computer languages (e.g., C, FORTRAN) for solving technical problems. MATLAB is an interactive system whose basic data element is an array, and almost all problems can be solved in MATLAB using that one data element.
  • UVa Licensed SAS on the Ivy Linux VM

    SAS Overview SAS is a command-driven software package used for statistical analysis and data visualization. It is available in . It is one of the most widely used statistical software packages in both industry and academia. You may use it if you have a large number of statistical algorithms. It is not limited to an industry, and could be used in both scientific and non-scientific contexts. We only offer the Teaching & Research version at the moment. Common Usage For this example we will use a common scenario from SAS Clinical Standards Toolkit, which is used for supporting clinical research activiites.
  • UVa Licensed SAS on the Ivy Windows VM

    SAS Overview SAS is a command-driven software package used for statistical analysis and data visualization. It is available in . It is one of the most widely used statistical software packages in both industry and academia. You may use it if you have a large number of statistical algorithms. It is not limited to an industry, and could be used in both scientific and non-scientific contexts. We only offer the Teaching & Research version at the moment. Common Usage For this example we will use a common scenario from SAS Clinical Standards Toolkit, which is used for supporting clinical research activiites.
  • Image Processing Software on Ivy Linux VM

    Pre-approved packages The following software packages are pre-approved for image processing on an Ivy Linux VM KNIME KNIME is open source analytics platform for data mining and pipelining. KNIME’s Image Processing Plugin allows users to perform common image processing techniques such as registration, segmentation, and feature extraction. KNIME is compatible with over 120 image file types and can be used alongside ImageJ. ImageJ ImageJ is a Java-based image processing program developed at the NIH. ImageJ can be used interactively through a graphical user interface or automatically with Java. OpenCV OpenCV is an open source library for computer vision applications.
  • Image Processing Software on Ivy Windows VM

    Pre-approved packages The following software packages are pre-approved for image processing on an Ivy Windows VM Axiovision Axiovision is software for microscopy image processing and analysis. Axiovision is highly configurableto meet the needs of your individual workflows. KNIME KNIME is open source analytics platform for data mining and pipelining. KNIME’s Image Processing Plugin allows users to perform common image processing techniques such as registration, segmentation, and feature extraction. KNIME is compatible with over 120 image file types and can be used alongside ImageJ. ImageJ ImageJ is a Java-based image processing program developed at the NIH. ImageJ can be used interactively through a graphical user interface or automatically with Java.
  • LibreOffice On Ivy Linux VM

    LibreOffice Overview Our Linux VMs come prepackaged with the open source alternative to Microsoft Office®, called LibreOffice. As of last writing, version 5 is installed, including the specific software suites mentioned below. LibreOffice is compatible with all Microsoft Office formats, and can be connected to services like Google Drive or DropBox. It is available under the Mozilla Public License. LibreOffice is full GUI software and would require you to RDP into your VM or use a graphical tool such as FastX in order to render it. LibreOffice Writer LibreOffice Writer is the word processor component of LibreOffice. It can save documents in .
  • Preinstalled Java SDK on Ivy Linux VM

    Java SDK Overview Ivy Linux VMs are installed with Java SDK 1.8. Java is a popular Object Oriented programming language and is used in a multitude of scenarios. It is available under the GNU General Public License for all users. The SDK consists of a large number of tools such as javac that help in application development. Running Java commands from the Command Line Open a Command Line Terminal and enter java followed by the desired command. E.g. to find the version of the SDK java -version Running your code To compile java code, first cd to the location of your .
  • Preinstalled Java SDK on Ivy Windows VM

    Java SDK Overview Ivy Windows VMs are installed with Java SDK 1.8. Java is a popular Object Oriented programming language and is used in a multitude of scenarios. It is available under the GNU General Public License for all users. The SDK consists of a large number of tools such as javac that help in application development. Running Java commands from the Command Prompt Open a Windows Command Prompt and enter java followed by the desired command. E.g. to find the version of the SDK java -version Running your code To compile java code, first cd to the location of your .
  • Preinstalled Perl on Ivy Linux VMs

    Perl Our VMs have Perl 5.16.3 available as part of the base linux VM. Licensed as open source under the GPL, it is most often used to develop mission critical software, and has excellent integration with markup languages such as HTML, XML, amongst others. Since it is both Object Oriented as well as procedural, it could be used within a multitude of programming projects. It includes built in database integration via its DBI module. Other than DBI, it has thousands of modules, making it one of the most extensible languages. Due to its interpreted nature, Perl is similar to Python and would be easy to understand for those familiar with Python.
  • Preinstalled Rodeo on Ivy Linux VM

    Rodeo Overview Our Linux VMs are installed with Rodeo version 2.5, as of the last update. Rodeo is a lightweight, Python based, IDE for data science. It has a very streamlined code-to-plot workflow, with easily extensible packages that make it simple to analyze difficult patterns in data. It includes many data analysis features under one roof, and adopts features from iPython Notebook (it actually runs atop the iPython kernel). Like most Python projects, it is open source and available for free. Launching Rodeo You can launch Rodeo from the Applications menu. It is a self contained IDE that would not require any knowledge of the command line.
  • Preinstalled Rodeo On Ivy Windows VM

    Rodeo Overview Our Windows VMs are installed with Rodeo version 1.3, as of the last update. Rodeo is a lightweight, Python based, IDE for data science. It has a very streamlined code-to-plot workflow, with easily extensible packages that make it simple to analyze difficult patterns in data. It includes many data analysis features under one roof, and adopts features from iPython Notebook (it actually runs atop the iPython kernel). Like most Python projects, it is open source and available for free. Launching Rodeo You can launch Rodeo from the Start menu. It is a self contained IDE that would not require any knowledge of the command line.
  • Preinstalled Strawberry Perl on Ivy Windows VM

    Perl Our VMs have Strawberry Perl 5.24 available as part of the Windows VM, as of the last writing. Licensed as open source under the GPL, it is most often used to develop mission critical software, and has excellent integration with markup languages such as HTML, XML, amongst others. Since it is both Object Oriented as well as procedural, it could be used within a multitude of programming projects. It includes built in database integration via its DBI module. Other than DBI, it has thousands of modules, making it one of the most extensible languages. Due to its interpreted nature, Perl is similar to Python and would be easy to understand for those familiar with Python.
  • Sumatra PDF on Ivy Windows VM

    Sumatra PDF Overview Sumatra PDF is an open source software to view PDF files in Windows. It could be used to view PDF documents stored within the Ivy VM. As of the latest version, Sumatra supports multiple formats including PDF, EPUB, MOBI, and XPS. Running Sumatra PDF From the Start menu, go to All Programs and search for Sumatra PDF. Click on the icon to run it. More Information For more information, visit the Sumatra PDF official website.
  • Preinstalled R on Ivy Linux VM

    R Overview R is an open source programming language, used by Data Miners, Scientists, Data Analysts, and Statisticians. It is available under the GNU GPL V2 license from the Comprehensive R Archive Network R can be used for many statistical, modeling, and graphical solutions. It is very Object Oriented in nature and is easily extensible. Running the command line R console Type R at the terminal to launch the R console. Installing packages Our Linux VMs come equipped with R preinstalled. Most major R packages are also installed and further could be installed from CRAN using (from within the R console)
  • Preinstalled R on Ivy Windows VM

    R Overview R is an open source programming language, used by Data Miners, Scientists, Data Analysts, and Statisticians. It is available under the GNU GPL V2 license from the Comprehensive R Archive Network R can be used for many statistical, modeling, and graphical solutions. It is very Object Oriented in nature and is easily extensible. Running Rstudio from the desktop You can start R in a Graphical interface using the RStudio application from the desktop Running the command line R console Type R at the command prompt to launch the R console. Installing packages Our Windows VMs come equipped with R preinstalled.
  • Preinstalled Python 2 and Python 3 with Anaconda on Ivy Linux VM

    Anaconda Our VMs have python 2 and 3 available as part of the Anaconda distribution. Anaconda comes installed with many packages best suited for scientific computing, data processing, and data analysis, while making deployment very simple. Its package manager conda installs and updates python packages and dependencies, keeping different package versions isolated on a project-by-project basis. Anaconda is available as open source under the New BSD license. It also ships with pip, the common python package manager. Installing packages Packages could be installed via pip or conda package managers Installing packages on a Linux VM A) Using conda Open the bash terminal, and type:
  • Preinstalled Python 2 and Python 3 with Anaconda on Ivy Windows VM

    Anaconda Our VMs have python 2 and 3 available as part of the Anaconda distribution. Anaconda comes installed with many packages best suited for scientific computing, data processing, and data analysis, while making deployment very simple. Its package manager conda installs and updates python packages and dependencies, keeping different package versions isolated on a project-by-project basis. Anaconda is available as open source under the New BSD license. It also ships with pip, the common python package manager. Installing packages Packages could be installed via pip or conda package managers Installing packages on a Windows VM A) Using conda From the Start menu, open a new Command Prompt (or Anaconda prompt) window, and type:
  • 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 RC can help: Lower pricing - UVA has an Internet2 discount available for educational use. Contact us to create an account for you or your research project. Cost estimates - Cloud storage is not free. Consideration should be made to the size of your files and how often they will be retrieved.
  • Commercial Data Sharing and Archiving Solutions

    Box® Non-sensitive cloud storage UVA Box is a cloud-based storage and collaboration service that gives eligible members of the University community the ability to access, store, and share up to 1 TB of non-sensitive/moderately sensitive University files securely—anywhere, anytime, on any device. Read more DropBox®/Sookasa® Sensitive Data (PHI/PII) storage If you plan on storing sensitive data such as PHI or PII, UVA Health System offers a secure encrypted storage for Health System affiliated researchers, students, and staff. “DropBox Sookasa” is a free cloud-based service hosted on Dropbox that can be accessed over the internet on any device. Highly sensitive data such as a HIPAA compliant dataset or PHI/PII must be stored in a Sookasa folder.
  • Preinstalled Office 2016 on Ivy Windows VM

    Microsoft Office Overview The Ivy Windows VMs are installed with Microsoft Office 2016. Features such as OneDrive are not available since Ivy is not connected to the public internet. Therefore in order to load documents in and out of the VM, you would have to use the Globus DTN. Softwares available The following software are available for use on the Ivy Windows VM: Word 2016 Excel 2016 PowerPoint 2016 Access 2016 OneNote 2016 Outlook 2016 Publisher 2016 Running Office All Office software could be accessed from the Start menu using Start > All Programs More Information For more Information about Microsoft Office, please visit its official website.
  • Secure Computing

    UVA School of Medicine Research Computing can assist medical researchers in both understanding what HIPAA compliance requires of their work, and how to implement technical solutions to achieve and verify such compliance. Review & Assessment From a compliance perspective, RC offers three levels of review/assessment: Security Plan - Having a security plan in place is important to your success at UVA School of Medicine. If your lab or department doesn’t have a plan in place Research Computing Information Security will be happy to help you develop such a plan. Security Review - If you have a security plan in place already we can help you verify that your computing resources are functioning as documented in your security plan.
  • User Guides

    High Performance Computing Standard and high security HPC to run your code, generally written in R, Python or shell scripts. Get Started › Secure Computing Secure virtual machines and interactive notebooks for processing HIPAA and other sensitive data. Get Started ›
    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? Need an environment provisioned in short-order? We can help you build in the AWS cloud.

  • Perl

    Perl Our VMs have Perl 5.16.3 available as part of the base linux VM. Licensed as open source under the GPL, it is most often used to develop mission critical software, and has excellent integration with markup languages such as HTML, XML, amongst others. Since it is both Object Oriented as well as procedural, it could be used within a multitude of programming projects. It includes built in database integration via its DBI module. Other than DBI, it has thousands of modules, making it one of the most extensible languages. Due to its interpreted nature, Perl is similar to Python and would be easy to understand for those familiar with Python.