/tag/ivy

  • UVA High Security Zone 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 lang R is a free software environment for statistical computing and graphics. anaconda lang This module points to Miniforge. - The conda/mamba executables are included. - The default channel is conda-forge. For details see https://www.rc.virginia.edu/2024/10/transition-from-anaconda-to-miniforge-october-15-2024/ ant devel Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other.
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  • 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 and 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
    Read more →
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  • Ivy Secure Environment

     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, FERPA, CUI or ITAR requirements.
    Facilities Statement - Are you submitting a grant proposal and need standard information about UVA research computing environments? Get it here. Overview Ivy consists of both virtual computing environments and secure storage. In order to obtain access to either system, users must
    Submit an account request, Complete the Information Security Awareness Training, and Ensure their personal computer meets all High Security VPN requirements.
    Read more →
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  • Workshops

     UVA 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 experts and are freely available to UVa faculty, staff and students.
    New to High-Performance Computing? We offer orientation sessions to introduce you to the Afton & Rivanna HPC systems on Wednesdays (appointment required).
    – Wednesdays 3:00-4:00pm Sign up for an “Intro to HPC” session Upcoming Workshops DATE WORKSHOP INSTRUCTOR There are currently no training events scheduled. Please check back soon! Research Computing is partnering with the Research Library and the Health Sciences Library to deliver workshops covering a variety of research computing topics.
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  • 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 & personal workstations Rivanna/Afton HPC clusters High-Security Research Standard Storage Lab / departmental storage Tape archives Cloud storage Off-campus resources (ACCESS, 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/Afton or your personal computer.
    Are your data stored at a different institution? At a supercomputing facility? All you need is your institution’s login credentials.
    Read more →
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  • 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 and 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
    Read more →
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  • 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.
    Facilities Statement - Are you submitting a grant proposal and need standard information about UVA research computing environments? Get it here. High Performance Computing - Rivanna and Afton A traditional high performance cluster with a resource manager, a large file system, modules, and MPI processing. Get Started with UVA HPC Secure Computing for Highly 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.
    Read more →
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  • Pricing

     Below is a schedule of prices for Research Computing resources.
    High Performance Computing Allocations Type SU Limits Cost SU Expiration Standard None Free 12 months Purchased None $0.01 Never Instructional 100,000 Free 2 weeks after last training session A service unit (SU) resembles usage of a trackable hardware resource for a specified amount of time. In its simplest form 1 SU = 1 core hour, but the SU charge rate can vary based on the specific hardware used. Resources like GPUs and memory may incur additional SU charges.
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  • High Performance Computing

     Research Computing supports all UVA researchers who are interested in writing code to address their scientific inquiries. Whether these programming tasks are implemented interactively, in a series of scripts or as an open-source software package, services are available to provide guidance and enable collaborative development. RC has specific expertise in object-oriented programming in Matlab, R, and Python.
    Examples of service areas include:
    Collaborating on package development Reviewing and debugging code Preparing scripts to automate or expedite tasks Developing web interfaces for interactive data exploration Advising on integration of existing software tools UVA has three local computational facilities available to researchers: Rivanna, Afton, and Ivy.
    Read more →
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  • How To Guides for Ivy Users

     Transfer Files to or from Ivy Using Globus
    Read more →
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  • Frequently Asked Questions

     General Do you have a general computing question?
    Read our FAQ› Rivanna and Afton High Performance Computing Platforms
    Read our FAQ › Ivy Secure Data Computing Platform
    Read our FAQ › Storage Research Data Storage & Transfer
    Read our FAQ ›
    Read more →
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  • How To

     General General tips and tricks for computational research.
    General HowTos › Rivanna and Afton High Performance Computing platforms
    HPC HowTos › Ivy Secure Data Computing Platform
    Ivy HowTos › Storage Research Data Storage & Transfer
    Storage HowTos ›
    Read more →
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  • Research Data Storage

     $(document).ready(function() { $("#status-message").hide(); updateStatusMessages(); setInterval(checkStatusMessages, 6000); }); function updateStatusMessages() { $.getJSON(‘https://tja4lfp3da.execute-api.us-east-1.amazonaws.com/api/messages' , function(data) { var messageData = ‘'; $.each(data, function(key, value) { var converter = Markdown.getSanitizingConverter(); var timestamp = value.body.substr(0,19); var messageBody = value.body.substring(timestamp.length+1).replace("<br>", "
    “); var messageLength = messageBody.length; if ( messageLength = millisPerDay) { var datestr = now.toDateString(); } else { var datestr = post_date.toDateString(); } msg = “[” + datestr + “] “+ msg; } } $('#status-message-'+keywords[j]).html(converter.makeHtml(msg)); } }); }); }; There are a variety of options for storing research data at UVA. Public and internal use data storage systems can be accessed from the Rivanna and Afton high performance computing systems.
    Read more →
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  • Software on Ivy Linux Virtual Machines

     Each Linux Virtual Machine (VM) comes with a set of preinstalled software applications. Each VM can further be customized via installation of optional software packages.
    An overview of available software packages for Windows VMs is provided here.
    Preinstalled Software Software Versions Description Anaconda2023.07-py3.11 The open-source Anaconda Distribution is the easiest way to perform Python/R data science and machine learning on Linux, Windows, and Mac OS X. R4.3.1 R is a free software environment for statistical computing and graphics. RStudio Server2023.06.2 RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server.
    Read more →
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  • Software on Ivy Windows Virtual Machines

     Each Windows Virtual Machine (VM) comes with a set of preinstalled software applications. Each VM can further be customized via installation of optional software packages.
    An overview of available software packages for Linux VMs is provided here.
    Preinstalled Software Software Versions Description Miniconda4.11.0 (Python 3.9.7) The open-source Anaconda Distribution is the easiest way to perform Python/R data science and machine learning on Linux, Windows, and Mac OS X. R4.3.1 R is a free software environment for statistical computing and graphics. RStudio1.4.1106 RStudio is an integrated development environment for R, with a console, syntax-highlighting editor that supports direct code execution, and tools for plotting, history, debugging and workspace management.
    Read more →
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  • Data Transfer

     Data transfer Public & Moderately Sensitive Data Transfer Secure Copy (scp) scp uses secure shell (SSH) protocol to transfer files between your local machine and a remote host. scp can be used with the following syntax:
    scp [source] [destination]
    scp SourceFile mst3k@login.hpc.virginia.edu:/scratch/mst3k
    scp SourceFile mst3k@login.hpc.virginia.edu:/project/Grouper_group_name
    Detailed instructions and examples for using scp are listed here.
    Secure File Transfer Protocol (sftp) sftp is a network protocol for secure file management. Instructions and examples for using sftp are located here.
    Graphical File-Transfer Applications Filezilla and Cyberduck, and MobaXterm are examples of open source SFTP client software for file management through an interactive graphical user interface.
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  • Secure Computing for Surgical Research

     RC is working with Dr. Eric Schneider to create a secure computing environment for the research of the Healthcare Surgical Outcome team. Data from this project will contain HIPAA identifiers, as well as Medicare information, and requires more security and control of data ingress/egress than projects previously hosted on the Ivy platform. After successful implementation of this project, RC will create a similar computing environment for DoD blast and traumatic brain injury data collected by Dr. Schneider before he joined UVA.
    PI: Eric Schneider (Department of Surgery)
    Read more →
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  • Highly Sensitive Data Storage - Ivy

     Overview Residing within the High Security Zone (HSZ), the Ivy secure computing environment is designed to fit your highly sensitive research computing needs and meets HIPAA, FERPA, CUI and ITAR compliance standards. Within the HSZ, researchers can store their highly sensitive research data in High-Security Research Standard Storage.
    Ivy Central Storage Ivy Central Storage (ICS) was an HSD parking zone and central storage pool with a capacity greater than 1PB. This storage space was available for researchers with highly sensitive data and could be mounted on an Ivy Virtual Machine.
    As of 10/15/24, ICS will be upgraded to High-Security Research Standard Storage.
    Read more →
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  • 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] (/userinfo/ivy/ivy-linux-sw/bioinformatics/bowtie2)
    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
    Read more →
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  • 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] (/userinfo/ivy/ivy-windows-sw/bioinformatics/bowtie2) –>
    HISAT2 Requires approval before installation. For more information on HISAT2, please click here
    Read more →
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  • 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] (/userinfo/ivy/ivy-linux-sw/data-analysis/matlab)
      SAS SAS is large platform independent software with multiple components, and is used for statistical analysis, data ETL operations, as well as several other
    Read more →
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  • 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] (/userinfo/ivy/ivy-windows-sw/data-analysis/matlab)
      SAS SAS is large platform independent software with multiple components, and is used for statistical analysis, data ETL operations, as well as several other
    Read more →
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  • 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.
    Read more →
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  • 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.
    Read more →
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  • 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:
    Read more →
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  • 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:
    Read more →
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  • User Licensed Stata on Ivy Linux VMs

     Stata Overview Stata is a graphical data analysis tool developed by StataCorp, and is short for Statistics 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.
    Users requesting an installation of Stata are required to provide their own license. Please consult with us before
    requesting an installation.
    You may also request a Stata license from the UVa Software Gateway
    Installing programs from SSC Please first run the following commands to use the proxy:
    Read more →
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  • User Licensed Stata on Ivy Windows VMs

     Stata Overview Stata is a graphical data analysis tool developed by StataCorp, and is short for Statistics 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.
    Users requesting an installation of Stata are required to provide their own license. Please consult with us before
    requesting an installation.
    You may also request a Stata license from the UVa Software Gateway
    Installing programs from SSC Please first run the following commands to use the proxy:
    Read more →
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  • 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
    Read more →
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  • 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.
    Read more →
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  • 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
    Read more →
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  • 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
    Read more →
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  • 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 activities.
    Read more →
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  • 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 activities.
    Read more →
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  • 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.
    OpenCV includes modules for image processing, video analysis, machine learning, and much more.
    Read more →
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  • 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.
    Read more →
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  • 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 .
    Read more →
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  • 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.
    Read more →
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  • 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.
    Read more →
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  • 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.
    Read more →
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  • 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. Please refer to this page for more information.
    Read more →
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  • 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)
    Read more →
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  • 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.
    Read more →
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  • 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:
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  • What is Research Computing?

     UVA Research Computing (RC) 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).
    One of our driving philosophies is that researchers already have medical and scientific expertise, and should not have to become computing experts on top of that.
    Read more →
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  • 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.
    Available Software The following software packages 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.
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  • 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 highly 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.
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  • Computing Environments at UVA

     Research Computing (UVA-RC) serves as the principal center for computational resources and associated expertise at the University of Virginia (UVA). Each year UVA-RC provides services to over 433 active PIs that sponsor more than 2463 unique users from 14 different schools/organizations at the University, maintaining a breadth of systems to support the computational and data intensive research of UVA’s researchers.
    High Performance Computing  UVA-RC’s High Performance Computing (HPC) systems are designed with high-speed networks, high performance storage, GPUs, and large amounts of memory in order to support modern compute and memory intensive programs. UVA-RC operates two HPC systems, Rivanna and Afton.
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