• 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,

  • 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.

  • 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.

  • 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

  • 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 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

  • 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 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 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.
    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:

  • 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 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

  • 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 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.

  • 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 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.

  • 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 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 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:

  • 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 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.