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

SoftwareVersionsDescription
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.
R4.0.4R is a free software environment for statistical computing and graphics.
RStudio1.4.1106RStudio 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.
Strawberry Perl5.22.1.2Perl is Larry Wall's Practical Extraction and Report Language.
Visual Studio Code1.66.0Visual Studio Code, also commonly referred to as VS Code, is a source-code editor made by Microsoft for Windows, Linux and macOS.
Microsoft Office Professional Plus2016
SumatraPDF3.1.1Sumatra PDF is a free and open-source document viewer that supports many document formats.


Optional Software

In addition to the preinstalled software, researchers may request installation of the following approved software packages for their Virtual Machine.


Bioinformatics

SoftwareVersionsDescription
Bowtie2Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
HISAT22.3.0HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).


Data Analysis

SoftwareVersionsDescription
Rodeo1.3.0Rodeo is a Native Python IDE for Data Science.
MatlabMATLAB is a multi-paradigm numerical computing environment and proprietary programming language developed by MathWorks. Matlab usage by UVA affiliates is covered by a site license.
SASSAS is a statistical analysis package. A limited number of SAS licenses are available on a first-come-first-serve basis.
STATAStata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. Installation requires user-provided software license.
IDLIDL is an interpreted programming language used to create analyses and visualizations of numerical data. A limited number of IDL licenses are available on a first-come-first-serve basis.
Apache cTAKEScTAKES is an open-source Natural Language Processing system that extracts clinical information from electronic health record unstructured text.
SPSSThe SPSS® software platform offers advanced statistical analysis, a vast library of machine learning algorithms, text analysis, and open source extensibility. A limited number of SPSS licenses are available on a first-come-first-serve basis.


Database Software

SoftwareVersionsDescription
MariaDBMariaDB is a community-developed, commercially supported fork of the MySQL relational database management system.
MongoDBMongoDB is a cross-platform document-oriented database program. Classified as a NoSQL database program, MongoDB uses JSON-like documents with optional schemas.
PostgreSQLPostgreSQL is an advanced, enterprise-class, and open-source relational database system. PostgreSQL supports both SQL (relational) and JSON (non-relational) querying.
MySQL WorkbenchMySQL Workbench is a unified visual tool for database architects, developers, and DBAs. MySQL Workbench provides data modeling, SQL development, and comprehensive administration tools for server configuration, user administration, backup, and much more.
Microsoft SQL ServerMicrosoft SQL Server is a relational database management system developed by Microsoft. Installation requires user-provided software license.


Engineering

SoftwareVersionsDescription
COMSOLThe COMSOL Multiphysics® software provides specialized functionality for electromagnetics, structural mechanics, acoustics, fluid flow, heat transfer, and chemical engineering.
SolidWorks2019SolidWorks is a solid modeling computer-aided design and computer-aided engineering computer program.
MadymoMadymo is the worldwide standard software for analyzing and optimizing vehicle safety designs and consists of a unique combination of MB, FE, and CFD technologies.
LS-DYNALS-DYNA is a general purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries.


Image Processing

SoftwareVersionsDescription
ImageJImageJ is a scriptable image processing program, bundling a lot of plugins that facilitate scientific image analysis.
DaVinci Resolve17DaVinci Resolve is a software tool that combines editing, color correction, visual effects, motion graphics and audio post production. Installation requires user-provided software license.
MRtrix3MRtrix3 provides a large suite of tools for image processing, analysis and visualisation, with a focus on the analysis of white matter using diffusion-weighted MRI.