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 |
|---|
| Miniconda | 4.11.0 (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. |
| R | 4.0.4 | R is a free software environment for statistical computing and graphics. |
| RStudio | 1.4.1106 | 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. |
| Strawberry Perl | 5.22.1.2 | Perl is Larry Wall's Practical Extraction and Report Language. |
| Visual Studio Code | 1.66.0 | Visual 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 Plus | 2016 | |
| SumatraPDF | 3.1.1 | Sumatra 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.
| Software | Versions | Description |
|---|
| Bowtie2 | | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. |
| HISAT2 | 2.3.0 | HISAT2 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
| Software | Versions | Description |
|---|
| Rodeo | 1.3.0 | Rodeo is a Native Python IDE for Data Science. |
| Matlab | | MATLAB 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. |
| SAS | | SAS is a statistical analysis package. A limited number of SAS licenses are available on a first-come-first-serve basis. |
| STATA | | Stata 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. |
| IDL | | IDL 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 cTAKES | | cTAKES is an open-source Natural Language Processing system that extracts clinical information from electronic health record unstructured text. |
| SPSS | | The 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
| Software | Versions | Description |
|---|
| MariaDB | | MariaDB is a community-developed, commercially supported fork of the MySQL relational database management system. |
| MongoDB | | MongoDB is a cross-platform document-oriented database program. Classified as a NoSQL database program, MongoDB uses JSON-like documents with optional schemas. |
| PostgreSQL | | PostgreSQL is an advanced, enterprise-class, and open-source relational database system. PostgreSQL supports both SQL (relational) and JSON (non-relational) querying. |
| MySQL Workbench | | MySQL 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 Server | | Microsoft SQL Server is a relational database management system developed by Microsoft. Installation requires user-provided software license. |
Engineering
| Software | Versions | Description |
|---|
| COMSOL | | The COMSOL Multiphysics® software provides specialized functionality for electromagnetics, structural mechanics, acoustics, fluid flow, heat transfer, and chemical engineering. |
| SolidWorks | 2019 | SolidWorks is a solid modeling computer-aided design and computer-aided engineering computer program. |
| Madymo | | Madymo 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-DYNA | | LS-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
| Software | Versions | Description |
|---|
| ImageJ | | ImageJ is a scriptable image processing program, bundling a lot of plugins that facilitate scientific image analysis. |
| DaVinci Resolve | 17 | DaVinci Resolve is a software tool that combines editing, color correction, visual effects, motion graphics and audio post production. Installation requires user-provided software license. |
| MRtrix3 | | MRtrix3 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. |
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