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.
R is a free software environment for statistical computing and graphics.
RStudio
1.0.136
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.
RStudio Server
1.2.1335
RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server.
LibreOffice is a free and open-source office suite, a project of The Document Foundation.
FastX Server
2.4.16
FastX enables users to start an X11 desktop environment on a remote system.
JupyterHub
1.1.0
JupyterHub is multi-user, multi-notebook server for Jupyter Notebooks.
JupyterLab
0.32.1
JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface.
Optional Software
In addition to the preinstalled software, researchers may request installation of the following approved software packages for their Virtual Machine.
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).
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.
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 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.
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.
KNIME is a free and open-source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining concept.
