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
Anaconda(Python 3) 5.2.0 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.
R3.6.0 R is a free software environment for statistical computing and graphics.
RStudio1.0.136 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 Server1.2.1335 RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server.
Perl5.16.3 Perl is Larry Wall's Practical Extraction and Report Language.
OpenJDK 81.8.0 Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
Atom Text Editor1.14.3 Atom is a free and open-source text and source code editor.
Rodeo2.5.2 Rodeo is a Native Python IDE for Data Science.
Emacs24.3.1 A text editor characterized by its extensibility.
LibreOffice5.3.6.1 LibreOffice is a free and open-source office suite, a project of The Document Foundation.
FastX Server2.4.16 FastX enables users to start an X11 desktop environment on a remote system.
JupyterHub1.1.0 JupyterHub is multi-user, multi-notebook server for Jupyter Notebooks.
JupyterLab0.32.1 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.


Bioinformatics

Software Versions Description
Bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
HISAT22.3.0 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
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.


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.


Image Processing

Software Versions Description
Knime 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.
ImageJ ImageJ is a scriptable image processing program, bundling a lot of plugins that facilitate scientific image analysis.
OpenCV OpenCV is an open-source BSD-licensed library that includes several hundreds of computer vision algorithms.