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 | 2023.07-py3.11 | 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 | 4.3.1 | R is a free software environment for statistical computing and graphics. |
| RStudio Server | 2023.06.2 | RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server. |
| Perl | 5.26.3 | Perl is Larry Wall's Practical Extraction and Report Language. |
| OpenJDK | 12 | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. |
| Atom Text Editor | 1.14.3 | Atom is a free and open-source text and source code editor. |
| Rodeo | 2.5.2 | Rodeo is a Native Python IDE for Data Science. |
| Emacs | 24.3.1 | A text editor characterized by its extensibility. |
| LibreOffice | 5.3.6.1 | 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 | 3.1.1 | JupyterHub is multi-user, multi-notebook server for Jupyter Notebooks. |
| JupyterLab | 3.6.3 | 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. |
| Matlab | 2023b | 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. |
| Apache cTAKES | 4.0.0.1 | cTAKES is an open-source Natural Language Processing system that extracts clinical information from electronic health record unstructured text. |
| Knime | 3.7.2 | 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. |
| Fiji | 1.53t | Fiji is a scriptable image processing program, bundling a lot of plugins that facilitate scientific image analysis. |
| PostgreSQL | 14.5 | PostgreSQL is an advanced, enterprise-class, and open-source relational database system. PostgreSQL supports both SQL (relational) and JSON (non-relational) querying. |
| MRtrix3 | 3.0.2 | 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. |
| PeakSeq | 1.31 | PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments. |
| PLINK | 2.00a20230303 | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |
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. | |
| HISAT2 | 2.2.1 | 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). |
| Bedtools | Bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. |
Data Analysis
| Software | Versions | Description |
|---|---|---|
| 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. |
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. | |
| 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. |
Engineering
| Software | Versions | Description |
|---|---|---|
| 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 |
|---|---|---|
| OpenCV | OpenCV is an open-source BSD-licensed library that includes several hundreds of computer vision algorithms. | |
| AFNI | AFNI (Analysis of Functional NeuroImages) is a software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of multiple MRI modalities. | |
| QIT (Cabeen) | QIT is a software package of computational tools for the modeling, analysis, and visualization of scientific imaging data. | |
| FSL | FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |