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
<tr>
<td><a href="/userinfo/ivy/ivy-linux-sw/anaconda" style="color: #0275d8";>Anaconda</a></td>
<td>(Python 3) 5.2.0</td>
<td>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.</td>
</tr>
<tr>
<td><a href="/userinfo/ivy/ivy-linux-sw/r" style="color: #0275d8";>R</a></td>
<td>3.6.0</td>
<td>R is a free software environment for statistical computing and graphics.</td>
</tr>
<tr>
<td>RStudio</td>
<td>1.0.136</td>
<td>Webster's defines RStudio as...</td>
</tr>
<tr>
<td>RStudio Server</td>
<td>1.2.1335</td>
<td>Webster's defines RStudio Server as...</td>
</tr>
<tr>
<td><a href="/userinfo/ivy/ivy-linux-sw/perl" style="color: #0275d8";>Perl</a></td>
<td>5.16.3</td>
<td>Perl is Larry Wall's Practical Extraction and Report Language.</td>
</tr>
<tr>
<td>OpenJDK 8</td>
<td>1.8.0</td>
<td>Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.</td>
</tr>
<tr>
<td>Atom Text Editor</td>
<td>1.14.3</td>
<td>Atom is a free and open-source text and source code editor.</td>
</tr>
<tr>
<td><a href="/userinfo/ivy/ivy-linux-sw/rodeo" style="color: #0275d8";>Rodeo</a></td>
<td>2.5.2</td>
<td>Rodeo is a Native Python IDE for Data Science.</td>
</tr>
<tr>
<td>Emacs</td>
<td>24.3.1</td>
<td>A text editor characterized by its extensibility.</td>
</tr>
<tr>
<td>LibreOffice</td>
<td>5.3.6.1</td>
<td>LibreOffice is a free and open-source office suite, a project of The Document Foundation.</td>
</tr>
<tr>
<td>FastX Server</td>
<td>2.4.16</td>
<td>FastX enables users to start an X11 desktop environment on a remote system.</td>
</tr>
<tr>
<td>JupyterHub</td>
<td>1.1.0</td>
<td>JupyterHub is multi-user, multi-notebook server for Jupyter Notebooks.</td>
</tr>
<tr>
<td>JupyterLab</td>
<td>0.32.1</td>
<td>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.</td>
</tr>
</tbody>
</table>
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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
<tr>
<td>Bowtie2</td>
<td></td>
<td>Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.</td>
</tr>
<tr>
<td>HISAT2</td>
<td>2.3.0</td>
<td>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).</td>
</tr>
</tbody>
</table>
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Data Analysis
Software
Versions
Description
<tr>
<td>Matlab</td>
<td></td>
<td>MATLAB is a multi-paradigm numerical computing environment and proprietary programming language developed by MathWorks.</td>
</tr>
<tr>
<td>SAS</td>
<td></td>
<td>SAS is a statistical analysis package.</td>
</tr>
<tr>
<td>STATA</td>
<td></td>
<td>Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.</td>
</tr>
<tr>
<td>IDL</td>
<td></td>
<td>IDL is an interpreted programming language used to create analyses and visualizations of numerical data.</td>
</tr>
<tr>
<td>Apache cTAKES</td>
<td></td>
<td>cTAKES is an open-source Natural Language Processing system that extracts clinical information from electronic health record unstructured text.</td>
</tr>
</tbody>
</table>
- - -
Image Processing
Software
Versions
Description
<tr>
<td>Knime</td>
<td></td>
<td>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.</td>
</tr>
<tr>
<td>ImageJ</td>
<td></td>
<td>ImageJ is a scriptable image processing program, bundling a lot of plugins that facilitate scientific image analysis.</td>
</tr>
<tr>
<td>OpenCV</td>
<td></td>
<td>OpenCV is an open-source BSD-licensed library that includes several hundreds of computer vision algorithms.</td>
</tr>
</tbody>
</table>
