BioVM is a virtual machine based on Ubuntu Linux with pre-installed and pre-configured software for Bioinformatics.

Features

Pre-installed Bioinformatics software

Current released versions of Bedtools, Bowtie, BWA, Clustal Omega, Cutadapt, EMBOSS (including Jemboss and Emboss Explorer GUI's), FastQC, FASTX-Toolkit, Mummer, Muscle, NCBI BLAST+, Primer 3, Samtools, TreeviewX, Trimmomatic, UGENE.

The Galaxy web platform

Galaxy is an open web-based platform for computational biomedical research. BioVM includes a pre-configured and ready to use instance of Galaxy with PostgreSQL as the database system and Apache as the proxy server.

Run Docker containers of Bioinformatics software

BioVM has the current stable version of Docker installed. The biovm user is setup for running Docker containers.

Python, PERL, R and system tools

Python
Create virtual Python environments with Virtualenv / Virtualenvwrapper. Install packages from PyPI. Write and debug Python programs using the PyCharm IDE (Community edition). Work with BioPython, Numpy, Scipy, Matplotlib, IPython and Jupyter Notebooks.
PERL
Use BioPerl, Install additional packages from CPAN without the need for root privileges.
R
Write and debug R scripts using the open source edition of RStudio. Install Bioconductor and CRAN packages without the need for root privileges.
System tools
Basic tools and libraries for compiling software (gcc, make), the Git version control system (including GUI).

Minimal installation of Ubuntu Linux

Ubuntu Linux (16.04 LTS, MATE edition) installed with a minimal selection of packages and customisations for a better user experience in a virtual environment.

Getting started with BioVM

Get started with BioVM in 3 steps!

Step 1 - Verify requirements

  • VirtualBox installed on your computer.
  • RAM - 4 GB or more is recommended.

Step 2 - Download appliance


Download the virtual machine

Format:
Open Virtual Appliance (OVA)
File size:
2.7 GB
Checksum (SHA-256):
de3de57a948be87275f472781742fe34a69dddd25775e5659cfc8c527c18c200
Download tip
BioVM does not receive any funding at the moment. If this
project will save you time and effort, please consider
making a donation.
or donate a custom amount.

Step 3 - Launch BioVM

Click on the downloaded .ova file. If that does not launch VirtualBox, open VirtualBox and then use the File -> Import Appliance option and select the downloaded file.

If you would like to change the number of CPU's or the amount of RAM for the appliance, you can do so at this stage.

Once the import is complete, select BioVM in the VirtualBox main window and the click on the Start button to launch BioVM.

The virtual machine will boot directly to the desktop as shown in the screenshot below.

The BioVM desktop

The BioVM desktop (more screenshots)

Questions?

For queries relating to the included software, please consult the documentation or website related to the software itself.

BioVM's documentation: https://biovm.readthedocs.io.

A copy of the documentation can also be accessed from within the VM (Menu -> Bioinformatics -> BioVM Help).

If your query is not answered in the documentation, please post it in the Support forums.

Screenshots

EMBOSS explorer web interface and Jemboss graphical user interface

EMBOSS explorer web interface and the Jemboss graphical user interface.

Start page of the Galaxy instance

Home page of the local Galaxy instance at http://localhost/galaxy (note: needs to be enabled)

Main window of the UGene program

Main window of the UGENE program

IPython Notebook demo

IPython Notebook

Source code

BioVM is an Open Source project released under the GPLv3 license. Source code is available on GitHub.