BioVM is a virtual machine based on Ubuntu Linux with pre-installed and pre-configured software for Bioinformatics.
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
- 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.
- Use BioPerl, Install additional packages from CPAN without the need for root privileges.
- 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).
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
- Open Virtual Appliance (OVA)
- File size:
- 2.7 GB
- Checksum (SHA-256):
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.
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.