AlignmentPlugin

VISNAB: Visualization of Network Alignments using BioFabric

Image: Mus Musculus (4370 nodes, 9116 edges) aligned to Arabidopsis Thaliana (5897 nodes, 13381 edges)

Overview

VISNAB is a BioFabric plugin that allows you to visualize network alignments.

Preparations

VISNAB is written as a BioFabric plugin, and requires that your first install BioFabric Version 2 Beta Release 2 (or higher). Note that the current production Version 1.0 of BioFabric is not designed to support plugins; at least Version 2 Beta Release 2 is required. BioFabric is written in Java, and can be run on your Windows, Mac, or Linux computer. Starting with Version 2 Beta Release 2, the Java runtime (OpenJDK 12) is bundled with BioFabric on all platforms, so a separate Java download is no longer required.

BioFabric Version 2 Beta Release 2 is currently available either as a zip file for Windows (named BioFabric20B2.zip), as a mountable disk image for Mac (named BioFabricInstallImageV2BetaRel2.dmg), or as a tgz file for Linux (named BioFabric-2.0.B.2.tgz). These are all available from the BioFabric GitHub repository release page.

• Windows: Unzip the BioFabric20B2.zip file as a folder on your desktop. Go into the folder. If you want to install BioFabric in the Windows Program Files folder, you will need to run the BioFabricInstaller as an Admin user. To do that, right-click on the BioFabricInstaller program and choose Run as administrator. If you are not an Admin, you will need to install it somewhere within your home directory by changing the install location as part of the installation. Once the installation is complete, you can right-click on the BioFabric program and select Create shortcut, then e.g. drag it to your desktop.

• Mac: Double-click the downloaded BioFabricInstallImageV2BetaRel2.dmg disk image file to mount it, and then open a Finder window for the mounted disk. From the Finder window, drag the BioFabric icon inside onto your desktop (or, if you prefer, into your Applications folder). If Mac Gatekeeper has been set to restrict to only App Store, you will need to launch System Preferences, click on Security & Privacy, and on the General tab set Allow apps downloaded from: App Store and identified developers. If you take this step, you probably want to reset it back to App Store after starting BioFabric the first time.

• Linux: Untar the BioFabric-2.0.B.2.tgz file (tar xvzf BioFabric-2.0.B.2.tgz). The shell script to run the program is BioFabric/BioFabricV2BetaRel2.sh.

Installing the Plugin

The VISNAB plugin is a Java JAR file. This compiled JAR file is available on the VISNAB GitHub repository release page. To install it, download the sVISNAB-V1.1.0.0.jar file, then simply drop that file into a directory on your computer. (Note that there should be only one copy of the VISNAB JAR file in that directory.) Start BioFabric, and use File->Set Plugin Directory... to point to the directory where you have placed sVISNAB-V1.1.0.0.jar. Restart BioFabric, and the VISNAB commands will appear in the Tools->Network Alignment menu.