What does BioFabric do? It displays a network where nodes are depicted as horizontal lines, not as points! Take a look at the Super-Quick Demo to see how it works in under 60 seconds:
BioFabric uses a novel network presentation method that represents nodes as horizontal line segments, one per row. For example,
this is the
Try BioFabric Online
BioFabric can be downloaded as a standalone executable and run on your Windows or Mac computer; see below.
However, if you just want to have a look, it can be run from the following link using Java WebStart. Once it is running, you can import
Click HERE to run BioFabric (version 1.0.0, released 07/27/12, REQUIRES Java 5 or above; Java 6 highly recommended for Macs) using Java Web Start.
If you are working with very large networks, you will need the huge memory version (4 GB allocated for the Java heap) along with the hardware to make this feasable. Click HERE to run this version (version 1.0.0, released 07/27/12, REQUIRES Java 5 or above; Java 6 highly recommended for Macs).
BioFabric is written in Java, and can be run on your Windows, Mac, or Linux computer. Note that all these downloadable executables require that you first download and install the Java Runtime Environment (JRE), which can be downloaded from here (click the "Free Java Download" button). On MacOS X, Java should already be factory-installed on all new Macs, but Java 6 is highly recommended for Macs so that large-scale views do not render so lightly as to be almost invisible. Note that all of the following versions are configured for 2 GB Java heap space.
Choose from the following download options:
We are continuing to add to the gallery of BioFabric networks. Go and check them out!
Version 1.0.0 of BioFabric has just been released, and the user documentation is... lagging (sorry!). Since the program is just a viewer and
not an editor, all you really need to do to get started is to import a tab-delimited
BioFabric-users Google GroupThis group is intended to answer questions, and to provide a forum for feedback and discussions about BioFabric. The group home page is:
BioFabric BlogThe blog Combing the Hairball is active, with new posts about various BioFabric topics:
BioFabric for Gaggle
The Gaggle is a framework, developed at the Institute for Systems Biology, "...for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data." BioFabric supports Gaggle, and the link below will launch the program with the Gaggle feature enabled. Launch the Gaggle Boss and other Gaggle-aware applications using the links on the Gaggle Blank Slate page.
Click HERE to run the Gaggle-enabled BioFabric (version 1.0.0, released 07/27/12, REQUIRES Java 5 or above; Java 6 highly recommended for Macs) using Java Web Start.
A variety of
The network described in Case Study III of the BioFabric paper is available here (32 MB).
WARNING! This is a compressed zip file of a network with a huge number (over 1,000,000) of links, and is a poor example for
learning how to use BioFabric. It requires the Java WebStart "huge memory version" of BioFabric to run (link provided above), and a computer
with enough physical memory to handle it. It is only included here because the BMC Bioinformatics supplementary materials site does not support files
this large. Instead, use the
Please cite BioFabric using [Longabaugh 2012] if you use it in your research:
A tar file of the current version of the source code is available here, but it lacks the toolbar image files that are needed to get the program running. The entire project is now also hosted on GitHub.
Send FeedbackIf you have any feedback you wish to send along, such as questions, bug reports, feature requests, and usability issues, you can send email to:
Web browser launch code adapted from Bare Bones Browser Launch by Dem Pilafian (http://www.centerkey.com/java/browser/).
Windows executable created using the Launch4j Executable Wrapper by Grzegorz Kowal (http://sourceforge.net/projects/launch4j/).
BioFabric was made possible through the development of BioTapestry, supported by National Institute of General Medical Sciences Award Number GM061005. BioFabric development was also supported in part by Award Number U24CA143835 from the National Cancer Institute. This content is solely the responsibility of the author and does not necessarily represent the official views of the National Institute of General Medical Sciences, National Cancer Institute, or the National Institutes of Health.
License and Disclaimer
This software is licensed under the GNU Lesser General Public License (LGPL), which is a standard "free software" and "open source" license. A copy of the license agreement is available online here. Note that some of the toolbar icons are distributed under this license.
The downloadable Windows executable is wrapped in code that is made available by Grzegorz Kowal under this MIT License.
BioFabric is under continual development, and despite our best efforts there are bugs in the software. Please be advised that, as stated in the license agreement, the Institute for Systems Biology and the authors disclaim any liability stemming from the use of this software.
Last updated: October 28, 2013
wlongabaugh -a~t- systemsbiology -d~o~t- org