Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Software

Combing the hairball with BioFabric: a new approach for visualization of large networks

William JR Longabaugh

Author Affiliations

Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109-5234, USA

BMC Bioinformatics 2012, 13:275  doi:10.1186/1471-2105-13-275

Published: 27 October 2012

Additional files

Additional file 1:

File Format: ZIP archive containing a BioFabric.bif (XML format) file. Title of Data: Human Interactome Network for Case Study I. Description of Data: This is the BioFabric file of the network built from the Human_Interactome_May.sif file and associated node annotations file obtained from [15] and shown in Case Study I. Unzip the file and extract the HumanInteractomeMayAnnotShadConn.bif file (19 MB), which can be loaded into BioFabric.

Format: ZIP Size: 2.2MB Download file

Open Data

Additional file 2:

File Format: ZIP archive containing a BioFabric .bif (XML format) file. Title of Data: Reduced Network for Case Study III. Description of Data: This is a reduced version of the BioFabric file containing the TCGA CSACR network of paired gene expression associations for four different GBM subtypes (plus a fifth unified analysis) used in Case Study III. The full file could not be included due to space limitations, so this only contains correlations with an absolute value ≥ 0.6 (instead of 0.5 used in the example). However, as the illustrated CD44-MSN associations have a correlation coefficient of 0.5, they are not present in this file. Unzip the file and extract the GEXP_GBM_comb_6_5DIV_SHA_ConnLO.bif file (82 MB), which can then be loaded into BioFabric. The full file can be downloaded from the BioFabric project web site.

Format: ZIP Size: 8.2MB Download file

Open Data

Additional file 3:

File Format: ZIP archive containing three BioFabric.bif (XML format) files. Title of Data: Random Networks for Case Study IV. Description of Data: These are the three random networks shown in Case Study IV. Unzip the file and extract the three files (er1060.bif, er1010.bif, ba2K.bif), each can then be loaded into BioFabric.

Format: ZIP Size: 3.3MB Download file

Open Data

Additional file 4:

File Format: ZIP archive containing the version 1.0.0 BioFabric.exe executable for Windows computers. Title of Data: BioFabric Windows Executable. Description of Data: This contains the BioFabric application bundled for Windows, configured with a maximum Java heap space of 1 GB. As this is version 1.0.0, it is preferable to download the latest version of BioFabric from the project web site.

Format: ZIP Size: 640KB Download file

Open Data

Additional file 5:

File Format: Mac Disk Image. Title of Data: BioFabric Mac OS X Executable. Description of Data: This disk image contains the BioFabric application bundled for Mac OS X, configured with a maximum Java heap space of 1 GB. As this is version 1.0.0, it is preferable to download the latest version of BioFabric from the project web site.

Format: DMG Size: 10.3MB Download file

Open Data

Additional file 6:

File Format: Gzipped tar file containing packages of Java source code, image, and property files. Title of Data: Version 1.0.0 BioFabric Source Code. Description of Data: This file contains the source code needed to build BioFabric. If Gaggle support is not needed, it can be compiled with Java 1.4.

Format: GZ Size: 230KB Download file

Open Data