Additional file 1:

Multi-platform distribution of BiGGEsTS. A multi-platform distribution of BiGGEsTS. The archive biggests.zip contains a directory with several files, including installation files, the application, sample datasets and sessions, the Quickstart Guide to the software ("BiGGEsTS Quickstart.pdf") and a simple text file with installation instructions ("readme.txt"). In Windows (or Mac OS X) run the "install.bat" (or "install.sh" in Mac OS X) file, for installing the Graphviz dot application and the GO files, and then the "biggests.bat" ("biggests.sh") file, for running the software. For Linux and other operating systems, please install the Graphviz dot application first and edit the "install.sh" file to append the path of the dot executable file (typically /usr/bin/dot) to the last line. Then run the "install.sh" script followed by "biggests.sh". Detailed instructions on how to install and use BiGGEsTS are also available in the Quickstart Guide [see Additional file 2]. The latest version of the software is available at the official website.

Format: ZIP Size: 19.3MB Download file

Additional file 2:

BiGGEsTS Quickstart Guide. This document introduces users to BiGGEsTS, providing instructions on how to install and use this software, to analyze time series gene expression data using biclustering.

Format: PDF Size: 2.7MB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 3:

Source code of the BiGGEsTS software. The source code of BiGGEsTS. The archive contains two directories, named "biggests" and "smadeira", inside a main directory, named "src". Each of the directories contained in "biggests" and "smadeira" contains the source files of the classes included in the packages identified by the same names. The Javadoc documentation of the source code is available at the official website.

Format: ZIP Size: 689KB Download file

Additional file 4:

Sample expression dataset (from Gasch et al. [28]). This file contains a sample time series gene expression matrix corresponding to a short subset of a real dataset from Gasch et al. [28], concerning the yeast response to heat shock. The original dataset analyzes 6142 genes from Saccharomyces cerevisiae in 8 time points (5', 10', 15', 20', 30', 40', 60', 80'). The gasch_ yeast_hs1_short.txt file is also included in the multi-platform distribution. To load this dataset into BiGGEsTS, run the software and use the "Browse..." button on the panel on the right to browse the file in the file system. Once it is found, press the "Open" button followed by the "Load" button (a detailed description of the parameters is available in the Quickstart Guide [see Additional file 2]).

Format: TXT Size: 2KB Download file

Additional file 5:

Archive of a sample BiGGEsTS session. This file contains a BiGGEsTS session with matrices and biclusters obtained by manipulating the time series gene expression data also provided as additional material [see Additional file 4], using BiGGEsTS. The session was exported into this file also using BiGGEsTS. To load the session into BiGGEsTS and explore its contents, run the software, select the "Session" menu, and then the "Load session" menu item from the menu bar (on the top of the window). You will be prompted to provide the path to the session file, this file (gasch_yeast_hs1_short.zip). Click the "Open" button. Once the data is loaded into BiGGEsTS, you can see that the dataset tree (on the panel on the left) has grown and that it has new items. Read the Quickstart Guide [see Additional file 2], for details on how to use BiGGEsTS.

Format: ZIP Size: 24KB Download file

Additional file 6:

Case study: discovering transcriptional modules using BiGGEsTS. Case study describing how to use BiGGEsTS to discover transcriptional regulatory modules using the transcriptional response of Saccharomyces cerevisiae to heat stress. The results published in [6] are reproduced.

Format: PDF Size: 2.4MB Download file

This file can be viewed with: Adobe Acrobat Reader