Installation and configuration instructions for the TimeClust software (see Magni et al. Bioinformatics 2007). The TimeClust software can be downloaded freely for non-profit institutions from http://aimed11.unipv.it/TimeClust. Executable files for Windows and LINUX platforms are available. The program requires the user to install the MATLAB runtime libraries, that are distributed together with the TimeClust files. The installation steps are here detailed. TimeClust distribution. ----------------------- The following files can be downloaded from the TimeClust web site: - README (this file) that contains installation and configuration instructions. - TimeClust1.3-WIN.zip that contains all files necessary for Windows platforms. - TimeClust1.3-LINUXx86.zip that contains all files necessary for LINUX 32bits platforms. - TimeClust1.3-LINUXx86_64.zip that contains all files necessary for Linux 64bits platforms. - Example.pdf that contains a simple user's guide. - expressiondata.txt, genenames.txt, clonenames.txt and cellcyclephases.txt that contain a toy gene expression data set (20 genes) to evaluate TimeClust. - expressiondata2.txt, clonenames2.txt and cellcyclephases2.txt that contain a typical gene expression data set (about 800 genes) to evaluate TimeClust. How to install TimeClust. ------------------------- 1) Download the distribution file for the desired platform. 2) Extract all files from the zip file on a temporary directory. 3) Install the MATLAB libraries trough the MCRInstaller (if the same version of the MATLAB library files are not already installed) in the following way: - for Windows machines a) run the MCRInstaller.exe. The setup wizard starts. b) add the following directory to your system path (on Windows XP, this directory is automatically added to your path) \ver\runtime\win32 - for Unix machines a) copy the MCRInstaller.zip in the installation directory and unzip the MCRInstaller.zip file. b) update your dynamic library path as follows: *Linux x86 32bit* export LD_LIBRARY_PATH="//bin/glnx86://runtime/glnx86://sys/os/glnx86://sys/java/jre/glnx86/jre1.5.0/lib/i386/native_threads://sys/java/jre/glnx86/jre1.5.0/lib/i386/client://sys/java/jre/glnx86/jre1.5.0/lib/i386:" export XAPPLRESDIR="//X11/app-defaults" *Linux x86-64 64bit. export LD_LIBRARY_PATH="//runtime/glnxa64://sys/os/glnxa64://sys/java/jre/glnxa64/jre1.4.2/lib/amd64/native_threads://sys/java/jre/glnxa64/jre1.4.2/lib/amd64/client://sys/java/jre/glnxa64/jre1.4.2/lib/amd64:" export XAPPLRESDIR="//X11/app-defaults" Note. If you have already installed MATLAB on your machine there is a limitation regarding directories on your path: this tool requires that mcr_root directory is first on the path, MATLAB requires that the matlabroot directory is first on the path. 4) Copy the TimeClust executable file and the TimeClust.CTF file in your application root directory 5) Run for the first time the TimeClust executable file and close the application. In this step the TimeClust_mcr directory and its subdirectories are created. 6) Open the config.txt file in the TimeClust_mcr/TimeClust1.3 directory to configure your application. In particular, set: - at the line 2 of this file, the desired web site to open from the TimeClust tool (default site is www.geneontology.org) - at the line 4, the command line to start the preferred editor to show text files (this step is not necessary for Windows platforms, the default text editor will be used). - at line 6, the command line to start the web browser to use (this step is not necessary for Windows platforms, the default web browser will be used). 7) Run again the TimeClust executable file and try with the small data set distributed together the software tool if all works as reported in the user's guide.