All the tasks were run on a desktop computer equipped with an Intel Pentium 4 (3.00 GHz) CPU and 1 GB of RAM, purchased c. 2005, running openSUSE 11.1 and using the Java 1.6.0_22 32-bit virtual machine with a maximum heap size of 512 MB.
Users can also directly visualize the protein structure and the related Connolly surface [ 41] according to PDB data, using the Java 3D applet.
The hierarchical clustering analysis was conducted by using Cluster 3.0 and the results were intuitively visualized by using the Java TreeView 1.0.5.
The geometry file was created using the Java JDK 1.6 Applet available at http://neuroproteomics.scs.illinois.edu/imaging.html, as described previously.
Global array clustering was performed by the complete linkage method with Euclidean distance, and was visualized using the Java TreeView 1.1.0 software; the gene expression values are displayed as normalized log ratios.
The staining scores from immunohistochemistry and TUNEL assay were converted into scaled values centered on zero in Microsoft excel (Microsoft, Seattle, CA, USA), and the results were visualized using the Java TreeView 1.0.5 (http://jtreeview.sourceforge.net/).net/
Randomisation of sites (sampling without replacement) was performed using the Java application SiteSampler v1.1 [ 56] Support for the different partitioning schemes was examined by assessing Bayes factors, calculated using a harmonic-mean estimator in the software Tracer v1.6 [ 57, 58].
Hierarchical clustering was performed using a correlation matrix and centroid linkage using the Cluster 3.0 algorithm (121) and visualized using the Java TreeView program (122).
A hierarchical cluster was created using the Cluster 3.0 [ 27] and viewed using the Java TreeView [ 28].
Lipid structures were generated using the Java application SMILIB v2.0 (Schüller et al., 2007) which combines SMILES (Weininger, 1988) representations of chemical substructures.
