APID (Agile Protein Interaction DataAnalyzer) is an interactive bioinformatic web-tool that has been developed to allow exploration and analysis of main currently known information about protein-protein interactions integrated and unified in a common and comparative platform. The analytical and integrative effort done in APID provides an open access frame where all known experimentally validated protein-protein interactions are unified in a unique web application that allows an agile exploration of the interactome network and includes certain calculated parameters that weight the reliability of a given interaction (i.e. the "edges" of the interactome network) between two proteins, and also qualify the functional environment around any given protein (i.e. the "nodes" of the interactome network) .

IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.

Analysis and visualization of biological networks, such as protein-protein and protein-DNA interactions, are crucially important toward obtaining a thorough understanding of living systems. Here, we present an integrative software platform , eXpanda , which enables an analysis of a very broad range of biological networks , with a special focus on the extraction of characteristic topologies which potentially function as units in the networks. eXpanda is provided as a Perl library which gives full-automatic connections to various biological databases via a Perl programmable interface and can perform topological analysis based on graph theory. The results of these analyses are visualizable by vector graphics.