Performance of six graph tools loading scale free networks of increasing size. Each point in the plot corresponds to the average elapsed time (in seconds) required to load one of these networks. The inset shows the first 10 s of the same tests (± standard deviation, n = 10). The networks were obtained by the function 'barabasi.game' available in the R package igraph . Briefly, each network has ϖ vertices and ε edges generated by a step-model where the first step generates a single vertex and no edge; the subsequent steps generate one vertex linked to an old vertex according to a probability distribution proportional to the degree of the nodes; therefore, in the end there are ϖ-1 edges. The networks were obtained and set prior to the performance tests, and only with minimum information in order to guarantee equal conditions among the software (that is, without any graph attribute, such as color, size, and so on). Versions tested: R version 2.14.1, RedeR_1.0.3, igraph_0.5.5-4, RCytoscape_1.4.3, Cytoscape 2.8.1, CytoscapeRPC 1.7, Rgraphviz_1.32.0. Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit). Hardware: MacPro4.1 2 × Quad-core Intel Xeon 2.26 GHz, 6 GB RAM. The source code used to run the complete analysis is available in Additional files 2 and 3.
Castro et al. Genome Biology 2012 13:R29 doi:10.1186/gb-2012-13-4-r29