Cytoscape plugins

The authors of Cytoscape, a software platform for the analysis and visualisation of networks, have just published an overview of Cytoscape plugins in Nature Methods. Although many of these plugins might be most relevant for biological networks, there might be some original and useful Humanities applications to be developed as well. The overview covers 152 plugins, that should be plenty for the more creative among us to explore and play around with.

Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set of tools. We present a travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5–2.8. We also describe ongoing efforts to distribute, organize and maintain the quality of the collection.

Citation analysis: winner takes all

A small group of papers (1%) often gets a disproportional amount of attention and citations (17%). This pattern has been identified a long time ago (have a look at the Web of Science selection procedure as an example of this trend). A short correspondence by Barabási, Song and Wang published recently in Nature revealed that this pattern only emerges after some time and that those top 1% of papers are not necessarily cited a lot immediately after they emerge. The authors argue that this pattern might be a result of our changing reading habits now that academic publications are so abundant, easily searchable and as a result easily accessible: “Researchers increasingly rely on crowd sourcing to discover relevant work, a process that favours the leading papers at the expense of the remaining 99%”.

Read the full correspondence on the Nature website.

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