Fındex __TOP_

NDEx 2.0 is the latest release of the Network Data Exchange (NDEx; refs. 1, 2) online resource (www.ndexbio.org), a framework in which users can store, share, access, and disseminate networks. In this article, we discuss workflows and methods used by NDEx in the context of its role as an online data commons and its mission to foster the emergence of network-centered communities of scientists involved in all aspects of disease biology, from basic research to personalized medicine.

File/folder structural change (in an effort to provide the different NDEX creations on both STEX and LEX with a unified folder structure) and added readme and texture index image. The contents of this upload haven't been changed otherwise.

Fndex

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For NDEx to provide a useful expo, other users must be able to find networks that are relevant to them. Thus, when networks are uploaded, NDEx indexes text strings for network descriptions, the user and group that manages the network, the genes or proteins represented by the nodes, the relations represented by the edges, and references cited. Users can initiate searches from NDEx homepage by entering names of cell processes or names of genes or proteins. This will bring up a table listing a number of networks. Figure 6 shows the results of a search for three circadian genes, per2, cry2, and bmal1. This returned 165 networks in which at least one of these genes is included. The table shows the name of the network, the number of nodes and edges, whether the network is public or private, the owner, and the date it was last modified. When one hovers a mouse over the name of a network, a popup window appears with a description of the network if one has been provided. If there is an icon in the Ref. column, it links to a publication in which the network appeared. One can proceed to download the network by selecting the icon with a white downward arrow. 006ab0faaa