The following file-formats are accepted by the system:

  • Edge list in one text file (.txt)
  • Zipped text files (.zip)
  • XGMML files (generated by Cytoscape) (.xgmml)
  • Cytoscape session files(both 2.x and 3.x) (.cys)

Edge list contains lines with node names separated by space to define an edge between them. Lines starting with '#' considered as comments.

The zip file must contain two text files named edges.txt and nodes.txt. In the edges file each row defines one edge in the graph, the source and target IDs are separated by space. In the nodes file each line defines one node, ID and name are separated by space (be careful not use spaces in the name part).

XGMML files are xml based graph files, usually exported by Cytoscape.

Cytoscape session files are session files used by Cytoscape.

The uploaded files can contain multiple graphs. The application selects the first, but you can change between them later. Only graphs with no loops can be used at the moment(which can be represented as a DAG(Directed Acyclic Graph)).

Nodes with no child element appears as blank circles, and nodes which has further child elements appears as filled circles. Left-clicking on a node opens its child elements, right-clicking opens all the child elements of the node(if graph has no more than 100 node) or opens until grandchilds(if graph has more than 100 nodes).

Here is a list of example files that can be uploaded directly:

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