13. Release Notes

13.1. GraphSpace 2.0

13.3.1. Highlights

  • We have added features in the layout editor that allow a user to select nodes and edges based on color and shape in order to edit their visual properties. This functionality is available in conjunction with the features that allowed a user to arrange the positions of the nodes in a variety of shapes.
  • We have brought the JSON format accepted by GraphSpace in line with Cytoscape.js (this JSON format is also compatible with Cytoscape).
    • We separate the structure of the network (nodes and edges) from the description of the visual styles of the nodes and edges.
    • Cytoscape.js supports a network-level data section in the JSON file specifying the network structure. We allow users to include network-specific attributes in this section, e.g., PMID, authors, and organism.
    • Cytoscape.js supports a data section within each node. Currently, GraphSpace recognizes an attribute called \aliases” in this section, through which the network creator can specify a list of aliases for the node.
    • GraphSpace now supports CSS-based Cytoscape.js JSON files for specifying the style of the graph. GraphSpace users can import these files either in the Upload section or the Layout Editor section.
    • We have deprecated support for the JSON format supported only by GraphSpace.
  • We have streamlined the search interface and made it more efficient. We have added support to search for networks that match a specific attribute (key-value pair) in addition to nodes. The search also includes the \aliases” attribute of nodes. We have disabled support for Exact searches: GraphSpace now supports only case-insensitive and substring searches.
  • Concomitant with these changes, we now allow Cytoscape users to export their visually-coded networks from Cytoscape and to import them directly into GraphSpace.
  • We have added support to allow a group owner to invite another person to a group via a signup link.
  • To facilitate bulk uploads of networks to GraphSpace, we have implemented the Graphspace python module that a user can install from PyPI.

13.2. GraphSpace 1.1

13.2.1. Bug Fixes

  • Fixed bug reported when trying to use the Forgot Password functionality.

13.3. GraphSpace 1.0

13.3.1. Highlights

  • This is the first public release of GraphSpace.