• An option to initialize node coordinates with visible positions of Cytoscape nodes has been implemented, thus EntOpt layout optimization could be applied by starting with the resulting node positions of another layout plugin.

• Memory usage was significantly reduced with sparse representation of the adjacency matrix and calculating overlaps on the fly instead of caching overlap matrix.
• The implementation of the underlying numeric optimization algorithm has been restructured to improve speed.
• Calculating with edge weights taken from a user selectable node column is implemented.
• Besides position, width and normalization factor of the nodes can also be optimized to achieve better layouts.
• The main diagonal of the adjacency and the overlap matrix now can be ignored or considered twice during the calculations depending on the characteristics of the visualized network.
• Data ordering (one dimensional optimization of node positions) is implemented.
• The gradual improvements in the quality of the network layout during the optimization process can be followed with the use of the global and componentwise normalized relative entropy values displayed in the network table and a new table dedicated to the various network components.
• It is now possible to perform the network visualization on an adjacency matrix raised to the second power by the plugin before the actual layout task is taking place.
• An issue preventing small components to be optimized properly has been fixed.

Fixing layout calculation for special graphs with: loops, parallel links, nodes with no links.

Initial version