v1.4.3

Fixes a bug where the PathLinker control panel failed to start in Cytoscape v3.8+.

Specifically, the approach we were using to start the PathLinker control panel from the 'Apps' menu tab broke in Cytoscape v3.8+ causing the GUI to be inaccessible. To get around the issue, we removed that functionality and simply run the app and build the control panel as soon as Cytoscape starts.

v1.4.2

Fixes a bug where the PathLinker app failed to start in Cytoscape v3.7+.

v1.4.1

Version 1.4.1 adds an option to treat all edges in the network as undirected edges.

This release matches the version of the PathLinker CyRest API app published in F1000 Research.

Add cyREST API Functionality

Major update to PathLinker which includes new cyREST API functions, code refactors, and bug fixes.

PathLinker app version: 1.3 -> 1.4
PathLinker API version: 1.0 (new!!!)

Feature:

• Now Compatible with Cytoscape 3.6 (Not backward compatible with Cytoscape 3.5).
• Restrict k and edge penalty text field to only allow integer and double numerical inputs from user.
• Implement two REST API function "run", one for selected network and one takes user input network SUID.
• Include Jupyter Notebook examples on using the automation features

Development:

• Refactor runKSP, create subgraph/view processes into task classes, now better align with OSGi design.
• Refactor validation and error handling codes for reducing duplicated codes.
• Reorder the packages for organization purposes.
• Update pom.xml file to include new features and be compatible with Cytoscape 3.6

Bug fix:

• Fix the issue where submit button enables when there aren't any inputs in the source/target fields.
• Remove unneeded error messages "source/target empty".
  fix the issue where more than one space between nodes in source/target text field results in adding additional node with empty name.
• Fix the issue where the network combo box is not updated correctly with selected item after creating a new network

v1.3

Version 1.3 adds the following features:

• The subnetwork generated by the PathLinker app will contains the same style of the parent network that it is generated from.
• Paths with the same/tied score in the results are now sorted based on alphabetical order of node names.
  • This change will allow results to be more interpretable and reproducible, however results from previous versions of the app could differ from results of this version due to the fact tied paths were not sorted earlier. Using the “Include tied paths” check-box will ensure all paths with a tied score are in the results.
• Added Junit tests to ensure updates do not break the core PathLinker algorithm.

Bug Fixes

• Fixed a bug where node attributes in the parent network were not carried over to the subnetwork.
• Fixed a bug where edge penalty can be set to less than 1 for the edge weight option “weights are probabilities”.
• Fixed a bug where multiple edges between two nodes were deleted by the app.

New Features

Control Panel

• Aesthetic and usability improvements including scroll-bars and help, about, clear and exit buttons.
• Added “Add selected source(s)” and “Add selected target(s)” buttons for the sources and targets input field. The button allows the user to select nodes in the network view and add their names into the input field.
• Added “Edge weight column” drop-down box in “Edge Weights” sub-panel. The user can select a column by name in Edge Table through the drop-down menu to be use as the input fields for edge weights.
• Added “Include tied paths” check-box in the “Output” sub-panel. Checking this option makes the app to include more than k paths if the path length/score is equal to the kth path’s length/score in the result.
• Added tooltips to all buttons and fields.
• Removed the check box “Generate subnetwork” → “Disable subnetwork generation”. Now PathLinker always generates the subnetwork.
• The “Submit” button is not enabled until required inputs are entered.

Table Panel

• Implemented new attribute “path index” in the “Edge Table”. The attribute assigns an index of the first path in which each edge appears. This feature will be useful in the CyGraphSpace app (not yet released) when users upload networks computed by PathLinker app via the CyGraphSpace app to GraphSpace.

Results Panel

• PathLinker results are now shown in a table in the “Results Panel” rather than as a pop-up window.
  Added buttons to export and delete results.
• Selecting paths inside the results table will highlight the paths in the network view accordingly.

v1.2.5

• The PathLinker app now works with both directed and undirected edges by creating a copy of the original network in which undirected edges are converted to bi-directed edges. The app then runs as before.

v1.2.4

This release described the version of the PathLinker app published in F1000 Research.

Version 1.2.4 adds the following features:

• Allows user to press Apps > PathLinker > Open to make PathLinker the selected tab in the CytoScape panel
• Fixes bug that made the "Allow sources in paths" setting persistent across different runs of the app.

v1.2.1

Version 1.2 adds the following features:

• The app automatically displays the subnetwork computed by PathLinker as a hierarchical layout (as long as k <= 200).
• The app quits if there are no valid sources/targets.
• If the edge penalty is left blank, the app assumes the default value for this parameter.