PathLinker

Reconstructs signaling pathways from protein interaction networks
<h1>PathLinker</h1> <br> <p>Implements the PathLinker algorithm for reconstructing signalling pathways from protein interaction networks.</p> <br> Please refer to the [documentation](http://pathlinker-cytoscape-app.readthedocs.io/en/latest/PathLinker_Cytoscape.html) for detailed descriptions, instructions, an example workflow with screenshots, as well as a Jupyter notebook showcasing how to use the CyREST-based PathLinker API. <br> <h2>Contact Information</h2> <p>If you have any problems using PathLinker or any suggestions for improvement, please contact us by email at jeffl@vt.edu or murali@cs.vt.edu</p>

1.4.1

Works with Cytoscape 3.6

Release Notes

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

1.4

Works with Cytoscape 3.6

API   pom.xml   Javadocs

Release Notes

PathLinker API version: 1.0 (new!!!) - Now Compatible with Cytoscape 3.6 (Not backward compatible with Cytoscape 3.5). - Implements two Cytoscape Automation cyREST API functions. One for running PathLinker on the currently selected network and one for running PathLinker on an input network SUID. Bug fixes: - 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.

1.3

Works with Cytoscape 3.2

Release Notes

Version 1.3 adds the following features: - 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. - 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.

1.2.4

Works with Cytoscape 3.2

Release Notes

Version 1.2.4 adds the following features: <ul> <li>Allows user to press Apps > PathLinker > Open to make PathLinker the selected tab in the CytoScape panel</li> <li>Fixes bug with persistent allow sources in paths setting</li> </ul>

1.2.1

Works with Cytoscape 3.2

Release Notes

Version 1.2.1 adds the following features: <ul> <li>Hierarchical layout only applied with k less than or equal to 200, due to slow rendering for large networks.</li> </ul>

1.2

Works with Cytoscape 3.2

Release Notes

Version 1.2 adds the following features: <ul> <li>Subnetwork is now automatically displayed as a hierarchical layout.</li> <li>Plugin now quits if there are no valid sources/targets.</li> <li>If the edge penalty is left blank, the plugin will assume the default value.</li> <br> </ul>

1.1

Works with Cytoscape 3.2

Release Notes

Version 1.1 adds the following features: <ul> <li>Adds support for graphs with multiple directed edges connecting the same pair of nodes. Now, multiple edges are replaced with a single edge whose weight is the average of the multiple edges.</li> <br> <li>Adds option for the user to specify an edge penalty for both additive and multiplicative options. For the multiplicative option this parameter will penalize each path by a factor of (number of edges in path)^(edge penalty) and for the additive option by a factor of (number of edges in path)*(edge penalty). <br> Note: to obtain the same results as v1.0 of the PathLinker plugin, please use a value for the argument equal to the total weight of edges in the network.</li> <br> <li>Fixes a bug with empty node/edge table entries being left behind after PathLinker is run.</li> </ul>

1.0

Works with Cytoscape 3.2

Release Notes

First version of PathLinker plugin.

CYTOSCAPE 3

Version 1.4.1

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Released 14 Apr 2018

Works with Cytoscape 3.6

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