Reviewer response for version 1
The paper of Gil et al. describes a new Cytoscape App, Pathlinker, which is the Cytoscape implementation of the previously published approach by the Murali group with the same name. 
It is always useful for the community to implement network analyzing algorithms to Cytoscape.
The paper and the abstract is well written and clear. 
The figures were well selected.
In order to facilitate the application of the PathLinker App, it would be useful to provide more, tutorial type comments and guidelines for new users. 
Given the important task PathLinker is meant to solve, many users would find it useful. 
Currently the Methods section contains the key steps but it does not read as a protocol or suggest alternatives for troubleshooting.
The current version of the paper does not contain the limitations of PathLinker. 
When this App should not be used, for which datatypes it is not good, or cases when the user should pay attention to any bias or problem?
The comparison with existing Apps focuses on the differences in the algorithms. 
As this is an App paper, it would be useful to include a comparison of the functional differences (features) between the Apps.
If possible, maybe for a new version, it would be nice if the App allows to input the source and target node names by node selection function, instead of typing it in (or pasting it in) to the requested fields.
Finally, a small bug in the App: When the user select the checkbox to generate a sub-network as an output, it does not generate a subnetwork within Cytoscape but a new network. 
The problem with this that it means the attributes of the original network will be lost. 
This should be fixed easily.
I believe PathLinker will be a popular and often used App for the biomedical and systems biology communities. 
I think the next step to increase its impact is to make the application of it as clear and as didactical as possible.
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