Reviewer response for version 1
AutoAnnotate is a Cytoscape app that can make complex networks easier to interpret by clustering nodes and labelling the clusters with relevant terms. 
Clusters can be collapsed into single nodes, greatly simplifying the network. 
The app is easy to use and allows configuration of quite of number of settings. 
The clusters are labelled based on the most frequent words in a (configurable) node column, using functionality from the WordCloud app.
The proper labelling of the clusters can require some toying with the parameters and manual curation, both in AutoAnnotate and WordCloud. 
For instance, using the AlzheimerEM.cys network from the WordCloud tutorial a cluster was labelled with the terms “interphase cycle”, where “cell cycle” would be more appropriate. 
The word “cell” was omitted due to the default “Normalize” setting of the WordCloud app that prevented very frequent words to be present in a label. 
Lowering this setting from 0.5 to 0.3 changed the label to “cell cycle”. 
This is described in the quite elaborate AutoAnnotated User Guide.
I have also tested the app with the SeedNet network (http://netvis.ico2s.org/dev/seednet/#/static/Data) which is a co-expression network that has 8,621 nodes with 502,173 interactions. 
The nodes were pre-clustered with MCODE into 136 clusters. 
It took AutoAnnotate a few minutes to annotate the clusters (on a MBP 2012), which is acceptable, and then about 10 seconds to generate a summary network. 
The produced cluster labels were based on the annotation of the clustered genes. 
The labels were not very informative because there were hardly any common words in the annotations. 
This was obvious from the words in the labels, and from the output of the WordCloud app for a cluster. 
For a future version of the app it might be an idea to scale the font of the label by the frequency of the chosen words (now the font can be scaled by the cluster size), to indicate how descriptive a label is for a certain cluster.
The manuscript is well written and to the point.
In the following two lines the plural “they” refers to the singular “user”:
“The USER may create as many Annotation Sets as THEY like, and can easily switch between them.”
AutoAnnotate is a useful addition to the collection of Cytoscape apps, and will undoubtedly help many users to create an informative summary of a complex network.
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