shorthest path length

[Marko Radulovic]

Dear All,

This group contains a few discussions related to the "shorthest path length", but all rather dated.
The plugins mentioned: ShortestPath and PathExplorer do not seem to work with the latest Cytoscape versions. The integrated NETWORK ANALYZER calculates
the "average shortest path length" for each node, but not the "shorthest path length" for particular interactions

I greatly appreciate any suggestions

cheers,
Marko

[Tim Hull]

Did you try PathExplorer recently, and if so what problems did you have? It is available for Cytoscape 3.x in the App Store - you should be able to install it from the App Manager...

Tim

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[Marko Radulovic]

Many thanksTim for your prompt answer.
I tried to install PathExplorer in the latest 3.2.1 Cytoscape, the installation goes smoothly, the system indicates it as INSTALLED, but PathExplorer still does not show in the APPS tab?!
Maybe a conflict with another application, although I only have several installed, does not work with the latest version, who knows?

regards,
Marko

[Tim Hull]

Did you look on the node right-click menu? That's where I see it after installing - it doesn't appear on the Apps menu...

Tim

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[Marko Radulovic]

Many thanks Tim, I see it PathExplorer now on the node right click, but still can not use it as, for example if I choose "FIND PATHS TO HERE" - it blinks for a second with selected nodes, but it is not clear where are the results stored? Can not find  manual

Anyway, after a look at its functions it is unlikely that PathExplorer can do the job. I actually need to calculate, for example - shortest paths between 100 nodes within a 1000-node network. The NETWORK ANALYSER application that is integrated within Cytoscape does it nicely for the whole network. However, when I select only a part of the network- the AVERAGE SHORTEST PATH column in the results table - remains empty, although it does calculate many other parameters.
 If you have any ideas on how to fix this I would be extremely grateful!

cheers,
Marko

[Tim Hull]

I don't know much about PathExplorer - you may want to get in touch with the authors of that app (linked on the App Store website) if you have further questions.

As far as the Average Shortest Path column in NetworkAnalyzer, I'm not sure - does anyone know if there might be a reason this is empty when analyzing a subset of nodes?

Tim

[Marko Radulovic]

Many thanks Tim! Since nobody is replying I will create a new post about the Network analyzer issue to make it more visible.
cheers,
Marko