Path Explorer help

[Miquel Oltra]

Hello.
I am using Cytoscape 3.1, and I want to highlight connected paths on my network. I have tried PathExplorer and it works (the connected path between two nodes is highlighted), but I can not do anything else after that action. For instance, to create a subnetwork, or to undo the highlighted I have done before.

Any suggestion or help about the use of this app? There are other apps to accomplish this basic tasks?

Thanks in advance,
Miquel Oltra

[piet molenaar]

Hi Miquel,

I'm seeing the same behavior in 3.2; since this is an app specific problem I'd suggest you contact the authors directly:

contact details of the main developer are here: https://github.com/Ritisha?tab=repositories

Cheers,

Piet

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Piet Molenaar
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Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
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[Giovanni Scardoni]

Hi,

you can use the Pesca app. It finds all the shortest paths between two or more of nodes.

It will be released in few weeks. You can find a beta version (working) here:

http://www.cbmc.it/~scardonig/pesca/

Please let me know any suggestion!

Giovanni

Giovanni Scardoni
The Center for BioMedical Computing (CBMC)
www.cbmc.it/~scardonig/
University of Verona
Strada le Grazie, 15 -37134
Verona -Italy

Try these Cytoscape apps!
CentiScaPe: http://www.cbmc.it/~scardonig/centiscape/centiscape.php
Interference: http://www.cbmc.it/~scardonig/interference/Interference.php

[Miquel Oltra]

Hi Piet!

Thanks for your answer. I haven't realised because I'm not still used to google groups discussions..

Finally, I decided to use the Pesca app in order to find the paths connecting one node to the rest of the network, and it is working quite well.

Giovanni, first of all I want to congratulate you for your job make in the app. It has been very helpful for me! The only thing that, in my opininon, is quite improvable is the "directed" check option.

For example: if I import in Cytoscape a network directly from Reactome (in BioPAX3 format), and then I use the Pesca app with "directed" option, the behaviour is not always the same. I mean that for edges types like "contains" or "member" it's difficult to follow the directions.

Anyway, thanks a lot for your job!

Best regards,
Miquel Oltra

[Suchetana Gupta]

Hi

Can we use Pesca to do calculations on a weighted network (the node and edge weight information is stored in an excel file)?

Any tutorial for the same?

Regards

Suchetana

[Giovanni Scardoni]

Hi Miquel,

sorry for delay answer. The directed option depends on the attribute of the edge. So it cannot decide 

the direction of an edge as contains or member. 

thank you for the suggestion, we will consider it for the next release.

Giovanni

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[Giovanni Scardoni]

Hi Gupta,

Pesca can be used for weighted networks. 

http://www.cbmc.it/~scardonig/pesca/

here a brief tutorial

Giovanni

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[Suchetana Gupta]

Thanks Giovanni.