FW: [cytoscape3 - Bug #4189] (Triaged) PSICQUIC

[Barry Demchak]

 

So, what I am doing it is to import a PPI network from the dabase, then filter it for human and degree connection, use clustermaker for separating cluster of genes. I need to find the central node that is in the list of genes I did indicate initially. Do you have any advice on how to find quickly the central nodes of each cluster that i get?

Thank you!

Rolando

 

2018-05-17 9:38 GMT-06:00 Barry Demchak <idekerlab...@gmail.com>:

Hi, Rolando –

 

No problem … many people think my e-mails are spam J

 

Yes, you would use a degree filter for this. You would most likely use “in+out” if your graph is undirected.

 

Good luck!

 

From: Rolando Pasquariello <rolando.pa...@gmail.com>
Sent: Thursday, May 17, 2018 8:24 AM
To: Barry Demchak <idekerlab...@gmail.com>
Subject: Re: [cytoscape3 - Bug #4189] (Triaged) PSICQUIC

 

Hello Barry,

sorry for my delay in the answer but your e-mail was in the spam! Anyway, thank you very much to be so nice. So i figured the problem out and was related to the internet connection at work that have had problems in the last period. It is not a problem related to cytoscape and so sorry about that! I was learning a new pipeline of analysis and started to have this problem was stressful! But it is ok now!

 

I have a quick question, how can I define a filter for the network to choose only those genes that have more that five connections? Should I use the degree filter?

 

Thank you for your help!

Rolando

 

2018-05-10 13:06 GMT-06:00 Barry Demchak <idekerlab...@gmail.com>:

Hi –

 

For the first problem, I’m not sure what you’re describing … let’s start differently. I have made a video of how the PSICQUIC feature should work:

 

https://www.screencast.com/t/Qa9BfsF1

 

Can you take a look at the video and tell me where you Cytoscape isn’t working the same?

 

Also, regarding the ontology feature, it is not available in Cytoscape 3.6.0 and 3.6.1 because it is broken. We’re working on fixing it and re-introducing it in a later version. We’re sorry for not having it available now.

 

From: cytoscape....@gmail.com <cytoscape....@gmail.com>
Sent: Thursday, May 10, 2018 4:41 AM
Cc: rolando.p...@gmail.com
Subject: [cytoscape3 - Bug #4189] (Triaged) PSICQUIC

 

--Reply above this line--

Issue #4189 has been updated by Barry Demchak.

• Status changed from New to Triaged
• Assignee set to Barry Demchak

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Bug #4189: PSICQUIC

• Author: Barry Demchak
• Status: Triaged
• Priority: Normal
• Assignee: Barry Demchak
• Category:
• Target version:
• Tags:
• Difficulty:
• Feature Risk:
• Testing Risk:
• Reviewer:

OS: Mac
Cytoscape version: 3.6.0

Hello,I am using cytoscape v3.6.0 to generate protein-protein work but I cannot access to any PSICQUIC databases in the last period. I have a white windows if I go to file -> import -> network -> public databases although I indicate the genes that I want to use for building the network. So I think there is a problem of communication between my macbook and cytoscape. How can I figure the problem out?I would like to use also the function \'ontology and annotation...\' but it is not present when I do File -> import -> \'ontology and annotation\'. I can only choose between network, tables and style. How can I get this function as well?I did attach here the cytoscape task history if it can help.Thank you for your help!Rolando

Reported by: Rolando
Email: rolando.p...@gmail.com

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