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cytoscape-helpdesk

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Welcome to the Cytoscape Helpdesk. This group is intended for discussions pertaining to the installation and operation of Cytoscape. If you are developing or maintaining your own Cytoscape app, then please consider the cytoscape-app-dev group. Questions about cytoscape.js should go to stackoverflow. Newbie questions are welcomed!

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Installing Cytoscape

Using Cytoscape

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General

If you are new to posting, following the Posting Guidelines will help you get quicker and more useful responses.

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10/1/18

Helpdesk Posting Guidelines

These guidelines can help you find answers to your questions, as well as provide Cytoscape staff with

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Helpdesk Posting Guidelines

These guidelines can help you find answers to your questions, as well as provide Cytoscape staff with

10/1/18

Eliot Ragueneau, Christopher Churas2

Jun 2

Custom protocol handler

Hi, Thanks for the feedback. That is a good idea. Adding the ability to launch Cytoscape desktop via

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Custom protocol handler

Hi, Thanks for the feedback. That is a good idea. Adding the ability to launch Cytoscape desktop via

Jun 2

Johanna Villén, … Scooter Morris27

May 15

Cytoscape not starting

Erika, Cytoscape 3.10 requires Java 17. Can you install that and let me know how it goes. -- scooter

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Cytoscape not starting

Erika, Cytoscape 3.10 requires Java 17. Can you install that and let me know how it goes. -- scooter

May 15

Shraddha Pai, Ruth Isserlin3

May 1

Multiple EnrichmentMap - custom palette?

Hi Ruth, Thanks, "Change Colours" did the trick. Also I didn't realize I had to set

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Multiple EnrichmentMap - custom palette?

Hi Ruth, Thanks, "Change Colours" did the trick. Also I didn't realize I had to set

May 1

guillerm...@gmail.com, … Odinaka Chris Iwuozo5

Apr 21

MetScape server down?

Hello, I just wanted to follow up, did the MetScape work on your end? I am still encountering the

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MetScape server down?

Hello, I just wanted to follow up, did the MetScape work on your end? I am still encountering the

Apr 21

Hema Latha Govada, … Christopher Churas6

Apr 17

Cytoscape app website not working

Hi, Sorry about that. Is it still down for you? I just checked and it seems fine for me. thanks,

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Cytoscape app website not working

Hi, Sorry about that. Is it still down for you? I just checked and it seems fine for me. thanks,

Apr 17

Nicholas Provart, … Nicholas Provart3

Apr 8

PSIMI 25 style has disappeared from Cytoscape?

Ah, thanks, Ruth! I think that is part of the problem - BioGRID's PSICQUIC webservice is down, so

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PSIMI 25 style has disappeared from Cytoscape?

Ah, thanks, Ruth! I think that is part of the problem - BioGRID's PSICQUIC webservice is down, so

Apr 8

Ruth Isserlin, Scooter Morris7

Mar 26

Issue with group attribute aggregation

Hi Ruth, I tried to reproduce the issue and I wasn't able to. I was using the Yeast Perturbation

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Issue with group attribute aggregation

Hi Ruth, I tried to reproduce the issue and I wasn't able to. I was using the Yeast Perturbation

Mar 26

Kristina Hanspers2

Mar 24

Join NRNB for Google Summer of Code 2025!

The contributor application period for GSoC starts today! Application deadline is April 8 18:00 UTC.

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Join NRNB for Google Summer of Code 2025!

The contributor application period for GSoC starts today! Application deadline is April 8 18:00 UTC.

Mar 24

Petlu Swetha, Scooter Morris2

Mar 15

Hi Petlu, You have several questions in there. When you say that you can't download CyPlot, can

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Hi Petlu, You have several questions in there. When you say that you can't download CyPlot, can

Mar 15

Petlu Swetha, Scooter Morris2

Mar 15

unable to download cyplot

There was an app store outage earlier -- I just tested and it's working for me, now. -- scooter

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unable to download cyplot

There was an app store outage earlier -- I just tested and it's working for me, now. -- scooter

Mar 15

John Muirhead-Gould

Mar 15

Introducing Nodes.bio: A Simple Implementation of Cytoscape.js

Dear Cytoscape Community, I'm thrilled to share Nodes.bio—a brand-new platform built to simplify

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Introducing Nodes.bio: A Simple Implementation of Cytoscape.js

Dear Cytoscape Community, I'm thrilled to share Nodes.bio—a brand-new platform built to simplify

Mar 15

Rashid Jusoh, Scooter Morris3

Mar 13

unable to update KEGG in cluego plugin

Dear scooter, thank you very much for your kind reply, I did search the link provided in the web

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unable to update KEGG in cluego plugin

Dear scooter, thank you very much for your kind reply, I did search the link provided in the web

Mar 13

Nicolai Karcher, Kozo Nishida2

Mar 8

incomplete import of KEGG pathway via keggscape

Hi, Thanks for your message. I have just replied to https://github.com/idekerlab/KEGGscape/issues/31

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incomplete import of KEGG pathway via keggscape

Hi, Thanks for your message. I have just replied to https://github.com/idekerlab/KEGGscape/issues/31

Mar 8

Shraddha Pai, … Odinaka Chris Iwuozo7

Feb 26

STRING app Customizing network appearance

Hello Chris, Thank you for your email. The suggestion was helpful. I have been able to launch the

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STRING app Customizing network appearance

Hello Chris, Thank you for your email. The suggestion was helpful. I have been able to launch the

Feb 26

Rimo Ghosh, Kristina Hanspers2

Feb 3

GSOC 2025 guidance

Hi Rimo, For information on getting started with Cytoscape development, see https://cytoscape.org/

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GSOC 2025 guidance

Hi Rimo, For information on getting started with Cytoscape development, see https://cytoscape.org/

Feb 3

Gautam Manchandani, Chris Churas3

Jan 31

GSOC'25 Guidance Related

Thank you , I will go through the details! On Thursday, 30 January 2025 at 22:23:48 UTC+5:30 Chris

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GSOC'25 Guidance Related

Thank you , I will go through the details! On Thursday, 30 January 2025 at 22:23:48 UTC+5:30 Chris

Jan 31

Sean So, Scooter Morris4

Jan 23

Grouping nodes close together in an automated fashion

Just as I sent that message above, I realised that I can achieve a nice visualisation within each

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Grouping nodes close together in an automated fashion

Just as I sent that message above, I realised that I can achieve a nice visualisation within each

Jan 23

Shivam Sundram, Scooter Morris2

Jan 22

Introduction and Guidance for contributing

Hi Shivam, I would suggest that you get started by going through the app development ladder: https://

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Introduction and Guidance for contributing

Hi Shivam, I would suggest that you get started by going through the app development ladder: https://

Jan 22

Ruth Isserlin, … Christopher Churas13

Jan 22

concentric circle layout

Hi Ruth, Okay that took a lot of correcting of chatgpt output, but got a prototype working. If you

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concentric circle layout

Hi Ruth, Okay that took a lot of correcting of chatgpt output, but got a prototype working. If you

Jan 22

xiangmin, Scooter Morris2

Jan 15

Why can't display "String: protein query" in network panel?

Can you tell us what version of stringApp and Cytoscape you are using? There was a recent change in

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Why can't display "String: protein query" in network panel?

Can you tell us what version of stringApp and Cytoscape you are using? There was a recent change in

Jan 15

Shraddha Pai, Mike Kucera3

Jan 9

EnrichmentMap: AutoAnnotate greyed out

Hi Mike, Yes, that helped - I installed the Pipeline collection and was able to successfully use

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EnrichmentMap: AutoAnnotate greyed out

Hi Mike, Yes, that helped - I installed the Pipeline collection and was able to successfully use

Jan 9

Rupesh varshney, Kristina Hanspers2

Jan 6

Introduction and Request for Guidance on Contributing to the Projects for GSOC 2025

Hi Rupesh, Thank you for your interest in Cytoscape and NRNB. Google has not yet announced GSoC 2025,

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Introduction and Request for Guidance on Contributing to the Projects for GSOC 2025

Hi Rupesh, Thank you for your interest in Cytoscape and NRNB. Google has not yet announced GSoC 2025,

Jan 6

Balasubramaniam Namasivayam, … Mike Kucera7

Jan 6

Getting Autoannotate cluster names in node table

Hi Mike, Thanks for the new version. I can confirm that it works as intended! I greatly appreciate

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Getting Autoannotate cluster names in node table

Hi Mike, Thanks for the new version. I can confirm that it works as intended! I greatly appreciate

Jan 6

HFazel, … Nadezhda Doncheva32

Jan 1

string-db data load error

Hi, We just released version 2.2 of stringApp, so you need to update to that one for things to work.

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string-db data load error

Hi, We just released version 2.2 of stringApp, so you need to update to that one for things to work.

Jan 1

Hashan Jayarathne, … Scooter Morris3

12/18/24

multi-omics analysis

Typically, the way I would approach this is by importing all of the data and then doing some simple

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multi-omics analysis

Typically, the way I would approach this is by importing all of the data and then doing some simple

12/18/24

liu xn, … Scooter Morris5

12/18/24

How to create a circular network with evenly distributed nodes (Not Just Around the Rim)

Hi Liu, In the far left-hand side of your control panel should be a series of icons "Network

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How to create a circular network with evenly distributed nodes (Not Just Around the Rim)

Hi Liu, In the far left-hand side of your control panel should be a series of icons "Network

12/18/24

Junyi Chen, Christopher Churas3

12/18/24

Fail to import Edge

Hi, Out of curiosity what was wrong? chris On Wed, Dec 18, 2024 at 1:25 AM 'Junyi Chen' via

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Fail to import Edge

Hi, Out of curiosity what was wrong? chris On Wed, Dec 18, 2024 at 1:25 AM 'Junyi Chen' via

12/18/24

Saad Khan, Scooter Morris7

12/11/24

Unable to make enhanced graphics work for circos

Look at the node visual property: Size->Fix custom graphics to node size and make sure that's

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Unable to make enhanced graphics work for circos

Look at the node visual property: Size->Fix custom graphics to node size and make sure that's

12/11/24

Brandon Tylke, Christopher Churas4

12/9/24

https://nrnb-nexus.ucsd.edu/ Certificate Expired

Hi Chris, Thank you for addressing this so quickly! Best, Brandon Tylke On Thursday, December 5, 2024

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https://nrnb-nexus.ucsd.edu/ Certificate Expired

Hi Chris, Thank you for addressing this so quickly! Best, Brandon Tylke On Thursday, December 5, 2024

12/9/24

Hayat Mohammed, Scooter Morris4

11/21/24

Yes, I found it a bit complicated also. I don't use ClueGO much, so maybe others on the list can

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Yes, I found it a bit complicated also. I don't use ClueGO much, so maybe others on the list can

11/21/24

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