What does core and all mean in network?

[yuewu...@gmail.com]

When I import a network from xml, there is always a core and an all network. The network is larger. I am note quite sure about what these terms mean.

Thanks.

Best.

Yue 

[Scooter Morris]

Hi Yue,
    What XML file are you importing, and what app are you using to import it?  Internally, Cytoscape doesn't have a concept of "core" nodes and "all" nodes, so this must be coming from either the program that generated the XML file or the app that's reading it in.

-- scooter

[yuewu...@gmail.com]

Thanks a lot.

I am using a file related to iJDZ836.xml, which is kind of a flux balance model.

I am just import it by cytoscape import(it shouldn't be any "app").

You kind of remind me it might probably come from xml file.

Best.

Yue Wu

[Barry Demchak]

I think we could give a better opinion if we had a copy of a sample file. Is there something you can e-mail to this forum or give us a link to??

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[Scooter Morris]

OK, pretty sure that the core vs. all is coming from the xml file itself.  What program generated the xml?

-- scooter

--

[yuewu...@gmail.com]

Sure, I will do that. The file are made by "https://github.com/jdreyf/fast-automated-recon-metabolism".  It is in attachment

On Friday, March 9, 2018 at 11:14:00 AM UTC-5, Barry Demchak wrote:

I think we could give a better opinion if we had a copy of a sample file. Is there something you can e-mail to this forum or give us a link to??

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of yuewu...@gmail.com
Sent: Friday, March 09, 2018 7:50 AM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: [cytoscape-helpdesk] Re: What does core and all mean in network?

 

Thanks a lot.

 

I am using a file related to iJDZ836.xml, which is kind of a flux balance model.

 

I am just import it by cytoscape import(it shouldn't be any "app").

 

You kind of remind me it might probably come from xml file.

 

Best.

Yue Wu

On Thursday, March 8, 2018 at 11:44:45 AM UTC-5, Scooter Morris wrote:

Hi Yue,
    What XML file are you importing, and what app are you using to import it?  Internally, Cytoscape doesn't have a concept of "core" nodes and "all" nodes, so this must be coming from either the program that generated the XML file or the app that's reading it in.

-- scooter


On Wednesday, March 7, 2018 at 7:45:20 PM UTC-8, yuewu...@gmail.com wrote:

When I import a network from xml, there is always a core and an all network. The network is larger. I am note quite sure about what these terms mean.

 

Thanks.

Best.

Yue 

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[yuewu...@gmail.com]

As reply to scooter

On Friday, March 9, 2018 at 11:14:00 AM UTC-5, Barry Demchak wrote:J

I think we could give a better opinion if we had a copy of a sample file. Is there something you can e-mail to this forum or give us a link to??

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of yuewu...@gmail.com
Sent: Friday, March 09, 2018 7:50 AM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: [cytoscape-helpdesk] Re: What does core and all mean in network?

 

Thanks a lot.

 

I am using a file related to iJDZ836.xml, which is kind of a flux balance model.

 

I am just import it by cytoscape import(it shouldn't be any "app").

 

You kind of remind me it might probably come from xml file.

 

Best.

Yue Wu

On Thursday, March 8, 2018 at 11:44:45 AM UTC-5, Scooter Morris wrote:

Hi Yue,
    What XML file are you importing, and what app are you using to import it?  Internally, Cytoscape doesn't have a concept of "core" nodes and "all" nodes, so this must be coming from either the program that generated the XML file or the app that's reading it in.

-- scooter


On Wednesday, March 7, 2018 at 7:45:20 PM UTC-8, yuewu...@gmail.com wrote:

When I import a network from xml, there is always a core and an all network. The network is larger. I am note quite sure about what these terms mean.

 

Thanks.

Best.

Yue 

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[Scooter Morris]

Hi Yue Wu,
    OK, from your description, and the fact that this is an SBML file, you are probably using the cySBML app, which does divide things up into "All", "Base", and "Kinetic" networks.  You can read about this app here: https://www.ncbi.nlm.nih.gov/pubmed/22772946.  If you use the Cytoscape importer without having the app installed, you won't see those three networks, but you also won't get the automatic styling and side panel that cySBML provides.  I had to edit the file to get the base SBML reader to work since we currently are using a *very* old version of the jsbml library that doesn't support groups.

-- scooter

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[yuewu...@gmail.com]

thanks a lot.