HELP FOR CYTOSCAPE!!!!

[lbuon...@tin.it]

Alex,

I wrote to you few weeks ago about our problems with Cytoscape, which have not been solved.

Let me start from the beginning.

We have downloaded the latest version available at the Cytoscape website (2.8.2). Obviously, we do not have a network file. Therefore, ss indicated in the Manual, we have imported the file galExpData.pvals using the path: File, Import, Attribute from Table.

After identifying the individual columns (gene, common,....), NO KEY ATTRIBUTES ARE SHOWN IN THE WINDOW at bottom left of the page. IS THIS NORMAL?
Moreover, when we select the import button, NOTHING IS IMPORTED.

CAN YOU HELP US? WE ARE UNABLE TO MOVE FORWARD.

I have sent you an invitation through SKYPE. Please, accept it. Talking would be much simpler to explain. I promise, I will not bother you more than necessary.

Best

Luigi
  



----Messaggio originale----
Da: ap...@gladstone.ucsf.edu
Data: 21-set-2011 0.34
A: <cytoscape...@googlegroups.com>
Ogg: Re: [cytoscape-helpdesk] Cytoscape splash screen and plugin loading

The splash screen disappears when all plugins are loaded and Cytoscape is
initialized. You can simply wait for it to disappear.

Or, do you mean how to detect programmatically as a plugin developer?

- Alex


On 9/20/11 3:07 PM, "ranjman" <ran...@gmail.com> wrote:

> I'm not sure how best to wait for Cytoscape to finishing loading and
> the intro/splash screen to disappear before loading my file (via a
> plugin menu). Is there a way to check for the splash window at
> startup?
>
> Any suggestions would be appreciated.
> Thanks


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[allan_k...@agilent.com]

Luigi – I can talk with you via skype for the next half hour, i.e. until around 9:45PM your time.   My skype id is allan.kuchinsky.    Give me a call and we’ll see if I can help you.

 

Allan Kuchinsky

[allan_k...@agilent.com]

By the way, you need to import a network before you import attributes.   Then you will have nodes that the attribute values can be attached to.

 

AllanK

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of lbuon...@tin.it
Sent: Wednesday, September 21, 2011 3:26 AM
To: cytoscape...@googlegroups.com
Subject: [cytoscape-helpdesk] HELP FOR CYTOSCAPE!!!!
Importance: High

 

Alex,

[Jason Montojo]

Hi Luigi,

What type of analysis are you trying to do?  When you import attributes, they need to be associated with nodes, edges or networks.  If you don't have a network, you won't have anything to attach the attributes to.

Thanks,

Jason

[Alexander Pico]

Here are the supported network file formats:
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Supported Network File Formats

1. You can start with networks provided as sample data distributed with the application
2. You can import a network using your data file (as text or xls) and just indicate your ID column as the “source” and leave type and “target” empty. This will give you a “network” of nodes with no connections.
3. You can also import networks from external databases:
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Importing Networks and Attributes from External Databases

There are only very specialized tools for turning specific datasets into networks. Most people come to Cytoscape with networks already or have their favorite network sources (e.g., PathwayCommons, WikiPathways, Protein interaction databases, etc)

 - Alex

On 9/21/11 8:40 AM, "lbuon...@tin.it" <lbuon...@tin.it> wrote:

Thanks for your reply.

The problem is that it is not very clear how to make the Network.

Luigi

----Messaggio originale----
Da: ap...@gladstone.ucsf.edu

Data: 21-set-2011 17.26
A: "lbuon...@tin.it"<lbuonaguro@tin.it>
Ogg: Re: HELP FOR CYTOSCAPE!!!!

Cytoscape is a network visualization tool. Without a network you will see nothing. Loading data without a network will show you nothing in Cytoscape.

I highly recommend that you start with the basic tutorials available from the website. These will help you step by step.

I don't have time for a Skype meeting this week.

 - Alex

On Sep 21, 2011, at 3:26 AM, "lbuon...@tin.it" <lbuon...@tin.it> wrote:

Alex,

I wrote to you few weeks ago about our problems with Cytoscape, which have not been solved.

Let me start from the beginning.

We have downloaded the latest version available at the Cytoscape website (2.8.2). Obviously, we do not have a network file. Therefore, ss indicated in the Manual, we have imported the file galExpData.pvals using the path: File, Import, Attribute from Table.

After identifying the individual columns (gene, common,....), NO KEY ATTRIBUTES ARE SHOWN IN THE WINDOW at bottom left of the page. IS THIS NORMAL?
Moreover, when we select the import button, NOTHING IS IMPORTED.

CAN YOU HELP US? WE ARE UNABLE TO MOVE FORWARD.

I have sent you an invitation through SKYPE. Please, accept it. Talking would be much simpler to explain. I promise, I will not bother you more than necessary.

Best

Luigi
  



----Messaggio originale----

Da: ap...@gladstone.ucsf.edu <mailto:ap...@gladstone.ucsf.edu>

Data: 21-set-2011 0.34
A: <cytoscape...@googlegroups.com>
Ogg: Re: [cytoscape-helpdesk] Cytoscape splash screen and plugin loading

The splash screen disappears when all plugins are loaded and Cytoscape is
initialized. You can simply wait for it to disappear.

Or, do you mean how to detect programmatically as a plugin developer?

- Alex


On 9/20/11 3:07 PM, "ranjman" <ran...@gmail.com> wrote:

> I'm not sure how best to wait for Cytoscape to finishing loading and
> the intro/splash screen to disappear before loading my file (via a
> plugin menu). Is there a way to check for the splash window at
> startup?
>
> Any suggestions would be appreciated.
> Thanks

------ End of Forwarded Message