cytoscape-helpdesk Google Group

RE: [cytoscape-helpdesk] loading excel data

allan_kuchin...@agilent.com — Sun, 29 Nov 2009 16:49:09 UT

The best way to get such networks is to use Cytoscape's Web Service Client Manager. This is described in the Cytoscape Help Document in the section entitled "Importing Networks and Attributes from External Databases". Here is one example using the IntAct database

Example #1: Retrieving Protein-Protein Interaction Networks from IntAct

loading excel data

ge2sa...@gmail.com (Gema) — Sat, 28 Nov 2009 12:04:13 UT

Hi, i´m new in cytoscape and i don´t know exactly how to upload my
dataset because i only have a protein list from a 2D-PAGE experiment
and i´d like cytoscape to show a network with my proteins list. I don
´t have previous knowledge about how interact my proteins among them
so I cant select source colum and target colum in the input dataset

Re: [cytoscape-helpdesk] Spring Embedded Bug 0002089

scoo...@cgl.ucsf.edu (Scooter Morris) — Mon, 23 Nov 2009 04:56:54 UT

Rono wrote:
Hi Rono,
The main recommendation I made in the bug was to use Force Directed,
which uses significantly less memory. There is no real way to fix the
out-of-memory problem, but I did fix it so that it doesn't throw an NPE
exception. The fix will be in the next release of Cytoscape - 2.7.0, or

Spring Embedded Bug 0002089

ronome...@network-ta.com (Rono) — Sat, 21 Nov 2009 04:58:06 UT

I'm seeing this bug with 2.6.3, so I searched the Bug Tracker and
found a description there. The problem is that the last update says
that it's been fixed, but there's no instructions, notes, or downloads
to implement the fix. Ho do I fix the spring embedded function?

Re: How to edit a file of edge attributes

zhaoyouwen1...@yahoo.com.cn (betty) — Sat, 21 Nov 2009 10:47:24 UT

I was so carless that I forgot to type a white space between the
sourece protein and the open parenthesis.After I corrected the error,I
imported the file successfully.

Re: How to import attribute from a file

zhaoyouwen1...@yahoo.com.cn (betty) — Sat, 21 Nov 2009 10:43:33 UT

I'm so soory.I was so carless that I forgot to insert a white space
between the source protein and the open parenthesis,which made the
file not be read correctly.
Thanks for the patient help.

How to edit a file of edge attributes

zhaoyouwen1...@yahoo.com.cn (betty) — Sat, 21 Nov 2009 08:38:08 UT

I am a new user of cytoscape. I edited a file of node attributes:
primarykey alias expressionstrength
a1 b1 0.3
a2 b2 0.4
a3 b3 0.5
The format is .xls.Then I imported the file sucessfully.But I came
across some problems when I tried to import a file of edge attributes:

Re: How to import attribute from a file

piet....@gmail.com (piet molenaar) — Thu, 19 Nov 2009 12:10:23 UT

Hi Betty,
I'm replying to your question via the helpdesk list;
as I stated already the id for an edge is in the format
nodeAId [space] (interactiontype) [space] nodeBId
In your primary key column the spaces are lacking:
a1(pp)a2 -> a1 (pp) a2
cheers,
Piet

--
Piet Molenaar
p.molen...@amc.uva.nl

Re: [cytoscape-helpdesk] Re: How to import attribute from a file

piet....@gmail.com (piet molenaar) — Thu, 19 Nov 2009 08:41:38 UT

Hi,
See here for supported network fileformats;
[link]

By far the easiest way however is to use import>File from Table (text/ms
excel):
[link]

Re: [cytoscape-helpdesk] Re: GML file w/ node coordinates

johannes.helm...@gmx.de (Johannes Helmuth) — Thu, 19 Nov 2009 01:13:17 UT

hey,

i appended two files (due to the 4MB restriction of this mailing list):
yEd.displayed.graph.jpg:export ed graph von yEd
input.graph.gml:the input graph

cheers

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Re: [cytoscape-helpdesk] Re: GML file w/ node coordinates

msm...@ucsd.edu (Mike Smoot) — Thu, 19 Nov 2009 00:24:02 UT

Can you send us the file in question and perhaps a screenshot of yEd with
what you expect to see?

thanks,
Mike

--
______________________________ ______________________________
Michael Smoot, Ph.D.
UCSD Department of Medicine
tel: 858-822-4756

Re: GML file w/ node coordinates

johannes.helm...@gmx.de (Johannes) — Thu, 19 Nov 2009 00:00:55 UT

for smaller gmls it just works fine. whats the matter?

Re: How to import attribute from a file

nit...@gmail.com (nitbio@gmail.com) — Wed, 18 Nov 2009 23:08:53 UT

Hello Bettey and Piet,

I am getting the same problem as Betty is. I do not know how to work
this problem out. I want to color my nodes on the basis of the
interactions strength but is not able to do it. Would be really great
if Piet could you send us a file format which we can download and run

Re: [cytoscape-helpdesk] Re: python scripting

david...@umich.edu (David Lawrence Epstein) — Wed, 18 Nov 2009 21:20:58 UT

Hi Keiichiro,

Thank you for your earlier response. I'm looking through the javadocs.
Are there more example scripts online or available besides those
listed at the site:

[link]

I may be able to do more if I can see how others have accomplished

Re: [cytoscape-helpdesk] How to import attribute from a file

piet....@gmail.com (piet molenaar) — Wed, 18 Nov 2009 15:21:13 UT

Hi Betty,
From the manual (
[link]
):

Edge names are all of the form:

sourceName (edgeType) targetName

Specifically, that is

*Table 10. *

sourceName space openParen edgeType closeParen space targetName