tool that supports level3 pathway visualization ...

[D Ashok Reddy]

Hi,

I would like to know the tool that supports BioPAX (level3) pathway
visualization.

Thanks,
Ashok

[Ozgun Babur]

Hi Ashok, ChiBE supports BioPAX L3. Its source code is available at
sourceforge. Which operating system are you using? I can create a
build for you with the latest sources.

Ozgun

[D Ashok Reddy]

Thanks you Ozgun.

I use windows and Ubuntu.

> > Ashok- Hide quoted text -
>
> - Show quoted text -

[Gary Bader]

Hi Ashok,
Cytoscape 2.7 also supports level 3 import (File->Import->Network).

Cheers,
Gary

http://baderlab.org
Donnelly Centre for Cellular and Biomolecular Research
University of Toronto - http://www.thedonnellycentre.utoronto.ca/

[D Ashok Reddy]

Hi Gary,

It is working with level2 files, but if I import Reactome (level3) and
Molecule Pages (level3) files, an error showing that 'Pathway is
empty!'.

Thanks,
Ashok

[Augustin Luna]

Hi Ashok,

Pathvisio has a plugin (http://pathvisio.com/wiki/BiopaxPluginHelp) in
beta stage that supports BioPAX L3.

Augustin Luna

[Igor Rodchenkov]

Hi Ashok, hi everybody,

Thanks for your question! Just downloaded Cytoscape 2.7.0 release, run, 

found two problems and how to fix them:

1. Reactome BioPAX L3 files contain 'bp:taxonXref' (BioSource's) property. This should be changed to 'bp:xref' (you can do manually)

(this is a fresh change, since BioPAX L2 v1.0 release, and I suspect this is going to be problem for many new BioPAX L3 files)

2. replace the core BioPAX plugin (biopax.jar) with the attached new one ;)

Let me know if it helps and if you have more questions. 

Cheers,

Igor.

--
Igor Rodchenkov
UofT
baderlab.org, biopax.org, pathwaycommons.org

[Igor Rodchenkov]

Please replace this Cytoscape plugin (PathwayCommons) as well: http://sourceforge.net/projects/biopax/files/cy_plugins/cpath2.jar/download

Igor R.

---------- Forwarded message ----------
From: Igor Rodchenkov <rod...@gmail.com>
Date: Thu, Aug 26, 2010 at 3:48 PM
Subject: Re: tool that supports level3 pathway visualization ...
To: dar...@gmail.com

Another fix for the core BioPAX plugin, biopax.jar: 

http://sourceforge.net/projects/biopax/files/cy_plugins/biopax.jar/download

(fixed: duplicate phys.entity nodes were created when importing biopax L2 data; - a bug introduced by the previous update...)

26-AUG-2010

Sorry...

--
Igor Rodchenkov
UofT