Fwd: BiNoM Plugin v2.0 released. Supports BioPAX Level 3

[B. Arman Aksoy]

Hi all,

For those of you who missed the news on the latest BiNoM Plugin release, here is some interesting news: https://twitter.com/#!/cytoscape/status/195591417853263872

[IgorRodchenkov]

In v2.8.1, if it's installed, then the core BioPAX plugin does not work (File->Import->Network (Multiple...) fails), but you can open a BioPAX file via Plugins->BiNoM I/O menu; when this plugin is removed, the core BioPAX works again 

(Paxtools parser conflicts with this plugin for some reason...)

IR.

[Eric]

Igor,

I've tried to load a BioPAX 3 file with cytoscape 2.8.2, without the BiNoM plugin installed, and it fails with an error message like this:

cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed: org.biopax.paxtools.util.BioPaxIOException: XMLStreamException ParseError at [row,col]:[11929,70] Message: Invalid byte 2 of 2-byte UTF-8 sequence.; Line number = 11929 Column number = 70 System Id = null Public Id = null Location Uri= null CharacterOffset = 920909 When the BiNoM plugin is loaded, it also fails to a BioPAX 3 file. Not sure why and where there would be a conflict... Eric

[Eric]

hi there,

I'm the current maintainer of the BiNoM plugin.

I tried with Cytoscape 2.8.2 to import a BioPAX3 file, without the
BiNoM plugin installed, but it fails with the error:

cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed:
org.biopax.paxtools.util.BioPaxIOException: XMLStreamException
ParseError at [row,col]:[11929,70] Message: Invalid byte 2 of 2-byte
UTF-8 sequence.; Line number = 11929 Column number = 70 System Id =
null Public Id = null Location Uri= null CharacterOffset = 920909

It also fails when the BiNoM plugin is loaded, with a different error
message though.

Eric

[IgorRodchenkov]

Hi Eric,

This is a different issue; - can be another bug, wrong file, or char encoding problem (must be "UTF-8", and if it's not your system default, 

try setting the Java option: -Dfile.encoding=UTF8 within the cytoscape script). 

Anyway, please try using one of simple examples at http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Level3/examples  (e.g., http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/raw-file/1356d2be5943/Level3/examples/biopax3-short-metabolic-pathway.owl) first.

Let me know how's going.

Regards,

Igor R.

On Friday, May 4, 2012 5:53:46 AM UTC-4, Eric wrote:

hi there,

I'm the current maintainer of the BiNoM plugin.

I tried with Cytoscape 2.8.2 to import a BioPAX3 file, without the
BiNoM plugin installed,  but it fails with the error:

cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed:
org.biopax.paxtools.util.BioPaxIOException: XMLStreamException
ParseError at [row,col]:[11929,70] Message: Invalid byte 2 of 2-byte
UTF-8 sequence.; Line number = 11929 Column number = 70 System Id =
null Public Id = null Location Uri= null CharacterOffset = 920909

It also fails when the BiNoM plugin is loaded, with a different error
message though.

Eric

On 3 mai, 22:51, IgorRodchenkov <rod...@gmail.com> wrote:
> In v2.8.1, if it's installed, then the core BioPAX plugin does not work
> (File->Import->Network (Multiple...) fails), but you can open a BioPAX file
> via Plugins->BiNoM I/O menu; when this plugin is removed, the core BioPAX
> works again
> (Paxtools parser conflicts with this plugin for some reason...)
>
> IR.
>
>

> ...

[Eric]

Hi Igor,

Thanks for your indications. I've modified the cytoscape startup as you indicated (via the Cytoscape.vmoptions file; I'm using a Linux Debian box). Now I can import the "canonical" files you've mentionned in your previous email. But it still fails on a biopax3 file exported from Reactome with the following message:

cytoscape[WARN]: Could not find RVC: cytoscape.visual.mappings.rangecalculators.StringRangeValueCalculator@b92a848
1	cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed: java.lang.NullPointerException
2	cytoscape.Cytoscape[WARN]: Network reader didn't return any nodes
3	cytoscape.Cytoscape[WARN]: Network reader didn't return any edges
4

cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed: org.biopax.paxtools.util.BioPaxIOException: XMLStreamException ParseError at [row,col]:[11929,70] Message: Invalid byte 2 of 2-byte UTF-8 sequence.; Line number = 11929 Column number = 70 System Id = null Public Id = null Location Uri= null CharacterOffset = 920909

5	cytoscape.Cytoscape[WARN]: Network reader didn't return any nodes
6	cytoscape.Cytoscape[WARN]: Network reader didn't return any edges
7

cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed: org.biopax.paxtools.util.BioPaxIOException: XMLStreamException ParseError at [row,col]:[11929,70] Message: Invalid byte 2 of 2-byte UTF-8 sequence.; Line number = 11929 Column number = 70 System Id = null Public Id = null Location Uri= null CharacterOffset = 920909

8	cytoscape.Cytoscape[WARN]: Network reader didn't return any nodes
9	cytoscape.Cytoscape[WARN]: Network reader didn't return any edges

Looks like there is some string formatting error ...

Now if I load the BiNoM plugin and re-try to load one of the "canonical" files, it indeed fails with this error message:

cytoscape[WARN]: Could not find RVC: cytoscape.visual.mappings.rangecalculators.StringRangeValueCalculator@1629ce8c
1	cytoscape[WARN]: Could not find RVC: cytoscape.visual.mappings.rangecalculators.StringRangeValueCalculator@1629ce8c
2	cytoscape.coreplugins.biopax.util.BioPaxUtil[WARN]: Import failed: org.biopax.paxtools.util.BioPaxIOException: Unexpected element at start: 6
3	cytoscape.Cytoscape[WARN]: Network reader didn't return any nodes
4	cytoscape.Cytoscape[WARN]: Network reader didn't return any edges

So as you said there seems to be some sort of conflict. I'm willing to help but have no clue where this conflict might originate from. Maybe some library that both modules are using??

All the best,

Eric

[IgorRodchenkov]

Hi Eric,

Let's move our discussion in private (I'll reply to you), because there is nothing do discuss here (not BioPAX issue but rather Cytoscape app's one); so we'll just have to create a ticket and find a solution/fix to this technical issue.

Anyone interested, please email me or Eric directly or use Cytoscape issue trackers: http://cbio.mskcc.org/cytoscape/bugs/ (for versions 2.8.x) or http://code.cytoscape.org/redmine/projects/cytoscape3/issues (new v.3.x)

Igor R.

On Wednesday, May 9, 2012 3:53:04 AM UTC-4, Eric wrote:

Hi Igor,

Thanks for your indications. I've modified the cytoscape startup as you indicated (via the Cytoscape.vmoptions file; I'm using a Linux Debian box). Now I can import the "canonical" files you've mentionned in your previous email. But it still fails on a biopax3 file exported from Reactome with the following message:

...