CyKEGGParser

KEGG pathway tuner: accurate, tissue- and protein-protein interaction-specific pathways
CyKEGGParser operates on pathways derived from the KEGG pathway database. Along with basic functionality of parsing and visualization of KEGG pathway maps in Cytoscape, it provides an option for semi-automatic correction of inconsistencies between KEGG static pathway images and accompanying KGML files, tissue-specific and protein-protein interaction (PPI) based tuning of the pathways, and exporting them in KGML and BioPAX formats. Please, feel free to tell us about any bug you find or an issue you face while using our app! Please, cite us with the link to our paper: http://f1000research.com/articles/3-145/v2

1.2.7

Works with Cytoscape 3.0

Release Notes

Database issue fixed for PPI tuning \\*** PPI database location has changed. Please, update CyKEGGParser to the this latest version!

1.2.6

Works with Cytoscape 3.0

Release Notes

User Manual updated. Tuning GUI updated.

1.2.5

Works with Cytoscape 3.0

Release Notes

Overwrite for sudden 1.2.4 upgrade. Sorted organism and pathways lists for more convenient web-retrieval.

1.2.4

Works with Cytoscape 3.0


1.2.3

Works with Cytoscape 3.0

Release Notes

Minor bug-fix for KGML-safety; supports KGML "coords" attribute parsing.

1.2.2

Works with Cytoscape 3.0

Release Notes

1. New options for tissue-specific and PPI based tuning 2. More detailed log for tissue-specific tuning. 3. Minor bug fix for BioPAX conversion. 4. Compatible with Java1.6 as well.

1.2.1

Works with Cytoscape 3.0

Release Notes

Bug fixed: platform independence for BioPAX conversion

1.2.0

Works with Cytoscape 3.0

Release Notes

New functionality: ability to convert KEGG pathways to BioPAX format. Several bug fixes and some improvements done in tissue-specific tuning, web-based loading, visual style and saving.

1.1.2

Works with Cytoscape 3.0

Release Notes

Minor bug fixes for tuning.

1.1.1

Works with Cytoscape 3.0

Release Notes

Database retrieval for protein-protein interaction based tuning is considerably sped up.

1.1.0

Works with Cytoscape 3.0


1.0.0

Works with Cytoscape 3.2


CYTOSCAPE 3

Version 1.2.7

License Click here

Released 17 Jun 2015

Works with Cytoscape 3.0

Download Stats Click here

CYTOSCAPE 2

Version 1.3

Released 14 Feb 2014

Works with Cytoscape 2.8

Download Stats Click here