CySBGN


CySBGN - SBGN diagrams in Cytoscape

Introduction

CySBGN imports, modifies and analyzes SBGN diagrams in Cytoscape, offering thus the large palette of tools available in this platform and its plug-ins to networks and pathways in SBGN format.

CySBGN is mainly developed and maintained by Emanuel Gonçalves and Martijn van Iersel at Saez-Rodriguez Group at EMBL-EBI.

CySBGN is now published! If you use CySBGN please cite:

Goncalves, E. J. V., Iersel, M. V., & Saez-Rodriguez, J. (2013). CySBGN: A Cytoscape plug-in to integrate SBGN maps. BMC Bioinformatics, 14(1), 17. doi:10.1186/1471-2105-14-17

Download

Download and place the following jars files in plugin folder of Cytoscape (v2.8.3):

CySBGN v1.2 (4.5 MB) - latest version
CySBGN v1.2 depends on CySBML plug-in version 1.2 to support the automated generation of SBGN diagrams of SBML models. 

CySBML v1.2 (9.9 MB) - homepage
Remove sbml-reader-2.8.3-jar-with-dependencies.jar from plugin folder.

CySBGN Tutorial
Detailed step-by-step guides and examples of the applicability of CySBGN



CySBGN is also available in Cytoscape App and in Sourceforge.


Table of Contents



Running CySBGN

How to import

File -> Import-> Network (Multiple File Types)

After CySBGN is installed the user can import a SBGN diagram by clicking in File -> Import -> Network (Multiple File Types) and then select the respective SBGN-ML file (as shown in the figure below).

Example file can be downloaded here and a few other SBGN diagrams files can be downloaded here.



After the diagram is successfully imported during the first import the user will be prompted with an information dialog regarding the rendering limitations of Cytoscape that affects the visualization of the SBGN diagrams. This dialog can be disable by ticking the Don’t show me this again box.


Simplify Diagram

Plugins -> CySBGN -> Create Simplified Network...

To render the diagrams as close as possible to the original, CySBGN creates some auxiliary nodes and edges to overlap the Cytoscape limitations (e.g. invisible ports to allow a edge to connect with another edge). Although, this auxiliary shapes represent some limitations to the correct operability of Cytoscape analysis or display methods (e.g. in a shortest path algorithm the auxiliary nodes are considered as one step as well).

To avoid this a simplification method was created that removes these auxiliary shapes as well as complex or compartments SBGN entities. The image below shows how a user can preform the simplification of a previously imported SBGN diagram.



After the simplification a view is generated and can be seen side-by-side with the original SBGN diagram.



At this point a Layout algorithm can also be applied.

SBGN-ML validation

Plugins -> CySBGN -> Validate network SBGN-ML...

CySBGN by using libSBGN enables the users to perform a syntactic validation of SBGN-ML documents. The validation function is accessible under the CySBGN menu in the Plugins menu and runs a syntax validation of the SBGN-ML file used to import currently selected SBGN-ML diagram.

Any issue found with the SBGN-ML file is listed in the Data Panel (bottom panel) in the CySBGN-Validation tab.

Automatic generation of SBGN diagrams from SBML models

Plugins -> CySBGN -> SBML to SBGN...

After installing CySBGN and CySBML plug-ins correctly (check CySBGN tutorial for detailed instructions) the user can complement SBML model visualization with an automated generated SBGN diagram of the model.

Through Plugins -> CySBGN -> SBML to SBGN... the user can select a SBML model and generate the respective SBGN diagram.
	The conversion process may take awhile

Since we are dealing with automated generation of diagrams the layout may need some manual correction. Here the overlapping nodes were moved to be completely visible. SBML model link.

Selected node information is visible in the Results Panel (right side panel) in CySBML tab, also Data Panel (bottom panel) shows SBML and SBGN node’s attributes.

	Some attributes may be hidden. Click Select All Attributes (  ) button to visualize all the attributes

The user can also take advantage of BioModels database as a resource of SBML models (check CySBGN tutorial for more details).

The example model mentioned above can be downloaded directly from the links below:

Screenshots

Central Plant Metabolism (libSBGN example file)



Using NetMatch plugin with SBGN diagrams



Using CytoHubba plugin with SBGN diagrams



Several examples of Entity Relationship Diagrams





CySBGN rendering comparison

CySBGN rendering can be compared here with other SBGN complaint tools. We re-used an extensive set of test cases covering the three supplementary languages of SBGN to validate the rendering of CySBGN.


CySBGN rendering comparison link



FAQ

Can I generate a SBGN diagram file (SBGN-ML file format) from a SBML model?

Yes. In CySBGN menu (under plugins menu) select SBML to SBGN, pick the desired SBML model and the SBGN file will be automatically generated and stored with the same name as the SBML file but with .sbgn extension.

Help me filling this section! Mail me your questions.

EBI - Saez-Rodriguez Group - link
Systems Biology Graphical Notation - link
Cytoscape - link
libSBGN - link
Systems Biology Format Converter - link
CySBML - link
BioModels database - link

CySBGN created by Emanuel Goncalves (emanuel@ebi.ac.uk)
Latest version 1.2 (26/11/2012)