Cytoscape
Cytoscape can read network/pathway files written in the following formats:
- Simple interaction file (SIF or .sif format)
- Nested network format (NNF or .nnf format)
- Graph Markup Language (GML or .gml format)
- XGMML (extensible graph markup and modelling language).
- SBML
- BioPAX
- PSI-MI Level 1 and 2.5
- Delimited text
- Excel Workbook (.xls)
Styles
Customising the way you visualise and manipulate networks is a key function of Cytoscape. This is achieved through the use of Styles:
The Style interface exists as a tab in the Control Panel and is divided into 3 tabs, for Node, Edge and Network properties. For each property, there are 3 columns describing the current Default (meaning the default value for the current mapping), Mapping and any Bypass. A pre-defined set of properties is displayed by default. Additional properties for display can be selected by clicking the Properties drop-down at the top of the list of properties. The Styles interface also lists any pre-defined styles in the drop-down at the top of the interface. The below figures shows the default style for the galFiltered session file.