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3. Importing data from from public databases. 4. Creating an empty network and manually adding nodes and edges. Import Fixed-Format Network Files. The Cytoscape User Manual copyright is owned by The Cytoscape Consortium, and is made available 3. Command Line Arguments · 4. Quick Tour of Cytoscape. Cytoscape 3.0.1 User Manual . This manual describes the installation and use of Cytoscape. 3. Cytoscape_3/UserManual 3. Importing networks from Web Service. 4. Creating an empty network and manually adding nodes and edges. Import Fixed-Format Network Files. Nature Methods paper by Cytoscape Consortium - a quick overview of Cytoscape App (Plugin) universe. Original Cytoscape paper (2003). User Manual. 3.x HTML 3. Importing networks from Web Service. 4. Creating an empty network and manually adding nodes and edges. Import Fixed-Format Network Files. This project contains the complete user manual for Cytoscape 3. There are versions of the manual based on specific versions of Cytoscape.