Installation | App template | YAML syntax | Variable substitution | Batch mode | Data files | Demos

Step-by-step instructions to use our demos:

1. Install Cytoscape
2. Install CyToStruct:
   • Open Cytosccape
   • Open the "Apps->App Manager" dialog box
   • In the "search" box in the main dialog box write "CyToStruct"
   • Once CyToStruct is found, select it, and hit the "install" button
3. Install a molecular viewer of your choice. Our demos work with PyMOL, UCSF Chimera, and Jmol (only installed molecular viewers will run).
4. In our demo scripts, we use the commands "pymolwin" to run PyMOL, "chimera" to run UCSF Chimera, and java (with the JMol.jar) to run Jmol; to launch a browser, we run "iexplore". Thus, it is necessary that the locations of the executables be included in the PATH environment variable. To verify that the PATH was successfully updated, run any of these command names (e.g., "pymolwin") in a cmd window: the molecular viewer should launch properly.
5. For our demos, download the *zip files.
6. Each zip file includes a directory with several types of files:
   • a *.cys file, which is the Cytoscape network file; double-clicking on it should open the network in Cytoscape.
   • a yaml_configuration file for that demo (in valid YAML)
   • a *.sif file, which is the raw data of the list of connected nodes, used as input to Cytoscape to construct the network
   • a node data file and/or an edge data file, with node-specific and edge-specific data used by CyToStruct
   • structure files
7. Right-clicking on an edge/node should open a menu, and then you can select CyToStruct and the command you wish to run (only installed viewers will run).
8. The YAML script for this network can be viewed by selecting within Cytoscape the menu "Apps->Configure CyToStruct". A copy of the YAML configuration is provided in the yaml_configuration file in the directory of each example. If the configuration file was erased, it can be re-loaded using the 'load from file' button, or simply by copy-pasting the content of the file.

• Protein-Protein interaction

• Domain network -- an example of more complex scripts for edges. Introduce variable unwinding, residue selection, and aligning of the structures (in PyMOL, also showing the alignment on the sequences themselves). Note: the zip file is 213MB.

• Toy example (example 3 in our manuscript)

• Another extra toy example -- uses CyToStruct to open text files associated with nodes in a text editor.

• 4-node toy example (same YAML as the toy example above)