VERSION 1.5 OF THE CYTOSEED PLUGIN WAS RELEASED ON FEBRUARY 24, 2015. SEE BELOW FOR DIRECTIONS FOR UNINSTALLING PREVIOUS VERSIONS AND INSTALLING VERSION 1.5.
Cytoscape Model SEED Plugin (CytoSEED) README
Installation:
1) Download and install Cytoscape 2.8.3 from http://www.cytoscape.org. The CytoSEED plugin is not compatible with earlier versions of Cytoscape.
2) Download the CytoSEED plugin from http://sourceforge.net/projects/cytoseed. Start the Cytoscape application and install the CytoSEED plugin by clicking on the Plugins -> Install Plugin from File menu item; then browse to and select the CytoSEEDplugin.jar file that you downloaded.
3) In order to format the KEGG maps properly, you must also install the KGMLReader plugin, which is available from within the Cytoscape application. Click on the Plugins -> Manage Plugins menu item; in the box labeled "Enter key words to search", type "kgml", then click on the "Search" button. Click on the arrow beside the "Network and Attribute I/O" folder, select the latest version of the KGMLReader plugin, and click on "Install".
4) If you installed both plugins correctly, you will now see new menu items listed under the Cytoscape Plugins menu as KGML Reader and SEED. Select the Plugins -> SEED -> Set Location of CytoSEED Folder menu item, and choose a location where the plugin can create a new folder named CytoSEED that will store the model and KGML data. Next you will be prompted to download the KGML files from KEGG; click on "Yes". This will take a few minutes. If there are problems with the download, you can restart it at any time from the Plugins -> SEED -> Download KGML Files From KEGG menu item.
Hot-keys "Cheat Sheet"
- Ctrl+Shift+L -- Load model and create session
- Ctrl+Shift+O -- Reopen model session
- Ctrl+Shift+S -- Save model session as
- Ctrl+S -- Save model session
- Ctrl+Shift+M -- Choose media
- Ctrl+H -- Hide selected nodes
- Ctrl+Shift+Z -- Zoom out to display entire current network
- Ctrl+Shift+T -- Tile all maps (Tiled view of all networks)
TO UNINSTALL CYTOSEED v.1.0 IN ORDER TO INSTALL A NEW VERSION:
In Cytoscape, use the "Plugins->Manage Plugins" menu item. Type "cytoseed" in the search box and click on Search. Open the Analysis folder and select "CytoSEED v.1.x" and click Delete. Restart Cytoscape and repeat the installation procedure above with the new version of CytoSEED.
Questions/Problems/Suggestions:
- If you have any questions, problems, or suggestions, please contact dejongh {at} hope.edu.
Licenses
- CytoSEED is released under the GNU General Public License.
