Install Cytoscape  Back to Top

Download and install Cytoscape v2.6.3 (v2.6.0 or above required) from here.

Install MetScape  Back to Top

There are several ways to install MetScape. You can use any one of them. Please click here for more information.

Startup Cytoscape  Back to Top

For Windows:
Click Start->All Programs->Cytoscape->Cytoscape OR you can go to Cytoscape/plugins directory, double click cytoscape.bat or cytoscape.exe.

Use MetScape  Back to Top

You need to install Cytoscape with MetScape on your computer before using MetScape if you have not done this before.

Startup Cytoscape ->click Plugins->MetScape->Build Network, you will see an input dialog box. There are three ways (corresponding to three tabs on MetScape main window) to generate compound networks.



Enter Compounds   Back to Use MetScape

Enter compounds, one per line. You can choose to search by "Compound Names" or "KEGG IDs" from drop down list of "Input Type". There are two radio buttons on the dialog box. If button "CR" is checked, both compounds and reactions are shown as nodes in network. Otherwise, if "CO" is checked, only compounds will be shown as nodes and reactions will be shown as edges. Click "Compound Lookup" button to browse all compounds. You can drag and drop compounds to MetScape input dialog box.

MetScape Tutorial Image 1



Feature 1: Show Attributes

Double click on a compound or reaction node, the details of the compound or the reaction will be shown on the Cytoscape result panel.

If reactions are shown as edges, double click on an edge, the reaction attributes will be shown on result panel.

MetScape Tutorial Image 2


Feature 2: Expand Network/Collapse Network

MetScape Tutorial Image 3


Feature 3: Mouse Over


Feature 4: Create Sub Network

Right click on a node to show the pop up menu, click "MetScape->Create Subnetwork", all highlighted nodes (yellow) and edges (red) will be displayed in a new window as a sub network.

MetScape Tutorial Image 4


Load Experiment File  Back to Using MetScape

Go back to MetScape input dialog box. Choose "Load Experiment File" tab, then click the button to choose a file to load. For input file with wide data range, you can choose to log the input data or scale the data from 0 to 10 to get better visualization result. The default option is "Original data". Please take a look of the file format, samples and data scale method used in MetScape.

Feature 5: Dynamic Expression

MetScape Tutorial Image 6


Feature 6: Pathway Filter

Right click on any node to get the pop up menu. Click MetScape->Pathway Filter. You will get a pathway list on the left panel. Choose pathway(s) and click Filter, Reactions that are involved in these pathways will be highlighted. Click "create subnetwork" button to create a pathway specific network on a new window.

MetScape Tutorial Image 7



Show Pathway  Back to Using MetScape

Click Show Pathway tab->expand drop-down menu->choose a pathway, at the top of list, you can choose "All" to show all pathways.

You will get all reactions in the pathway. Double-headed arrow means the reaction is reversible. You can change the radio buttons to show all compounds or only main compounds (default), show reaction as node or edge (default).

MetScape Tutorial Image 8


Top of Page