Tutorial:Introduction to Cytoscape 3-part3

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This tutorial is not up-to-date. All Cytoscape tutorials are now hosted at tutorials.cytoscape.org.

This tutorial will describe how to get started with importing networks in Cytoscape 3. There are many options for loading networks in Cytoscape, ranging from importing locally stored networks in a variety of formats, loading example networks, and building a network from public databases.

Welcome Screen

When first launching Cytoscape, you will see the Welcome to Cytoscape screen. The welcome screen is also available under Help → Show Welcome Screen....


The welcome screen is designed to help you quickly get started with Cytoscape 3 by giving you quick access to network import options and user resources like tutorials and manuals.

On the left side of the welcome screen, there are several options for starting a new session:

  • With Empty Network: This option lets you create a new empty network. Choose this option if you want to manually create a network from scratch.
  • From Network File: This option lets you import a network file in a variety of file formats: SIF, NNF, GML, XGMML, SBML, BioPAX, PSI-MI Level 1 and 2.5, Delimited text and Excel Workbook. For details on supported file formats, please refer to the manual. Choose this option of you have a local network file. For more details on network file import, see Loading a Simple Network.
  • From Network Database: This option lets import a network using either Interaction Database Universal Client (formerly PSICQUIC) or Pathway Commons Web Service Client. Choose this option if you want to analyze public network data or if you have a specific gene or set of genes you want to find interactions for. Details below.
  • Organism Networks: The set of icons underneath From Network Database represent a set of networks from model organisms taken from BioGRID.

On the right side of the welcome screen are a couple more options for loading existing sessions:

  • Open Recent Session: This is a list of all of the session files you have opened, in reverse chronological order. Note that "Sample Yeast Network" is always present and provides access to galFiltered.cys, which is often used to demonstrate Cytoscape features.
  • Open Session File: Allows you to browse your filesystem for Cytoscape session files to load.

From Network Database

Selecting the From Network Database option opens the Interaction Database Universal Client interface:

  • In the top section, enter your search conditions, i.e. the gene or set of genes you are interested in, for example "BRCA2".
  • In the Search Mode drop-down, you can also change the mode of the search to Search Interactome, which allows you to search for an entire interactome by species, and Search by Query Language (MIQL), which allows you to search using the Molecular Interaction Query Language.
  • The Select Database section will display available databases. After initiating the search by clicking Search in the Enter Search Conditions the results of the search will be visible in the Records Found column:
  • In the Select Databases section, select/deselect database results using the check box in the Import column. Click Import when ready.

You can choose to import all interactions, or choose a subset by deselecting resources from the list. Click 'Import to import the resulting network.

The Interaction Database Universal Client is also available under File → Import→ Public Databases....