Social Network Logo

Social Network App Download Page

Brief Description

The Social Network Cytoscape app creates a visual summary of how individuals are connected. Biological networks can be visualized and analyzed using Cytoscape. Often researchers want to go beyond the network of proteins or genes and also look at the inter-connectedness between colleagues and institutions. Who tends to publish together? What institutions are most collaborative? Are there inter-disciplinary connections in my institution? The app addresses these questions by building co-publication networks where the nodes represent authors, edges represent co-authorship and edge thickness represents how frequently co-authors collaborate.


The Social Network App only runs on the latest version of Cytoscape (Cytoscape 3.x). Instructions for downloading and installing Cytoscape 3.x can be found HERE.

Once Cytoscape 3.x is installed and running:

Voila! The app should now be installed.

Launching The App

In Cytoscape 3.x:

A new panel called Social Network will pop up on the left side of Cytoscape.

Getting Started

Social Network App User Panel (PubMed Search)

The Social Network App is divided into three main sections (Search, Information, Network):

  1. PubMed Search: Enter the key-word or query you want to build a network out of here (i.e. an author's last name and first initial).

  2. Max authors per pub: Specify the maximum number of authors you require in a publication here. Limit is set to 500 by default. This means that publications containing more than 500 authors will not be visualized by the app. Setting the limit to a high value increases the computational demands of the app and is therefore not recommended.

  3. Time Interval: Specify the time interval here. By default the maximum date is set to the current year and the minimum date is set to five years before the current year.

  4. Create Network: Once you've provided all the required information (i.e. Load File and Specify Network Name), click here to create your network. If the information you provided is found to be lacking, the app will notify you of this, and offer tips on how to remedy the situation.

  5. Network Summary Section: In this section, a summary of the network's attributes is provided:

    • # of nodes and edges in the network
    • Type of the network (InCites, Scopus or PubMed)

    • Various other attributes (i.e. a list of any unidentified faculty).

File Input

Social Network App User Panel (File Input)

  1. Select Database: Select a database here. There are only three databases available. As stated above, the Social Network App only supports reports generated by Incites, PubMed and Scopus at the moment.

  2. Load File: Provide a path to your data file here. To load a data file, click on the button marked (...). Here are some example files: InCites, PubMed, Scopus,

  3. Specify Network Name: Specify the name of your network here.

User Guide

Link to User Guide


Setting up Eclipse (or other IDE) for development of the app


Social Network App User Panel

Social Network App User Panel

Social Network App User Panel

Social Network App User Panel

Software/SocialNetworkApp (last edited 2015-10-08 00:16:32 by kofiav)

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