PSICQUIC Client Plugin for Cytoscape Quick Start

News

  • 3/13/2014: Now PSICQUIC Client is a built-in core feature in Cytoscape 3.1. You do not have to install plugins to use it.
  • 6/1/2012: New Cytoscape Plugin version 0.31 released. This update is recommended for all current users. Please use with latest version of Cytoscape (2.8.3).
    • Smart Label - Plugin adds more human-readable gene names to the node
    • Color coding based on species name
    • Bug fixes for edge score import function
  • 5/30/2012: Now PSICQUIC Client is part of Cytoscape 3 core!
  • 7/28/2010: version 0.25 released. This is compatible with Cytoscape 2.7.0 or later.

Introduction

http://psicquic.googlecode.com/svn/wiki/images/cytoscape_client_docs/cytoscape_client_31_ss1.png

Cytoscape is an open source platform for general network data integration, analysis, and visualization. It is widely used in systems biology community and is expandable by plugins. PSICQUIC Universal Client is a Cytoscape plugin for querying multiple PSICQUIC-compliant interaction data services from a simple user interface.

The advantage of using PSICQUIC services with Cytoscape client is you can save your work as a snapshot (session file) and also you can use its powerful visualization features. For more information about Cytoscape, please visit official web site.

Overview of Client User Interface

http://psicquic.googlecode.com/svn/wiki/images/cytoscape_client_docs/cytoscape_client_31_ss2.png

PSICQUIC Client for Cytoscape is a part of Cytoscape's web service client framework. You can access PSICQUIC databases just like other clients. From a single window, you can send your query to all of registered PSICQUIC services at once.

How to Use PSICQUIC Client

Install Plugin

The PSICQUIC Client Plugin is compatible with Cytoscape 2.7.0 or later. If you have older versions, please download the latest version. The Plugin is available from Cytoscape Plugin Manager. Select Plugin-->Manage Plugins and then you can find the plugin under Network and Attribute IO section --> PSICQUICUniversalClient

Start Plugin

To start the plugin, select the client from File-->Import-->Network from web services.... If PSICQUIC client is properly installed, you can find it in Data Source combo box:

http://psicquic.googlecode.com/svn/wiki/images/cytoscape_client_docs/data_source_box.png

Query Services

http://psicquic.googlecode.com/svn/wiki/images/cytoscape_client_docs/query_mode.png

There are two search modes in the client:

  • Search by Interactor ID
  • Search by Query (MIQL)

You can switch the mode from Search Property tab.

Search by Interactor ID(s)

In this mode, Cytoscape sends list of identifiers as query. You can simply copy and paste list of identifiers to the text box. After the search process, it pops up the following window:

http://psicquic.googlecode.com/svn/wiki/images/cytoscape_client_docs/search_result1.png

In this window, you can select which data sets you want to import. If the result is 0 or the service is inactive, it will be ignored. When the import process finished, you can edit the network titles in the following window:

http://psicquic.googlecode.com/svn/wiki/images/cytoscape_client_docs/import_result1.png

If you press Merge button, Advanced Network Marge plugin will be started and you can merge imported networks manually.

Search by MIQL

This mode supports MIQL syntax. You can simply type the query in the text field. For more information about MIQL, please read the reference page.

PSICQUIC Client in Cytoscape 3

The newly architectured Cytoscape 3 is now in developer beta status and PSICQUIC client feature is a built-in function from this version. To try the new version, please visit here.

Need Help?

Please join our user mailing list. All core developers of Cytoscape are available to answer your questions.

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