IDARE

IDARE is a Cytoscape 3 app (versions 3.4 and above), for subnetwork generation and data visualisation.

Features

• Automated layouting of data using a variety of layout types
• Available visualisation types include scatter plots, graphs, heatmaps, time series and bar charts
• Parseable formats include excel sheets, tab/comma separated value files and GEO SOFT files
• Generation of connected subnetworks and clickable links between these networks
• Addition of gene nodes and further information based on information from COBRA annotations in sbml files (see Schellenberger et al 2011 )

Availability

Cytoscape App store: http://apps.cytoscape.org/apps/IDARE
Compiled JAR https://github.com/sysbiolux/IDARE/releases/
Current available plugins https://sysbiolux.github.io/IDAREPlugins/
User Manual https://github.com/sysbiolux/IDARE/blob/master/UserManual.pdf
Example/QuickStart https://sysbiolux.github.io/IDARE-QuickStart
API: https://sysbiolux.github.io/IDARE/API
Source Code: https://github.com/sysbiolux/IDARE
Bug Tracker: https://github.com/sysbiolux/IDARE/issues

Installation

There are three options available:

• Use the Cytoscape Application manager. In Cytoscape open Apps → App Manager → Install Apps and search for IDARE.
• Download the Jar from the Cytoscape App store
• Download the Jar from the Github
  If you download it manually put it into the apps/installed folder of your Cytoscape configuration folder (commonly %HOME/CytoscapeConfiguration/3/apps/installed).

Building

To build the app, you will need to also download the cy3sbml app (http://apps.cytoscape.org/apps/cy3sbml). Determine the path of the jar file (likely in the CytoscapeConfiguration folder in your home directory) and install it to your maven repository.

mvn -e install:install-file -Dfile=cy3sbml-v0.3.0.jar -DgroupId=org.cysbml -DartifactId=cy3sbml -Dversion=0.3.0 -Dpackaging=jar

Adjust the X to the version you downloaded. IDARE works with version 0.3.0 but we can't guarantee that it works with newer versions.

To build IDARE:

git clone https://github.com/sysbiolux/IDARE.git IDARE
cd IDARE/METANODE-CREATOR
mvn install

Plugin Development

To develop plugins, you will have to install the application into your maven repository. Navigate to the location of the IDARE-2.0.1.jar file and run

mvn -e install:install-file -Dfile=IDARE-2.0.1.jar -DgroupId=IDARE -DartifactId=IDARE -Dversion=2.0.1 -Dpackaging=jar

In your pom.xml add

<Cytoscape-App-Dependencies>IDARE;2.0.1</Cytoscape-App-Dependencies>

to the properties field.

The IDARE dependency is added as follows:

<dependency>
	<groupId>IDARE</groupId>
	<artifactId>IDARE</artifactId>
	<version>2.0.1</version>
	<scope>provided</scope>	
</dependency>

Existing Plugins

Two plugins exist for the app:
A reader for GEO SOFT Files that converts them into a format useable by IDARE. The jar can be downloaded from here, the code can be found here.
The second plugin allows to create BarCharts as visualisation option and can be downloaded from here, with code available here

Relevant Literature

Galhardo, M.; Sinkkonen, L.; Berninger, P.; Lin, J.; Sauter, T. & Heinäniemi, M. Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network. Nucleic Acids Res, 2014, 42, 1474-1496 http://dx.doi.org/10.1093/nar/gkt998
Pfau, T.; Galhardo, M.; Lin, J.; Sauter, T. IDARE2—Simultaneous Visualisation of Multiomics Data in Cytoscape. Metabolites, 2021, 11, 300. https://doi.org/10.3390/metabo11050300