A GUI based tool for comparison of multiple biological interaction networks
Interaction networks are a convenient way of representing the complex nature of multi-component systems. Examples of such complex systems include biological pathways, social interactions, financial markets, management systems, multiple modules in a programming language, etc. Recognizing the similarities and differences between multiple interaction networks becomes easier when aided by proper visualization tools. we present a GUI based network comparison tool CompNet, which allows to visually compare multiple networks based on node and edge similarities. Additionally, the tool can compare individual networks on the basis of general network properties, node neighborhoods and community similarities. CompNet is expected to be a valuable addition in the field of visual data mining especially for users aiming to visually compare more than two interaction networks at the same time.
Dependencies : Before installing CompNet, it is pre-requisite to have R package installed along with the R igraph library. R package can be downloaded from here and the R igraph module can be downloaded from here
The tool can be downloaded as a zip file (containing the CompNet executable along with the associated programs and dependencies).
After downloading the appropriate zip file, users need to unzip the contents (using a software like 7zip). This would generate a directory, called CompNet_LINUX_32 or CompNet_LINUX_64 or CompNet_Windows (depending on the platform selected), containing the executable and the "case_studies" folder. To run the application for the first time, the permissions of the executable needs to be changed (on Linux systems). This can be done by right clicking on the executable, followed by selecting 'Properties' tab. Subsequently, users need to select the 'Permissions' tab, change all the access permissions to 'read and write' and select the check box that says 'Allow executing file as program'.Once the permissions have been changed, for all subsequent runs, users just need to double click the application and run it.
Linux users may also run the command (chmod 755 ./compnet_32 OR chmod 755 ./compnet_64) after opening the terminal in the directory where the CompNet executable is placed
If you use CompNet for your work please cite the following paper :
Kuntal BK, Dutta A, Mande SS. CompNet: a GUI based tool for comparison of multiple biological interaction networks. BMC Bioinformatics. 2016 Apr 26;17(1):185. doi: 10.1186/s12859-016-1013-x. PubMed PMID: 27112575; PubMed Central PMCID: PMC4845442.