Download & Run

NaviCluster

NaviCluster works on any operating system that has Java 6 installed.

Download NaviCluster: NaviCluster-bin.zip

To run NaviCluster, please follow the below guidelines:

  1. Install Java 6 (with update later than 10). Java is available via its website. You can check the version of Java installed in your computer by typing java -version in the Terminal (Mac OS X) or Command Prompt (MS Windows). Your computer has Java 6 installed if you get the following output: java version "1.6.0_XX" where XX denotes any numbers representing the update version.
  2. Download NaviCluster-bin.zip and decompress it. The compressed file contains NaviCluster.jar, the lib folder (containing libraries necessary for running NaviCluster), a property-information file (gene_ontology-100329-short.txt), and a sample dataset composed of a node file (yeastnet2-noIEA.node) which contains information about nodes and an edge file (yeastnet2-noIEA.edge) which contains a list of edges and their weights.
    • The property-information file is Gene Ontology (GO) derived from the OBO format available on the website Gene Ontology (GO) at 29 March 2010.
    • The sample dataset is the yeast Saccharomyces cerevisiae protein network YeastNet v.2 with 5,483 nodes and 102,803 edges.
    • GO annotations for nodes in the node file are obtained from Saccharomyces Genome Database (SGD).
  3. Double-click the navicluster.sh file (Mac OS X) or navicluster.bat file (Windows). You can also run NaviCluster via the command java -Xmx1024m -jar NaviCluster.jar
  4. NaviCluster runs the two-stage clustering algorithms on the sample dataset and shows the main window. At this stage, you can start navigating the network. See How to Use for more detail.

Note: For Linux users, please put the parameter -Dawt.useSystemAAFontSettings=on between java and -jar in the above command to force Java to use anti-alias rendering of all GUI components.


PSI-MITAB Converter

PSI-MITAB format is a standard format supported by many databases, e.g., DIP, MINT, IntAct, and BioGRID. To support users who want to import networks in PSI-MITAB format, we provide a Java that accepts a network in PSI-MITAB and convert it to the node and edge files used iœn NaviCluster. For detailed instructions on how to prepare the node and edge files by yourself, please proceed to the relevant sections in How to Use.

Download: PsiMiTabConverter.zip

Instruction:

Extract the file on your favorite place and type the following command in the terminal/command prompt: java -Xmx1024m -jar PsiMiTabConverter.jar <PsiMitabFilePath> <AnnotationFilePath> -needIEA