XINViewer

DIP XIN Protein-Protein Network Viewer

CH391L, Fall 2004

[See my other software on SOFTPEDIA.]

Abstract

XINViewer is a DIP XIN Protein-Protein Interaction Network viewer written in Java. It was written entirely from scratch as a final project for CH391L.

Documentation

Here is the final project report where we analyze clusters in H.pylori and E.coli using XINViewer.

Here is the user manual for XINViewer.

Source

The source for XINViewer is available here.

Here is how to compile the source:

Install and configure Apache Ant, version 1.6.2 or newer.
Install JUNG, version 1.5.2 or newer.
Install Apache Xerces, version 2.6.2 or newer.
Install COLT, version 1.0.3 or newer.
Install Jakarta Commons, version 3.1 or newer.
Install Prefuse, alpha or newer.
Download XINViewer-src.zip and save it somewhere on your hard drive.
Unzip it: this will create a subdirectory called "XINViewer".
Go to the XINViewer subdirectory.
Edit the file "build.xml" and change all the paths in the section "jars.classpath" to point to the paths where you installed the libraries above.
Type "ant" to build the XINViewer binary.

Binaries

In order to run XINViewer you need to have a Java Virtual Machine installed on your computer. The product has been tested only using Sun Microsystems' Java version 1.4.2, but it should work on newer virtual machines as well.

You can run XINViewer in two different ways (see below for details):

Command line: download and execute manually
Java WebStart: execute automatically

Command line execution

Check that you have a Java Virtual Machine installed by typing java -version. Here is an example:
```
C:\>java -version
java version "1.4.2_05"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_05-b04)
Java HotSpot(TM) Client VM (build 1.4.2_05-b04, mixed mode)
```
If you do not have a Java Virtual Machine installed, or if it is the wrong version, download one from here.
Download the following files and store them in the same directory anywhere on your hard drive:
- XINViewer.jar: the main binary
- colt.jar: the COLT library
- commons-collections-3.1.jar: the Commons library
- jung.jar: the JUNG library
- prefuse.jar: the Prefuse library
- prefusex.jar: the Prefuse Extensions library
- xercesImpl.jar: the Xerces library
- xml-apis.jar: the Xerces API library
- Ecoli20041003.xin: Sample DIP XIN protein-protein interaction network for E.coli
Launch XINViewer by typing java -jar XINViewer.jar in the directory where you stored all the binaries above. The main window will appear on the screen shortly. Open "Ecoli20041003.xin" and play with it.

Java WebStart execution

Java WebStart comes pre-packaged with Java 1.4.2 or higher. Check that you have Java WebStart installed by launching a demo application at the demos site.
Download the file Ecoli20041003.xin somewhere on your hard drive.
Launch XINViewer:

Note: You will be prompted with a window telling you that XINViewer needs unrestricted access to your local machine: this is because XINViewer must be able to load XIN files. Click "Start" to continue or "Exit" if you are not comfortable with this requirement.

The main window will appear on the screen shortly. Open "Ecoli20041003.xin" and play with it.