DIP XIN Protein-Protein Network Viewer
Razvan Surdulescu, Eva-Maria Strauch (c) 2004
AbstractXINViewer is a DIP XIN
Protein-Protein Interaction Network viewer written in Java. It was written entirely from
scratch as a final project for CH391L.
Here is the final project report
analyze clusters in H.pylori and E.coli using XINViewer.
Here is the user manual
SourceThe source for XINViewer is available here.
Here is how to compile the source:
- Install and configure Apache Ant, version 1.6.2 or
- Install JUNG,
version 1.5.2 or newer.
- Install Apache Xerces, version 2.6.2 or
- Install COLT, version
1.0.3 or newer.
- Install Jakarta Commons, version 3.1
- Install Prefuse, alpha or
- Download XINViewer-src.zip
and save it somewhere on your hard drive.
- Unzip it: this will create a subdirectory called
- 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.
BinariesIn 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
- 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:
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:
- 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
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
- Download the file Ecoli20041003.xin somewhere on your
- 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.