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Cobweb is licensed under the GNU General Public License version 3.

If you are using Cobweb, please give us the credit by linking to http://bioinformatics.charite.de/cobweb and citing the application note about Cobweb:
von Eichborn J., Bourne P.E. and Preissner R. (2011) Cobweb: a Java applet for network exploration and visualisation. Bioinformatics, 27, 1725-1726 [Paper]

If you just want to use Cobweb for your own work, please download the example applet by clicking on the corresponding section below. In this package there is everything you need to set up your local copy of Cobweb.
If you want to include enhanced feedback possibilities as well, please also download the JavaScript files and refer to the Tutorial.

Download Java source-code

The sources make up two packages, cobweb and particlesystem. The classes that belong to each package are shown below.

Please Note, that these sources need the processing core, the G4P library and commons codec to work. These libraries (called core.jar, guicomponents.jar and commons-codec-1.4.jar) can be downloaded below (click on "Download Java libraries (jar)").

Package: cobweb

Cobweb.java	Main class of the applet, imports the particle system and draws the network
GraphFunctions.java	Class that offers some graph-based algorithms
GraphMLParser.java	Class to parse GraphML-files and create the network
Parameters.java	Class to store parameters like the picture path given in the input file
SIFParser.java	Class to parse SIF-files and create the network
XGMMLParser.java	Class to parse XGMML-files and create the network

Package: particlesystem

Edge.java	Edge between two nodes
Integrator.java	Integrator, computes the positions for all nodes
Node.java	Class that represents one node
ParticleSystem.java	Main class of this package that uses all other classes to represent the network
Repulsion.java	Repulsion between two nodes
Vector2D.java	Implementation of two dimensional vectors

Additional files:

user_col_schema.png	The user-specified colour schema that is used for the control elements
font.ttf	The font that is used to show the node names

These source files may be not up to date. To get the newest version, please look at the Cobweb repository at Github (show repository).

Download java_sources.zip

Download JavaScript files

The following JavaScript files are needed for Cobweb to enable the enhanced feedback through the sidebar. Both of them have to be included in the page that contains the applet by adding <script type="text/javascript" src="./applet.js"></script> and <script type="text/javascript" src="./prototype.js"></script> to the top of the page.

applet.js	Contains a set of functions that is used by the Cobweb applet to communicate with the sidebar.
prototype.js	Core file of the Prototype JavaScript framework, it is needed for applet.js to work

Download javascript_files.zip

Download example applet

Complete example applet. After extracting it to your harddisk opening example.html opens the applet showing an example network. The code of this example applet can be used to understand how the applet can be implemented into a website.

The example applet contains:

example.html		Sample html-file showing how the applet can be implemented on a website
stylesheet.css		Style rules to define the look of the website
js		Folder containing JavaScript-files
	applet.js	JavaScript file containing functions that are necessary to control the applet via the website
	prototype.js	Prototype JavaScript framework
applet		Folder containing the applet libraries, for details please click on "Download Java libraries (jar)" above
	cobweb.jar
	particlesystem.jar
	core.jar
	guicomponents.jar
	commons-codec-1.4.jar

Download example_applet.zip

Download Java libraries (jar)

Libraries:

cobweb.jar	Main library for the applet, contains the code for user interaction and network drawing
particlesystem.jar	Contains the particle system logic behind the network, computes the nodes positions in the network
core.jar	3rd party library containing the core of the processing framework
guicomponents.jar	3rd party library for drawing control elements (G4P)
commons-codec-1.4.jar	3rd party library offering common encoding functions (Apache commons codec)

Download java_libraries.zip

Download example input files

Some example-files can be downloaded here. For general information about the structure of the files please have a look at the tutorial.

Example files:

apoptosis.xgmml	The apoptosis example (see here) in XGMML format.
apoptosis.graphml	The apoptosis example (see here) in GraphML format.
apoptosis.sif	The apoptosis example (see here) in SIF format.

Download example_input.zip