List of external Sources and Packages

Packages (Preliminary)

This is a list of all non-standard JRE items which have been included in this application. Additional information like the license texts and third party remarks you will find in the source code package.

available for download at

Developer Edition

http://Cm1.CELLmicrocosmos.org

Educational Edition

http://CE3.CELLmicrocosmos.org

Pathway Edition

http://Cm4.CELLmicrocosmos.org

Name

Version

Type

Description

Usage

License

More Info

jung-algorithms
jung-api
jung-praph-impl
jung-io
jungvisualization
2.0 Library 2D Network Layouts 2D Visualization of Tours and Networks
BSD License http://www.ung.sourceforge.net
collection-generic Library Part of the jung-package Apache License 2.0
axiom-api
axiom-impl
1.2.7 Library Webservice/MySQL Connection to Database.
These packages are only included in the Pathway Edition and Developer Edition
Apache License 2.0
axis-adb
axis-kernel
1.4 Library " Apache License 2.0
backport-util-concurrent 3.1 Library " CPL/EPL
commons-httpclient
commons-codec
3.1 Library " Apache License 2.0
commons-logging 11.1 Library " Apache License 2.0
concurrent Library " Public Domain
log4j 1.2.15 Library " Apache License 2.0
neethi 2.0.4 Library " Apache License 2.0
mysql-connector-java 5.15 Library " GPL
wsdl4j 1.6.2 Library " CPL/EPL
j3d-core, vecmath 1.5.2 Library 3D Graphics API for the Java Platform The CellUniverse/The 3D Visualization GPL 2 (with CLASSPATH exception) http://www.j3d.org
j3d-core-utils
1.5.2 Library Additional libraries for j3d-core Picking and Navigation BSD (without advertising clause) http://www.j3d.org
JDOM 1.1.1 Library
XML Java support Loading and saving of XML files Apache License (without acknowledgment clause) http://www.jdom.org
JFreeChart
JCommon
1.0.13
1.0.16
External Standalone Fast statistical visualization Visualization of the resulting percental lipid distributions and lipid/protein weights
LGPL 2.1 (or later) http://www.jfree.org/jfreechart/
Substance 4.0 Library A collection of Look & Feel's
The L&F of the GUI
BSD (without advertising clause)
http://substance.dev.java.net

Websites

The following websites are important for the functionality of CmME or include data used by CmME:

Name

Website

Usage

Publication

Cell Centered Database http://ccdb.ucsd.edu 3D cell components or complete cell models based on microscopic data sets are derived from images and 3d data from the CCDB Martone ME, Gupta A, Wong M, Qian X, Sosinsky X, Ludäscher B, Ellisman MH. A Cell-centered Database for Electron Tomographic Data. Journal of Structural Biology 138, no. 1-2 (2002): 145-155.