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
http://Cm1.CELLmicrocosmos.org
http://CE3.CELLmicrocosmos.org
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 |
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. |