12.4 List of external Sources and Packages

Packages

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 at

org.cellmicrocosmos.cm2.lib

available for download at

http://Cm2.CELLmicrocosmos.org

Name

Version

Type

Description

Usage

License

More Info

Infonode Docking Windows
1.6.1 Library A Window manager for a UI with multiple internal windows
Manages the different windows in the main GUI
GPL http://www.infonode.net
j3dcore-1, vecmath
1.6.0 Library JogAmp's 3D Graphics API for the Java Platform Displaying and picking of the 3D objects in the Membrane View
GPL 2
http://forum.jogamp.org/java3d-f3728156.html
jogamp-fat
2.3.2 Library JogAmp's 3D Graphics API for the Java Platform The JOGL project hosts the development version of the Java Binding for the OpenGL API, and is designed to provide hardware-supported 3D graphics to Java applications
New BSD 2-Clause License
https://jogamp.org/jogl/www/
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/
Jmol 14.15.2 Entire application as a jar-File
A pdb viewer that can be used standalone or
as a browser applet
External previewing of the membrane or single molecules; enables also 3D shape export to other graphics software
LGPL 2.1 (or later) http://jmol.sourceforge.net
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
Tools from JDK 1.8.0_25 Library
A collection of tools for Java Compiling of java files GPL 2 (with linking exception) http://openjdk.java.net

Websites

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

Name

Website

Usage

Publication

HIC-UP
http://xray.bmc.uu.se/hicup/ Some lipid models packaged with CmME are downloaded from HIC-UP Kleywegt GJ, Jones TA (1998) Databases in protein crystallography. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54, 1119-1131.
OPM
http://opm.phar.umich.edu Semi-automatic protein placement of transmembrane, intrinsic and extrinsic proteins Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: Orientations of Proteins in Membranes database. Bioinformatics 22, 623-625.
PDB
http://www.pdb.org Resource for all actual PDB structures, direct connection via the Search and Download PDB's dialog Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
PDB_TM
http://pdbtm.enzim.hu Semi-automatic protein placement of transmembrane proteins Tusnády GE, Dosztányi Z, Simon I. (2005) PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res. 33(Database issue), D275-278.

External Tools

The following tools might be interesting to use in combination with CmME

Name

Website

Usage

Publication

xmgrace
http://plasma-gate.weizmann.ac.il/Grace It can be used to visualize algorithm runtime graphs  
Gromacs
http://www.gromacs.org A very mighty Molecular Dynamics package which can be run on cluster computers. The PDB Settings dialog can be used to export compatible PDB files. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008): GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 4(3), 435447.