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 |
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. |
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), 435–447. |