project

The aim of CELLmicrocosmos is the interactive stereoscopic visualization of biological cells for a better understanding of their internal structures and their functioning.

Based on microscopic datasets, biological cells are reconstructed in 3D models. Via Virtual Reality (VR) techniques they can be explored interactively for educational and scientific purposes.   [more]

Cm2 MembraneEditor News

Welcome to the release page of the CELLmicrocosmos 2.2 MembraneEditor (CmME).

News 24. October 2017

News 19. May 2017

Fixed some minor installation bug with the Self-executable files.

News 7. May 2017: Cm 2.2.2_2 Release

We released a new version of the MembraneEditor. More info here.

News 3. May 2017

Because the old web start version ran out caused by an outdated certificate, I took the opportunity to get rid of the old Java 3D 1.5.X implementation and integrate the new JOGL-based Java 3D 1.6.0 final release with the help of the JogAmp team (in particular thanks go to Phil for creating a custom fix for us!). The official release will be later, but you can already continue your work. And the best thing: Mac OS X support! Web start works, and alternatively you can download the self-executables! Just go to the start page, there are also details about my test environments. Plus: stereo support if you own a professional graphic card and 3D monitor! Side-by-side stereo for those of you with consumer 3D-TVs (does not work on Mac by now, sorry!).

News 16. July 2014

We just got a new SSL certificate from COMODO and this one makes troubles. Java will complain and also the browser, if you are using the https protocol. We are working on this issue, but you can just continue to use our tools without any drawbacks - just ignore the warning during the application start.

News March 2014

The first minor update will come within the next days, scheduled for 17.03.2014. A few bug fixes and some nice improvements and features will be introduced.

News February 2014

Join our VizBi 2014 Tutorial about Molecular Modeling. Find out more.

Moreover, there is a new version 1.09 of the VesicleBuilder, check it out in our forum!

News January 2014

It is about time for Version 2.2.2! It will come with a number of very nice extensions. The full new release is scheduled for 27.01.2014, so check back again soon! Problems with the newest version of Oracle Java WebStart in version 1.7.0_51 caused a delay, but a temporary newer version is online now. You may have to reinstall the MembraneEditor by downloading here the new WebStart version.

The current version was successfully tested with Java 7 (64 bit)

  • Windows 7 and Windows 8, Oracle Java 1.7 Update 51
  • Xubuntu 12.04 and Ubuntu 12.04, Oracle Java 1.7 Update 51
  • OpenSuse 12.2 and 13.1, OpenJDK 1.7/IcedTea

Moreover, if you want to learn more about membrane modeling and how to generate initial membrane simulations, please have a look at our Tutorial at the VizBi 2014!

Start the Webstart Version 2.2.1

The new version of the MembraneEditor is now online. Just go ahead to the start page. Please read the instructions first.

16.07.2012 Cm2.2.1_2 (BGRS 2012 Release) out now!

The pre version of Cm2.2.2 is out now! It includes a large number of partly important updates. Only a few highlights: PDB_TM and OPM integration drastically improved; membrane topologies can be exported; two improved membrane packing algorithms support now absoulte values; Java 7 compatibility fix. More ...

In addition we changed the provider now. This website is now faster and (hopefully) more reliable then ever! More Information in our Forum.

06.03.2012 The Vesicle Builder

Brand new, first presented at the VizB 2012: the first version of the Vesicle Builder is out for testing! Download the Plugin, import it into your MembraneEditor and build vesicles in a fast an easy way! More you will find in the forum.

30.09.2011 Attention: Please Re-install Webstart

Note: If you are using the WebStart version and you did already the fix below, the new version will install automatically during the start-up of the program on your computer (of course it has to be online).

All Webstart users: Please just re-install the MembraneEditor. Thanks to Oracle, the company owning JAVA now, we had to make some changes on our Starting (JNLP) files. Therefore, since September 17th 2011, the Webstart application was corrupt. More Information in our Forum.

The Source Code Release

Our first major publication was published in the Journal of Chemical Information and Modeling (doi: 10.1021/ci1003619). This publication is accompanied by the full release of the source code of the MembraneEditor under GPL3 license. Just download the source code of Cm2.2.1 now. It's free!

Upgrade now!

Please keep in mind that the older version 2.2.0 is not supported anymore! On many systems like Windows the old version still will start, but there will be no more updates for this version. Your workspace will not be affected.

warningRemark OPM Orientation (12.08.2011)

The definition of the orientation of outer mitochondrial, chloroplast and nuclear membrane have changed in the OPM database. The CmME documentation in release 2.2.1 have to be updated. We are currently working on minor rlease 2.2.2 which will include this changes. Please refer to this page for the correct definitions:

http://opm.phar.umich.edu/about.php?subject=topology

Thanks go to Dr. Andrei L. Lomize for this information!

Workspace Upgrade

Hint: With the new version comes a new DefaultDatabase, containing the collection of lipids discussed in the JCIM publication. If you want to install this, just rename your current workspace (e.g. Cm2_Workspace_old) and start the new MembraneEditor again. The new workspace containing the new lipids will be installed and you can choose now which workspace you want to work with in future or just merge both workspaces manually.

 

Videos on YouTube

We provide now a first set of new videos on YouTube showing how to use CmME. Here is one example. The full list may be found here!

More?

To find out more about the CELLmicrocosmos project, please go to the official main page. Be aware that the MembraneEditor is our most mature product so far. If you want to stay informed according new develpments, please add yourself to the mailing list or contact This email address is being protected from spambots. You need JavaScript enabled to view it. .