This forum is aimed towards anybody who is working with the the MembraneEditor. Installation instructions are found here. Any questions, remarks or critics are welcome. Also this is a chance to get in contact with other users.
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Mailing List Archive (Release Updates)

Post by bjoern » 04.12.2011, 22:59

In this forum the emails sent to the MembraneEditor Interest group are archived.

Of course, if you want to stay up-to-date, you should join the email list, because the content of the email will always be posted here with at least one month delay.

Just join the email list by clicking here.

The actual email is found at the bottom of this page.

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CELLmicrocosmos 2.1 membraneEditor: PreRelease Invitation

Post by bjoern » 04.12.2011, 23:01

01.04.2009

CELLmicrocosmos 2.1 membraneEditor: PreRelease Invitation

Liebe Kollegen und Freunde, (English Version below)

Sie bekommen diese Mail, weil Sie maßgeblich beteiligt waren an der
Weiterentwicklung des CELLmicrocosmos membraneEditors, sei es durch
Kommentare, Kritik, Ideen oder einfach durch das Interesse, eines Tages
mit diesem Tool zu arbeiten. Zunächst möchte ich Ihnen herzlich für Ihre
Unterstützung und Ihre Interesse danken!

Es handelt es sich hier übrigens nicht um einen verspäteten 1. April Scherz,
auch wenn die bisherige Verzögerung des PreReleases eine solche Vermutung
nahe legen könnte.

Mit dieser Mail möchte ich Sie einladen, die Beta-Version zu testen. Da
das Programm bisher noch nicht publiziert wurde (außer zweier
Poster-Präsentationen auf der GCB und GCC 2008), haben wir uns
entschieden, einen personalisierten Zugang anzubieten. Alles, was Sie
dafür brauchen, ist eine Internet-Verbindung, eine aktuelle Java-Version
mit Webstart, einen User-Namen und ein -Passwort. Keine Angst - wenn
etwas davon sich etwas seltsam anhören sollte - wir werden Ihnen helfen,
Ihr System entsprechend einzurichten.

Wenn Sie nun interessiert sind, den membraneEditor zu testen, senden Sie
mir bitte einfach Ihren bevorzugten User-Namen und ihren
Passwort-Wunsch, und ich werde Ihren Account entsprechend einrichten.

Falls Sie zunächst aber noch ein paar Informationen zu dem
membraneEditor benötigen, haben wir eine Webseite für Sie eingerichtet:

Poster-Abstract der German Conference on Chemoinformatics 2008:
http://va.gdch.de/wwwdata/abstracts/5327/5327_0102.pdf

Cm2-Projekt-Homepage:
http://Cm2.CELLmicrocosmos.org

Wir hoffen, Ihnen wird die Arbeit mit dem membraneEditor genauso viel
Spaß machen wie uns!

Mit frendlichen Grüßen
Björn Sommer,
Tim Dingersen
& das CELLmicrocosmos Team



Dear Collegues and Friends,

you get this mail because you have been involved in the development of
the CELLmicrocosmos membraneEditor, through comments, critics, ideas or
simply by the interest to use this tool one day. First of all, I want to
thank you very much for your interest and support!

By the way - this is no late April Fools' Day Joke - although the long delay
of the PreRelease may provoke this idea!

Today I want to invite you to test the Beta Version. Because the tool
has not been published so far (except a poster presentation at the GCB
and GCC 2008), we decided to provide a personalized access. All you
need for this is an internet connection, an actual webstart-able Java
Version, a user name and a password. Don't worry - if something of this
sounds kind of strange to you, we will help you with setting up your system.

So, if you are interested in working with the membraneEditor, please
sent me your preferred login-name and -password, and I will create your
account soon.

If you first want to find out more about the membraneEditor, we prepared
a webpage for providing a first glance at it:

Poster-Abstract of the German Conference on Chemoinformatics 2008:
http://va.gdch.de/wwwdata/abstracts/5327/5327_0102.pdf

Cm2-Project-Homepage:
http://Cm2.CELLmicrocosmos.org

We hope you will enjoy working with the membraneEditor as we do!


Best regards,
Björn Sommer,
Tim Dingersen
& the CELLmicrocosmos Team

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CELLmicrocosmos 2.2 MembraneEditor: Happy Holidays!

Post by bjoern » 04.12.2011, 23:04

23.12.2009

CELLmicrocosmos 2.2 MembraneEditor: Happy Holidays!

Dear Colleagues and Friends,
merry-x-mas-membraneeditor-2009.jpg
Merry X-mas 2009 with the MembraneEditor
merry-x-mas-membraneeditor-2009.jpg (176.66 KiB) Viewed 23339 times
we wish you a merry christmas, many presents and of course a happy and successfull new year!

As a first small warming-up christmas present for all users and supporters of the MembraneEditor, you can just start its actually updated version 2.2 right now (a login is not needed anymore):

http://Cm2.CELLmicrocosmos.org

Changes from Version 2.1 to 2.2 (Excerpt)
  • advanced PDB format compatibility options enabling Molecular Dynamic Simulations
  • Backward-Parsing for PDB membranes simulated e.g. with Gromacs
  • support of rafts and multiple layers
  • access to the atomic level for Plugin-Algorithms
  • automatic alignment of many membrane proteins by using OPM and PDBTM data
  • simplified removing of overlapping molecules
  • every single lipid may be aligned now
  • external Jmol library used for previewing especially large membranes
  • different view modes (3D shapes, atomic spheres, lines)
  • high lipid densities by using atom based collision detection
  • improved performance
In the next year, the documentation will be updated to the newly added features and in addition we will prepare some videos showing how to use the MembraneEditor. And of course, we are already developing some new significant features ...

Thank you for your support and your critics and please just sent me an email if you got any questions or bug-reports.

Best regards and hope to meet you again in 2010!

Björn Sommer & team.CELLmicrocosmos.org

Meet us at:
BIOSTEC Bioinformatics, Valencia 20.-23.1.2010
EMBO Workshop Visualizing Biological Data (VizBi), EMBL Heidelberg, 3.-5.3.2010

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Re: Mailing List Archive

Post by bjoern » 04.12.2011, 23:11

22.11.2010

CELLmicrocosmos 2.2 MembraneEditor: GCC 2010 Update

Dear Colleagues and Friends,

the 6th German Conference on Chemoinformatics lies behind us and for all those who did not attend here is a short newsletter about the newest MembraneEditor developments:

New Videos on YouTube
membraneeditor-goes-youtube-2010.png
The MembraneEditor goes YouTube 2010
membraneeditor-goes-youtube-2010.png (78 KiB) Viewed 23339 times
Dedicated to all those who want to have a fast introduction to the main functionalities of the MembraneEditor. Included are direct links to the according pages in the manual:

http://www.cellmicrocosmos.org/index_cm ... =cm2videos

How to cite ...
Our first major publication is submitted. For the meantime we prepared a page with a citeable conference talk from the last GCC and in addition a german feature article published in the October issue of Nachrichten aus der Chemie:

http://www.cellmicrocosmos.org/index_cm ... blications

Cooperation on CmME MD Editon
Together with Dr. Jens Krüger from the Group of Prof. Gregor Fels/Paderborn we are working on the CmME MD Edition. First results has been presented at the 3rd EuCheMS in Nürnberg and the GCC 2010 in Goslar. A group of students is working now on the improvement of the workflow between Gromacs and CmME. Thanks go also to Dr. Lars Schäfer, who helped us in 2009 to make our membranes compatible to Gromacs!

Performance Installations
You have a very fast machine with 4GB Ram? Or you think, the MembraneEditor could run faster on your laptop? You are probably right! Just try the new Performance Installations, extending the size of the Java virtual memory used. This may increase the performance and also enable you to export larger membranes to PDB format. Just use the regular start page, cancel the standard installation and choose another option. And don't be afraid - if it does not run afterwards (because your configuration does not support the virtual memory settings), just use another installation option - your workspace won't be changed!

Improved Raft-Support
Algorithms can now be restricted to fill only the highlighted microdomain/raft with lipids. In addition, the area per lipid shown in the Properties window is now computed for the whole membrane or the selected microdomain, taking its outer shape into account. Of course also the PDB export can be restricted to the selected area. Watch the Microdomain video for more ...

Improved Statistics
In addition to the molecular weight and the percental lipid distribution, the Statistics show now also the absolute number of lipids. This might be interesting for example if you have to generate topology files.

Membrane Shifter Tool
membraneeditor-membrane-shifter-tool-2010.png
MembraneEditor Membrane Shifter Tool
membraneeditor-membrane-shifter-tool-2010.png (30.45 KiB) Viewed 23339 times
You simulated your membrane in Gromacs, re-imported it into the MembraneEditor for further analysis and it is not centered correctly? No problem, just use the Membrane Shifter Tool found in the algorithms! It is automatically computing the vertical center of you rmembrane, but you may also change it manually. In addition it may be needed to center the membrane horizontally - this is now possible with the Translation option it the Change Size dialog.

The MembraneEditor Main Page
The Program, Manual, Videos, Forum etc. can be found here:
http://Cm2.CELLmicrocosmos.org

Feedback needed!
We are curious to know what you are doing with the MembraneEditor! Do you use it to build and analyze bilayers? Are you inserting proteins? Do you simulate it with Gromacs or CHARMM etc.? Would you like to see a video for a special workflow on YouTube? Please help us to improve the MembraneEditor! If you find a bug, or you have an idea of a feature you really need, just tell us! Or your mailbox is full enough, no more interest in this email newsletter? Just let us know!

We wish you a lot of fun and productive work with the MembraneEditor!

With best regards,

Björn Sommer & team.CELLmicrocosmos.org

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CELLmicrocosmos 2.2.1 MembraneEditor: Publication and Source

Post by bjoern » 04.12.2011, 23:23

25.05.2011

CELLmicrocosmos 2.2.1 MembraneEditor: Publication and Source Code Release


Dear Colleagues and Friends,

there are some news about the development of the CELLmicrocosmos MembraneEditor (CmME) which may be interesting for your future PDB-based modeling and simulation work:

Publication on JCIM
Finally we published our first major article in the Journal of Chemical Information and Modeling. In addition, the Editorial Board was so kind to select an image from our publication as the cover picture.
JCIM-Cover-05-2011-MembraneEditor.png
JCIM Cover 05/2011 The MembraneEditor
JCIM-Cover-05-2011-MembraneEditor.png (119.89 KiB) Viewed 23339 times
So if you like to learn more about the theoretical background of CmME, just have a look at:

Sommer B, Dingersen D, Gamroth C, Schneider SE, Rubert S, Krüger J, Dietz, K-D:
CELLmicrocosmos 2.2 MembraneEditor (2011): A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems. J. Chem. Inf. Model. 51(5), 1165-1182.

Excerpt:
  • publication-based modeling of the inner and outer rat hepatocyte membrane in PDB format
  • semi-automatic placement of two proteins based on the OPM database
  • membrane packing problems and their theoretical background
  • investigation of the algorithmic runtime and performance
  • GROMACS MD simulation of a DPPC layer created with CmME
Source Code Release on GPL3
After some night shifts we managed to tidy up the code and to choose the correct license. The GNU GENERAL PUBLIC LICENSE 3 is a well known Open Source license which is often chosen in scientific contexts. So feel free to download the whole application at:

http://Cm2.CELLmicrocosmos.org

Changes
Since the last Xmas2010 update, there have been some improvements, which are shortly listed here:
  • 3D Stereoscopy Support added
  • PDB Writer refactored and enhanced
  • PDBTM and OPM Update issues with Linux and Windows fixed, canceling process improved, Contents Section in Downloads window improved
  • Source code completely refactored
  • MembraneAlgorithm package renamed to MembranePackingAlgorithm package, referring to our publication
  • Documentation extended and improved, citation and topology information for CmME, OPM, PDBTM and PDB added
  • Grace export integrated into protocol window for drawing algorithm runtime graphs
  • New compatibility information added into the PDB Output Settings for different PDB viewers
  • Parallel Projection and Uniform Background options added to 3D Settings
Upgrade Now!
The brand-new version 2.1.1 is now online also as Webstart Application. Please note: The former version 2.1 will not be supported anymore. On some systems, like Windows, you will still be able to start this version, but it will not be updated anymore. So please go to the Webstart page and download the new version. It is no problem to keep your old workspace! The new version will use your old workspace.
How to update the Cm2_Workspace
The new version comes with a new lipid library containing the lipids and proteins discussed in the publication. If you do not want to have a look at it, just keep your workspace and skip the following step. If you want to use the new files, just rename your Cm2_Workspace to something like Cm2_Workspace_old. The new workspace will automatically be installed after your started the new version of CmME. Then you can decide to merge the new and your old workspace manually.

If you have any questions, suggestions or bug-reports, feel free to contact us!

We hope that you will enjoy working with the MembraneEditor!

With best regards,

Björn Sommer & team.CELLmicrocosmos.org

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CELLmicrocosmos 2.2.1_1 MembraneEditor: GCC 2011 Release

Post by bjoern » 04.12.2011, 23:26

10.11.2011

CELLmicrocosmos 2.2.1_1 MembraneEditor: GCC 2011 Release

Dear Colleagues and Friends,

it was nice to meet some of you again at the German Conference on Chemoinformatics. For those, who did not attend, this email gives a short overview about the new developments of the MembraneEditor.

The GMX-Plugin
Attached you will find the poster regarding the GMX-Plugin, first presented at the GCC this year. It drastically improves the modeling and simulation workflow by connecting the MembraneEditor to Gromacs, and this can be done locally, via ssh or Unicore.

It is still a beta version, but for those of you who are interested it is possible to get already the jar file to make first tests with it. It works already quite fine. For more information, just have a look at the poster.
Re-installation needed
If you did not use the WebStart verson of the MembraneEditor for a few weeks, a re-installation is needed. Oracle, the company behind Java, changed a policy for Java3D, and therefore we had to change a few file paths. This makes no difference for the work with the MembraneEditor. Every file needed for the installation are hosted now directly at CELLmicrocosmos.org.

You just have to go back to the Cm2 Website and download the JNLP-file by going to "Start" and following the instructions. Your workspace will not be changed.

http://Cm2.CELLmicrocosmos.org

More information regarding this topic you will find in our forum:

http://www.cellmicrocosmos.org/Cmforum/ ... f=18&t=657

Release 2.2.1_1
If you already did the re-installation process, the update will be installed automatically during starting the MembraneEditor on your local machine while you are on-line.

The full list of new features and bug fixes:
  • save screenshot function added
  • stereo autofocus function added (for Java3D Stereo compatible graphic cards)
  • Statistics background adjust to the actual theme (dark or bright)
  • new OPM/PPM Server information added to Help and support implemented
  • new OPM alignment information added to Help
  • case-sensitive problem with directory Cm2/cm2images/icons solved
  • Cm2_IconDepot problems catched
  • problem with SortByType setting in ReversePDBParser solved
  • Developer Tutorial completely corrected
  • MyMembraneAlgorithm corrected (Example class of the Developer Tutorial)
  • Help slightly extended
  • JavaDoc comments of MembranePackingAlgorithm updated
  • 2 old lipids removed from library
  • backward compatibility with icon folder of the old Cm2_1 project added
  • Source Code: removed outdated TODO remarks
  • Source Code: version numbers in CHANGES.txt (this file) corrected
  • compatibility to optional GMX-Plugin version 1.1 (beta) for Gromacs added
So if you are interested in beta-testing the GMX-Plugin, please feel free to contact us.

Best regards,
Björn Sommer

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CELLmicrocosmos 2.2.2 MembraneEditor Release & VizBi 2014 ..

Post by bjoern » 17.04.2014, 15:58

29.01.2014

CELLmicrocosmos 2.2.2 MembraneEditor Release & VizBi 2014 Workshop Announcement

Dear Colleagues and Friends,

it is about time, now it is out:

CELLmicrocosmos 2.2.2 MembraneEditor Release
Cm2_2_2_release.jpg
Cm2_2_2_release.jpg (10.91 KiB) Viewed 23347 times
The open source tool for modeling PDB membranes based on Membrane Packing Algorithms comes now with the next major release.

After solving some issues with the brand new Oracle Java 7 (Update 51) and OpenJDK versions, the WebStart version comes now with a number of improvements. Only to list the most relevant ones:
  • APL@Voro integration (optional on Linux and Mac OS X)
  • The Wanderer Rookie for high-density membranes
  • Extended capabilities of the Membrane Packing Algorithm interface
  • Extended protocol capabilities
  • New Website
  • Many bug fixes
  • A full list you may find here
Just go on and give it a try:
http://Cm2.CELLmicrocosmos.org

VizBi Workshop Announcement - 3 days left!

If you or your students want to learn more about molecular modeling with the MembraneEditor, where to get data for compositions and how to use the PDB membranes with external tools like Gromacs, you can meet us at the VizBi in Heidelberg (04.03.2014). More information you will find here:

http://vizbi.org/2014/Program/#CELLmicr ... 20Modeling

So, hope to meet you soon again!

Happy Modeling!
Björn Sommer & team.CELLmicrocosmos.org

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CELLmicrocosmos 2.2.2_1 MembraneEditor Minor Release

Post by bjoern » 17.04.2014, 16:04

17.03.2014

CELLmicrocosmos 2.2.2_1 MembraneEditor Minor Release

Dear Colleagues and Friends,

the next minor release is out now:

CELLmicrocosmos 2.2.2_1 MembraneEditor Minor Release
Molecule Alignment and Performance Update, Bugfixes (17.03.2014)
Cm2_2_2_1_release.jpg
Cm2_2_2_1_release.jpg (13.02 KiB) Viewed 23347 times
Shortly, here the number of improvements and bug fixes:
  • All users of Linux distributions usind IcedTea for Java WebStart will be happy: the actual release was pre-compiled with Java 6 and it is not required anymore to install some alternative packages.
  • The direct APL@Voro integration did not work on all systems correctly, this problem is fixed now.
  • The lipid/protein alignment mode was extended. First, the area can be defined in which molecular structures around the molecule to align are shown. Second, the alignment can be manually changed by providing an axis-angle.
  • For all those people who want to work with larger numbers of molecular structures, a special mode was implemented based on work done during Philipp Unruh's diploma thesis. You will find it in the 3D Settings dialog.
Just restart the WebStart version of the MembraneEditor or install it from here:
http://Cm2.CELLmicrocosmos.org

Happy Modeling!
Björn Sommer & team.CELLmicrocosmos.org

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