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From Virtual Reality to Immersive Analytics in Bioinformatics

Call For Papers
Special Session at the Stereoscopic Displays and Applications XXIX (2018), Burlingame, California
Special Issue of the Journal of Integrative Bioinformatics, vol 15, de Gruyter Berlin

Bioinformatics usually deals with the smallest entities of life, therefore, visualization plays an important role in this field. Stereoscopic rendering has already been used for a long time for visualizing biological structures, dating back to the first hype of virtual reality technologies 25 years ago when the CAVE was invented and Head-Mounted Displays (HMD) became affordable. Triggered by the success of new, modern HMDs such as Oculus Rift and HTC Vive, Virtual Reality has recently gained a lot of attention again. On the other hand, a new generation of large-scale “computational microscopes” is being established, such as the CAVE2, representing large, nearly 360 degree-spanning visualization facilities.

At the same time, advanced “Visual Analytics” solutions have become an important tool in all areas of scientific data analysis, combining visualization, data mining and analysis methods, and user interaction. Uniting both VR and VA, “Immersive Analytics” now starts to make use of new technologies, immersing the scientist into the data, and, in the best case, enabling advanced insights.

This special issue will focus on:

  • What is the legacy of the past?
  • Which approaches (partly) failed, and which success stories were triggered by Virtual/Augmented Reality in the context of Bioinformatics?
  • Which new ideas exist to approach now immersive analysis of biological data?
  • Which methods, technologies and/or applications are expected to change the way we see and perceive biology?

More info here:

http://vr2iainbioinf.immersive-analytics.org

Please join us at the workshop BioNetVisA 2017 - From biological network reconstruction to data visualization and analysis in molecular biology and medicine in Basel at the 12th September 2017. We will give a talk there on "Multiscale Modeling and 3D Visualization of spatially-embedded Cytological Networks" together with a number of other exciting talks!

https://sysbio.curie.fr/bionetvisa/

The workshop is part of the [BC]2 Basel Compuational Biology Conference.

@cellmicrocosmos joins the Twitter family

To get the hottest info on CELLmicorocosmos and related projects, tools and conferences, join us now:

Or just have a look to:

https://twitter.com/cellmicrocosmos

IB Workshop: Bio Visualization with Blender and MembraneEditor

At the Integrative Bioinformatics Symposium in Odense (22.-23.06.2017) in Odense

http://www.imbio.de/ib2017

Mehmood Ghaffar and Björn Sommer will present a Blender/MembraneEditor workshop. Here is the introductory text:

The visualization of cells as well as their internal membranes are becoming an established field in the scientific community as many processes which cannot be captured by actual microscopy and spectroscopy techniques can be communicated by 3D modelling and animation.

Whereas at the mesoscopic level cells and their components can be visualized with Blender, at the molecular level, protein complexes or whole membrane structures can be easily modelled with the CELLmicrocosmos MembraneEditor. Often, the last-mentioned step is used for creating initial configurations for molecular simulations.

In the context of the Integrative Bioinformatics conference 2017 we are conducting two hands-on workshops for attendees who would like to learn how to visualize biomolecular processes with Blender and/or the MembraneEditor:

  • Workshop I: Hands-on Introduction
  • Workshop II: Web-based Bio Visualization and Virtual Reality with Blender

http://www.imbio.de/ib2017/bio-vis.php

We are happy to announce the Quad-2 Release of the CELLmicrocosmos MembraneEditor!

The most important change is the substitution of the old Oracle Java 3D libraries by JogAmp's Java 3D 1.6.0 implementation. Now the 3D visualization is faster, more reliable, and we can support now Mac OS X! Many thanks go to the whole JogAmp team for their support!

Second, the Web Start was re-initiated and optimized for Java 8, running on all major platforms including Mac OS X!

Then, Stereo 3D visualization is fully supported now. There is an extra version for professional graphics and 3D devices, but also the standard version is coming with side-by-side or top-bottom rendering for, e.g., 3D-TVs (sorry, does not work on Mac).

Moreover, we fixed the PDBTM update – as there was a new website release of PDBTM, the update functionality for the membrane placement matrices was broken. Now, you have again full support for automatic protein placement!

More details below here:

http://www.cellmicrocosmos.org/index.php/cm2help/11-more-about-the-editor/11-5-history

To start over, just go to:

http://Cm2.CELLmicrocosmos.org

More information about the JogAmp project please find at this website:

http://jogamp.org

Special thanks for the Java3D continuation go to Julien, Harvey and Phil of JogAmp!

Vive la France! ;-)
Bjorn

Last year we presented the Stereoscopic Space Map at the Stereoscopic Displays and Application conference:

http://www.ingentaconnect.com/contentone/ist/ei/2016/00002016/00000005/art00027

This time we were invited to give a talk regarding our visualization facilities. Therefore, we conducted a nice joint paper discussing the different projects we are working on. As you will see a number of co authors contributed their work:

3D-Stereoscopic immersive analytics projects at Monash University and University of Konstanz, Björn Sommer, Karsten Klein and Falk Schreiber, Monash University and University of Konstanz (Germany); David G. Barnes, Monash University and Monash Immersive Visualization Platform at Monash University; Sarah Boyd, Thomas Chandler, Maxime Cordeil, Elliott Wilson, Jon McCormack, Kim Marriott, Kingsley Stephens, Monash University; Toan Nguyen, Monash Immersive Visualization Platform at Monash University; Hieu Nim, Monash University and Australian Regenerative Medicine Institute of Monash University (Australia); Dany Vohl, Swinburne University of Technology (Australia)   [SD&A-109]

http://stereoscopic.org/2017/program.html

Just like last year, the presentation will be again in Stereo 3D.

Moreover, we will give a demo showing the Space Map by using - for the first time - a zSpace 300 which will be provided by

http://zspace.com

Also, zSpace will be there to present their own approaches.

Again back to Bielefeld, we will present "Web-based Visualization and Exploration of Cytological Localization Scenarios" at the IB 2016 (Conference on Integrative Bioinformatics). The Proceedings will be published during this year in our Journal of Integrative Bioinformatics (http://imbio.de/journal), so even if you are not able to attend you will be able to have a look at some of the interesting topics. http://www.imbio.de/ib2016/program.php

We will participate in the Shonan seminar on "Web-based Molecular Graphics". Here is the abstract of the meeting, so if you are interested in this topic - see you there!

Molecular graphics is a well established discipline used in many scientific fields (e.g., life sciences, biomedical research, chemistry, material sciences), including commercial research (e.g., pharmaceutical industry). A wealth of methods and tools have been developed, and are still actively developed – however until recently activity has focused on stand-alone software. This meeting will explore an emerging new frontier for molecular graphics, namely deployment in a server-client environment, which promises to make molecular structural information much more easily accessible to scientists. In addition, the recent hybrid approaches have revealed structures, functions and dynamics of very large molecules and cellular machineries, which are displayed as both atomic structures and molecular/cellular images, greatly extending the roles of molecular graphics. This meeting will bring together key players in this emerging field to explore the challenges and opportunities raised by web-based molecular graphics and new applications.

Organizers: Andrea Schafferhans, Seán I. O'Donoghue, Haruki Nakamura

At the HEC 2016 conference (Health - Exploring Complexity: An Interdisciplinary Systems Approach) we will present a short talk in the "Data Integration in Life Sciences" special session with the topic: Integration and Virtual Reality Exploration of Biomedical Data with CmPI and VANTED.

We will participate in the Shonan seminar (Japan) on "Dynamic Networks Visual Analytics". Here is the abstract of the meeting, so if you are interested in this topic - see you there!

There is an abundance of complex dynamic data across many domains. Often such data has a natural interpretation as a network, e.g. for applications in biology, the social sciences, telecommunication, finance, energy, and information security. Analysis of these dynamic networks is key to the understanding of complex processes both in fundamental research and for decision making. For example, neuroscientists try to unravel the inner workings of the human brain using activity correlation networks, regulators and finance companies investigate trading patterns at the stock market and their relation to information spread in social media, and energy providers monitor and analyze power generation, distribution, and consumption via sensor networks on electrical grids. Use-cases include real-time monitoring of events and processes as well as a posteriori analysis of recorded data to gain insight. This insight then can be used to explain the principles of an underlying system, to detect important artifacts, e.g. cases of emergency, or to predict future changes. Many of these cases require a human in the loop to make decisions, e.g. in emergency situations, or to allow experts to guide exploration and insight generation for complex processes. Lack of sufficient a priori knowledge, in combination with the complexity of the dynamics in multi-variate data hamper the use of purely rule-based systems for analysis and decision making. Thus, a visual analytics type approach is best suited for such cases.

More here: http://shonan.nii.ac.jp/seminar/085/

Organizers: Takayuki Itoh, Karsten Klein, Beppe Liotta

Our new approach combining the interactive zSpace 200 monitor with the impressive CAVE2 is online now. And it is online twice:

Here is the Open Access publication:

http://ist.publisher.ingentaconnect.com/contentone/ist/ei/2016/00002016/00000005/art00006

And here is the video:

http://www.youtube.com/watch?v=W5Xl6WC-dl0

Sorry, the video is not the shown stereo version by now. I hope the organization committee will soon also release the stereo versions.

The system was developed at Monash University and first presented at the Stereoscopic Displays and Applications conference XXVII. in San Francisco!

In 2014, we presented the first time at the Stereoscopic Display and Applications XXV. conference in San Francisco. There, we showed a first prototype of a quite simple cell visualization and discussed problems and its future potential in a paper entitled "Stereoscopic Cell Visuzalization: from mesoscopic to molecular scale" (http://spie.org/Publications/Journal/10.1117/1.JEI.23.1.011007).

Moreover, we discussed our approach of optimizing the stereoscopic effect in interactive environments, as implemented e.g. in our CellExplorer (http://Cm4.CELLmicrocosmos.org). Now, we extended this approach to large-scale stereoscopic environments. First results will be presented in our talk: "Stereoscopic Space Map – Semi-immersive Configuration of 3D-stereoscopic Tours in Multi-display Environments".

In parallel, we submitted our stereoscopic cell animation of a Chlamydomonas reinhardtii cell to be shown at the 3D cinema session. This was a larger project between Prof. Dr. Olaf Kruse and Dr. Anja Doebbe (Algae Biotechnology & Bioenergy, Bielefeld University), Prof. Dr. Thoma Huser (Biomolecular Photonics Group, Bielefeld University), and the Biomedical Informatics Department. The largest part of the modeling and visualization process was done by Niklas Biere, based on the knowledge acquired in the "Interdisciplinary Cell Visualization and Modeling" lectures, projects and seminars. A first preview was shown at the CELLmicrocsmos neXt workshop (http://neXt.CELLmicrocosmos.org):

https://pub.uni-bielefeld.de/download/2704602/2704608

Now, the full HD version is finished and will be shown (if accepted) at the SD&A 2016 confence, together with high quality stereoscopic videos from S3D experts from all over the world, such as Pixar. Afterwards, it will be made freely available on YouTube (of course, also in S3D).

More news you can find at:  http://www.stereoscopic.org/2016.

Together with Xavier Ho we - Kristina Johnson and Bosco Ho, initiated the Computer Graphics in the Web Meetup (Melbourne). There were already two meetings with four very interesting talks (which will be online available soon - check this message soon again):

http://www.meetup.com/Computer-Graphics-on-the-Web/

At 1st March, I will present a talk about Stereoscopic Visualization in the Web/Virtual Reality Techniques. Especially I expect to see some amazing approaches at the SD&A conference in San Francisco which will be also part of this talk.

http://cellmicrocosmos.org/index.php/home/cellmicrocosmos-news/225-15-17-2-2016-stereoscopic-displays-and-applications-xxvii

In case you are interested, please sign up soon, we have limited seats and attendance is for free B-)

P.S.: You missed the talk? No problem, watch it here - sorry, the Oculus Rift you need to get from somewhere on your own now to test the demos:

https://www.youtube.com/watch?v=Rox2RTb7JvM

Since VIZBI (Visualizing Biological Data) started in 2010, we have participated in this amazing conference each time it has taken place in Heidelberg. In 2013 we gave a workshop about MembraneEditor. This year, we will give an extensive Blender workshop at 8 March (conference: 9-11 March). “Extensive” means we are partnering with Chris Hammang, who already has a very good standing in the Blender community because of his very impressive biomedical animations. Just take a look at his website if you haven’t seen his work yet!

http://chrishammang.com.au

Also, Niklas Biere and I will present a poster discussing our stereoscopic cell animation. This animation will be shown for the first time in Full HD 3D at the SD&A conference in San Francisco just a month before VIZBI:

http://cellmicrocosmos.org/index.php/home/cellmicrocosmos-news/225-15-17-2-2016-stereoscopic-displays-and-applications-xxvii

However, the nice aspect about our Blender workshop is that it will have two parts.

The first part will be an introduction, so that even animation newbies can learn a lot. And in case you already have some experience with Blender, the second workshop will feature more advanced skills!

http://vizbi.org/2016/Program/#Mesoscopic_and_molecular_visualization_with_Blender_%E2%80%93_Basic_hands-on_workshop

I have given a number of Blender tutorials during my time as a lecturer at Bielefeld University, and some of my students, like Niklas for example, have already achieved great results!

In the second tutorial, Chris will talk about advanced approaches he is using in his amazing work and I will talk about stereoscopic visualization with Blender, and more:

http://vizbi.org/2016/Program/#Mesoscopic_and_molecular_visualization_with_blender_%E2%80%93_Advanced_hands-on_workshop

The workshop costs Just 100 EUR for each tutorial! If you are around in Heidelberg, you could participate in our workshop(s) without attending VIZBI - but then you will miss a great conference! Extended Registration Deadline is the 8 February and it is sill possible to apply for fellowships!

http://www.embl.de/events/2016/conferences/VZB16-02_Announcement/

So see you in Heidelberg!

Chris and Bjorn

During the IEEE International Symposium on Big Data Visual Analytics (BDVA) in Hobart, Tasmania, we will present a new exploration approach called Hybrid-dimensional Visualization and Interaction Integrating 2D and 3D Visualization with Semi-Immersive Navigation Techniques. Moreover, there will be a live demo presenting our new approach, enabling 3D-stereoscopic visualization combined with 3D interaction.

Our work will be presented during a special session called Immersive Analytics, following the homonymous initiative of Monash University/Faculty of Information Technology.

The Journal of Integrative Bioinformatics just published a special issue on Standards in Systems Biology. This is a quite interesting approach because, for the first time, it is possible to get a fast overview of the different standards in Systems Biology. Every specification comes with a short abstract which introduces the corresponding standard. Then, the complete specification follows. Therefore, the specification is citable. The complete special issue is - like all publications in JIB - open access.

http://imbio.de/journal/archive.php?pindex=12&iid=27

Although the CELLmicrocosmos project is not directly involved, CmPI provides SBML import capabilities, and SBML is one of the major formats discussed in this special issue.

In Beijing, from October 8 to October 12, the Sino-German Workshop on Multiscale spatial compunational systems biology will take place. The MSCSB2015 is jointly held by Harbin Institute of Technology and Brandenburg Technical University Cottbus – Senftenberg and funded by the Sino-German Center for Research Promotion. We will present there new about the CELLmicrocosmos project in the context of this workshop.

http://homepage.hit.edu.cn/pages/liufei/8

On Wednesday, 17 June 2015, starting at 2 p.m., we will present CELLmicrocosmos PathwayIntegration: Basics and New Approaches at the College of Computer Science & Technology in Hangzhou. For more information, please this site:

http://www.software.zjut.edu.cn/info.php?id=4876

This talk is part of a research stay at Ming Chen's Group of Bioinformatics at Zhejang University supported by the National Natural Science Foundation of China (NSFC).

Zhejiang University

http://www.cls.zju.edu.cn/binfo/index.htm

Together with Dr. Lifeng Xu we started to explore new perspectives for the PathwayIntegration.

On Wednesday, 13 May, 11am – 12.30pm, and then starting at 2pm, the new sensiLab will be opened to the public. Here, a number of very exciting projects will be presented showing new approaches towards an advanced interaction design for the 21st century. One of these projects will be a preview of the new version of our CelLExplorer/PathwayIntegration which was extended by new 3D interaction methods based on the feedback of a number of sensiLab researchers.

Learn more about the concept of the sensiLab here:

http://infotech.monash.edu/seminars/2014/sensilab.html
http://monash.edu.au/news/show/high-tech-lab-opens-up-the-senses

Fell free to join the presentation - many amazing projects and people are waiting for you!
Level 6, Building H at Monash University’s Caulfield campus from 11am – 12.30pm, 2pm with open end

The CELLmicrocosmos project moves a few miles from Bielefeld University to Monash University in Melbourne. Here, the New Horizons Building is shown which was just finished in the middle of 2013. At this location new horizons for the Cm project will be openend. Meanwhile, also in Bielefeld the development will continue: In the context of a PhD thesis, a new extension for CmPI is in preparation.

Because 1) important changes are coming very very soon and 2) Easter is only a bunny jump far away, 2 Easter eggs (code P.-R.) are hidden at CELLmicrocosmos.org. Who finds them?

Together with Lu Zhu - a new PhD student who just started working in the context of the German-Canadian DFG International Research Training Group (1906/1) - a small workshop is organized. In this workshop, we are going to discuss the methods and tools that help life scientists exploit the large biological datasets to gain insight into underlying biological and biomedical mechanical processes by using data visualization, networking analysis and protein subcellular localization. A number of very intersting talks will there be presented!

[More info]

From the 5th to the 16th of January we will give a winter short course in Interdisciplinary Cell Visualization and Modeling in Verona. Besides the lectures, there will be also a practical part with the focus to molecular modeling and simulation using the MembraneEditor, APL@Voro and GROMACS. This research exchange with the group of Prof. Alejandro Giorgetti is kindly supported by ERASMUS+.

If you are participating in this course and you have the login information, please proceed to the forum:

http://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=61&t=764

Please find the info with the DOIs to all extended abstracts here.

All abstracts are published at the Bielefeld University Library Service BieColl.

Towards a 3D Cell Model of Chlamydomonas reinhardtii
Niklas Biere,Anja Doebbe, Nils Rothe, Thomas Huser, Olaf Kruse, Björn Sommer (DOI: 10.2390/biecoll-next2014-2)

Celebrating 10 years of CELLmicrocosmos at the German Conference on Bioinformatics. Call for Abstracts out now!

http://neXt.CELLmicrocosmos.org

 

At the Eurographics Workshop on Visual Computing for Biology and Medicine (EG VCBM), Thomas Waltemate will present a new approach which was developed in cooperation with Prof. Mario Botsch in the context of Thomas' excellent Master thesis. The resulting publications - which will be published shortly after the conference - has the title: "Membrane Mapping: Combining Mesoscopic and Molecular Cell Visualization".

More about the workshop you will find here: http://www.vcbm.org

By the way, the idea of this approach goes back to a master thesis of Marion Zysik from 2007. However, during this time, it was by far not possible to reach the impressing results from this cooperation project with Mario and Thomas as well as related multiscale projects from external groups.

At the 2014 International Workshop and Summer School on Biological Big Bytes in Harbin (P.R. China) we will present a talk discussing our latest achievements in the Cm4 project (20th August) and a short hands-on workshop (21st August):

 http://www.cls.zju.edu.cn/binfo/C3/2014/index.html

5th International German/Russian Summer School on "Integrative Biological Pathway Analysis and Simulation"

During the IB-PAS 2014 in Bielefeld, we will present a talk discussing "Cell Visualization and Animation", showing state-of-the art cell visualizations from international experts and artists, as well as some of our own first approaches in this research field.

More about the interesting program you will find here:

http://www.techfak.uni-bielefeld.de/ags/bi/ibpas2014/workshop/

 

In İzmir, a workshop will take place discussing translational and health informatics. In this context, the subcellular localization concept of the CELLmicrocosmos 4 project will be discussed: Subcellular Localization and Visualization of Database-Derived Biological Networks. More information can be found here: http://wtbm.iyte.edu.tr/courses/

Meet us in Nottingham at the conference Molecular Simulations and Visualizations Conference/Faraday Discussion 169. During the poster session, we will present the new release 2.2.2 of the MembraneEditor and the way it works with APL@Voro!

Our poster discussing the combination of the MembraneEditor and APL@Voro just won a poster prize at the Molecular Simulations and Visualizations Conference/Faraday Discussion 169 in Nottingham. The poster you will find here, together with all other posters presented during the last years in conjunction with the CELLmicrocosmos 2 project.

The poster prize is a very nice Ramos W32 tablet, equipped with the Android OS and YASARA (Yet Another Scientific Artificial Reality Application), a molecular modeling suite. More information you will find here: http://www.yasara.org/android.htm

We made already first experiments with this tool. Obviously it provides sophisticated methods to create different conformations of lipids for our MembraneEditor. In our future release, we will include a compatibility option for the PDB export for YASARA.

Thanks a lot go to the conference committee as well as the sponsors from YASARA!!!

For not even two months ago the major release 2.2.2 of the MembraneEditor is online. And now, the next minor release is online!

A few small but important changes have been made.

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.

The complete list of changes can be found here. Or, just proceed to the Cm2 project page.

After our successfull presentation of the topic "Stereoscopic Cell Visualization" at the conference Stereoscopic Display and Applications XXV. - where we won the SD&A Award for Best Use of Stereoscopy in a Technical Presentation - our paper "Stereoscopic cell visualization: from mesoscopic to molecular scale" was now published in the Journal of Electronic Imaging. Just proceed here: doi:10.1117/1.JEI.23.1.011007

For the third time we will be back to the VIZBI - one of the leading conferences in biological visualization! But this time (04.-07.03.2014), there will be also something brand new from our side: we will present a tutorial with the title CELLmicrocosmos Workshop: Molecular Modeling. This workshop will cover several approaches using our MembraneEditor in conjunction with Blender and APL@Voro. So it is about time that you have a look at the VIZBI page now!

The registration for VizBi 2014 will close January 31 2014.

New deadline for the registration for tutorials: February 15!

After two seminar discussing stereoscopic 3D visualization, a manuscript was submitted to the Stereoscopic Display and Applications XXV. It was accepted and will be presented next year in February.

More news you can find at:  http://www.stereoscopic.org/2014.

The program preview can be found here! So see you on Monday, 3rd February 2014 in San Francisco!

It was about time for the new major relase 2.2.2 of the MembraneEditor. A large number of bug fixes were added, but also some nice features are introduced.

One special new approach is the use of Gunther Lukat's APL@Voro which has been recently published. If this nice tool is installed on your Linux/Mac OS X machine and you link it with the MembraneEditor, a simple click on a button provides a fast analysis of the area per lipid as well as the membrane thickness of your membrane patch by using APL@Voro.

But there are many more features, it should be mentioned, that the Wanderer Rookie - a high-density membrane packing algorithm - had been added.

In addition, the front page with its "old style" was replaced by a fresh new one. This layout will also be applied later to the other sub projects.

But now, have a lot of fun with the new release of the MembraneEditor!

1.11.2013 Back in Black

After nearly 7 years, the CELLmicrocosmos site is relaunched!

The major advantage of the old site: it was completely programmed from the scratch during the master thesis of Björn Sommer. Of course, it was extended during the last years. Especially, the new sub-domains for the 4 sub projects were already added. But there was a small problem: everything had to be edited and updated by hand.

In times of content management systems and a fast changing web, this approach seems quite archaic.

And here is the new site! It unites the eye-catching cellular design of the old website with new CMS technologies of Joomla and its add-ons. Back in Black!

And of course, this is only the beginning. During the next months, this site will be updated and extended. So have a lot of fun with our new site!

Today, Ralf Rotzoll, André Heissmann and Alexander Schäfer (heroes #1-3) presented there diploma theses in the seminar of the Bio-/Medical Informatics Department. All topics were associated with the CELLmicrocosmos MembraneEditor. In the future, a number of nice extensions will come.

Moreover, our new paper based on the diploma thesis of Gunther Lukath (hero #4) was accepted, who is now a PhD student in Hamburg. Find the pre-version here: http://pubs.acs.org/journal/jcisd8. And please do not forget: the paper is nice, but the software is better, just download it here: APLVORO.org!

So congratulations to all you guys!

And with that, the CELLmicrocosmos website version 1, ran since several years, is saying good bye! The rebirth is scheduled for tomorrow evening, let us see, what happens!

This time we will present our new work based on the diploma thesis of Gunther Lukat. The talk is scheduled for Tuesday with the title Membrane Simulation Analysis using Voronoi Tessellation.

The program associated with this topic is called APL@Voro and can be downloaded from http://www.aplvoro.bplaced.net/.  The new publication on this topic will be published soon in the Journal of Chemical Information and Modeling. More information according the conference you can find at https://www.gdch.de/gcc2013.

We will present our new developments according the CELLmicrocosmos 4.2 PathwayIntegration project during a poster and software presentation at the IB 2013. Moreover, hot news about the Journal of Integrative Bioinformatics will be introduced there.

Summarizing several years of student projects, discussions, lectures, theses, conference contributions, etc., a first overview is now online available; the dissertation of Björn Sommer, entitled: CELLmicrocosmos - Integrative Cell Modeling at the Molecular, Mesoscopic and Functional Level.

The dissertation contains the most important developments of the past few years, the biological and technical background, a large number of related works, theoretical observations, as well as future directions for cell modeling.

The abstract as well as the whole thesis can be freely accessed at PUB: http://pub.uni-bielefeld.de/publication/2557380

The second season of the new module at Bielefeld University is starting: InterZellVis. Some of the topics will be: Microscopy, Cytological History, 3D Stereoscopy, Java 3D, 2D/3D/4D Visualization, and much more!

It will be available for the following studies:

Naturwissenschaftliche Informatik, Bioinformatik und Genomforschung, Molekulare Biotechnologie, Medienwissenschaften, Medieninformatik und Gestaltung and it will contain these courses:

Additional information are found in the modul guide of the Technical Faculty.

Watch the 3D Intro at YouTube!

It is about time for our next PreRelease! After the PreRelease of the MembraneEditor some time ago - which is fully available since 2011 - now the PathwayIntegration will follow.

Together with the new publication in the Journal of Bioinformatics and Computational Biology which is now online, the project is now made freely available via Java WebStart. The FullRelease including the source code will follow in a few months with the publication of CmPI.

Read more and then: just start it!

Although this workshop is not devoted towards biological membranes, a poster will be presented entitled CELLmicrocosmos MembraneEditor and the GMX-Plugin - Modeling Membranes for MD Simulations. More information about this workshop can be found at http://www.nanolayer.org

In 2009, the MembraneEditor first visited the Model(l)ing 09. Now, it will return to Erlangen and we are looking forward to a very nice workshop. More information you will find at http://mmws2013.mgms-ds.de. More information about what we will present there you will find here later.

A chapter of CELLmicrocosmos is about to be completed: the defense of the PhD thesis of Björn Sommer entitled CELLmicrocosmos - Integrative Cell Modeling at the Mesoscopice, Molecular and Functional Level will take place at the CeBiTec building in G2-104.

Download the thesis here for free: http://pub.uni-bielefeld.de/publication/2557380.

This time we will present a brand new program developed by Gunther Lukat during his diploma thesis.

For this purpose, we submitted a last minute poster entitled APL@Voro: revealing lipid domains with planar subdivisions. For more information, please look at the GCC 2012 website.

APL@Voro, a very powerful tool to analyze the area per lipid behaviour of rectangular membranes simulated with Gromacs, can be found at: APLVORO.org.

Prof. Dr. Ming Chen, head of the Department of Bioinformatics at the Zhejiang University (Hangzhou, P.R.China) will give a a (english) block seminar in the context of the new module InterZellVis: Genome-wide biological Network Modeling and Analysis

More information can be found in the ekVV of Bielefeld Unviersity and the Cell Visualization Forum (incl. poster).

Like every semester, different short movies are presented in the CinemaxX Bielefeld produced from and with students during the UniVideoMagazin. But this time there is something special: a music video in stereoscopic 3D will be shown! And this was the chance we got to take: in the actual CELLmicrocosmos student's project, Tobias and Christian created a cell animation using the 3D software Blender. Somewhat a return to the roots, because the whole project once started with a cell animation!

After several weeks of hard work this video will now be shown in the CinemaxX as a special feature - in stereoscopic 3D!

More information on the 33. UniVideoMagazin ...

A talk and two posters will present the newest developments of the CELLmicrocosmos project. The BGRS - the 8th International Conference on Bioinformatics of Genome Regulation and Structure\Systems Biology - is a quite large multi conference providing a good overview of the actual scientific achievements in this area with a focus on the east/west cooperation.

More information on the BGRS at the official website ...

Already at the first VizBi (VIsualiZing BIological data) conference in Heidelberg in 2010 our project was attending with a poster. This time our poster will present the first version of the brand-new Vesicle Builder. Based on the plugin-interface of the MembraneEditor, an external Membrane Packing Algorithm was developed to create ellipsoid vesicles in a quite convenient way.

This time we will attend in addition a few very interesting workshops regardings Blender and Amira. Just go to the conference-page.

The following semester starting in April 2012, we will introduce a new modul at Bielefeld University: InterZellVis.

It will be available for the following studies:

Naturwissenschaftliche Informatik, Bioinformatik und Genomforschung, Molekulare Biotechnologie, Medienwissenschaften, Medieninformatik und Gestaltung and it will contain these courses:

Additional information are found in the modul guide of the Technical Faculty.

For the first time a sub-project of CELLmicrocosmos participated in the [science fair] - and won a prize! Hosted by Bielefeld University, this is a nice opportunity for especially young scientists to present their work.

The poster presented showed the latest developments of our CellExplorer Educational Edition (CE3) project, entitled: CE3: An eLearning Software for Cytological Education. Based on the CellExplorer, already part of a few publications, it is an approach to bridge the gap between university and common/grammar schools.

The poster contained information regarding the master theses of Marco Civico and Roland Orlik. Both thesis are based on the CELLmicrocosmos Cell Modeling project of SS2011 with four additional participants. We won in the category "best design" (best out of 30) and rumors say that we were also close to get the prize in the category "best interdisciplinary project". The prize money of 1.000 will be directly reinvested into CE3. More about the prize at the Bielefeld University News and more about the fair at <Perspektive 2011>. Congratulations from us to all winners!

The beta version of the project if located at CE3.CELLmicrocosmos.org

Never downloaded the MembraneEditor yet? See the preview videos first! A set of videos shows how to work with the MembraneEditor and gives some insights to its special features. In addition the according chapters in the user guide are linked, so that you are able to gain a deeper view into the application.

At 14:00 Marco Civico and Björn Sommer will present new developments of the CellExplorer Educational Edition project (CE3) at the IB-PAS 2011 in the ZIF (the full, extremely short conference title is: 2011 International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation). Results of the CELLmicrocosmos Cell Modeling project in SS2010 and following semesters will be presented as well as first achievements of Marco's master thesis.

At the 3rd International Workshop on Science Gateways for Life Sciences in London, Sebastian Rubert will present his talk Managing GROMACS Jobs through Grid Resources using the CELLmicrocosmos 2.2 MembraneEditor. The audience will be able to have a first glance on the final state of the tool of his master thesis. A first preview of his work was already presented at the Grid Workflow Workshop in Cologne in March.

The MembraneEditor is published now in the Journal of Chemical Information and Modeling. From today, the MembraneEditor is released on GPL3 and its source code is freely available to everybody.

To have a look at our publication, please visit the JCIM website.

To find out more about our cover graphic on JCIM, have a look at this website.

The Bio-/Medical Informatics Department returns to Novosibirsk. We will give their several talks during the opening session of the RCIBC Opening. At 11:40 we will give the presentation Visualization and Analysis of Biological Networks combining different Bioinformatic disciplines.

Sebastian Rubert will present a part of his Master Thesis at the Grid Workflow Workshop 2011 in Cologne. He implemented a prototype of an UNICORE interface between the MembraneEditor (CmME) and GROMACS. After the workshop a working paper will be published with the title: Grid Workflow Approach using the CELLmicrocosmos 2.2 MembraneEditor and UNICORE to commit and monitor GROMACS Jobs. This prototype is not part of the actual CmME Webstart application.

The talk in German language of Sebastian Rubert is online now at the SuGI portal.

During the year 2010 a manuscript was prepared, establishing a workflow between tools from the Bio-/Medical Informatics Department Bielefeld (including CELLmicrocosmos 4.2 PathwayIntegration) and the Institute of Cytology in Novosibirsk. The result is the puclication: Visualization and Analysis of a Cardio Vascular Disease- and MUPP1-related Biological Network combining Text Mining and Data Warehouse Approaches. The Supplementary Data and the link to the online publication can be found here.

Back to Goslar: For the third time the MembraneEditor visits the German Conference on Chemoinformatics. Together with Dr. Jens Krüger we will present a poster entitled Coarse-grained and All-atom MD Simulations with Gromacs Based on CELLmicrocosmos 2.2 Model Membranes (Poster MOM 22).

At the 3rd EuCheMS we will present and discuss new perspectives for the MembraneEditor using molecular modelling. We will present a poster entitled Development towards a CELLmicrocosmos 2.2 based M.D. Edition (Poster Va.013) and give a talk about CELLmicrocosmos 2.2 Application: Modelling of a Mitochondrial Bilayer Membrane (02.09.2010, 14 c.t., CCN West Saal Paris).

At the EMBO workshop Visualizing Biological Data (VizBi) we will give a short presentation entitled: CELLmicrocosmos 2010 Preview: Cell modelling based on enzymatic localization at the cellular and molecular level derived from life science relevant data.

We will present our Shortpaper CELLMICROCOSMOS 4.1 - An Interactive Approach to Integrating Spatially Localized Metabolic Networks into a Virtual 3D Cell Environment (Björn Sommer, Jörn Künsemöller, Norbert Sand, Arne Husemann, Madis Rumming and Benjamin Kormeier) at the BIOSTEC Bioinformatics Conference in Valencia at the Thursday Session.

For the exhibition of the Bundesministerium für Bildung und Forschung (BMBF) at the Grüne Woche in Berlin we present for the first time a plant cell built with the Cm 3.1 CellEditor. We significantly improved the software, the workflow as well as the quality of the cell components for this purpose. The abstract cell model will be shown with other works at an autostereoscopic display of the Frauenhofer Institute called 3D Kiosk.

We will present the brand-new version of the MembraneEditor during our talk at the German Conference on Chemoinformatics. It is scheduled at the Molecular Modelling Session and will start at 3:05 p.m. in the lecture hall of the Hotel Der Achtermann in Goslar.
Topic: CELLmicrocosmos 2.2: Advancements and Applications in Modeling of three-dimensional PDB Membranes.

For the first time in China there will be a small lecture concerning the Cm project at the 2009 International Summer School on Chips, Computers and Crops in Hangzhou.

During the Molecular Modelling Workshop we will present the MembraneEditor version 2.1 for the last time and already show some features of the new version 2.2 coming at the end of this year. In addition you may meet us at the Model(l)ing Conference 08.-11.09. afterwards.

The German Conference on Bioinformatics took place in Dresden and we presented a poster of the Cm2.1 project.

For ca. one week we will visit once again Novosibirsk and give a presentation about the actual state of work and talk about further cooperations at the Second International Autumn School for Young Scientists on Computational Systems Biology and Bioinformatics.

The Cm-Website has been extended to support the four different Cm projects 1-4 seperately. They are all directly available by their URLs, e.g. Cm2.CELLmicrocosmos.org, and by tabs on the right top of the site. Cm2 offers the PreRelease of Cm2.1 MembraneEditor (see 01.04.2009), Cm4 will soon offer the PreRelease of Cm4.1 PathwayIntegration. Cm3 CellEditor is at the moment only available as a module of Cm4 and Cm1 is still in development.

The Cover of the August issue of Informatik Spektrum was designed by combining the projects Cm2 MembraneEditor and Cm4 PathwayIntegration with visualization technics of Autodesk 3D Studio Max.

A few more information about this combination you will find in the printed August issue of Informatik Spektrum.

The following semester, we will restart our initial idea, the Cell Explorer. If you are interested, please come at 14:00 c.t. to C5-151. [more]

Finally we got our WebStart Version of the MembraneEditor running quiet well. If you are interested in testing our most advanced tool, just contact This email address is being protected from spambots. You need JavaScript enabled to view it. .

The lipid distribution extension and evaluation for the Cm2.1 project will be presented at 11:00 s.t. at D5-113.

We presented a poster at the 4. German Conference on Chemoinformatics / 22. CIC-Workshop held in Goslar and had a lot of fruitful discussions.

The preview for the CELLmicrocosmos 4.1 project has been at 14:00 c.t. at C5-151.

We presented our tools to our russian friends at the International Autumn School for Young Scientists on Computationals Systems Biology and Bioinformatics 2008 in the Institute of Cytology and Genetics.

The shortest preview on this page you will find here (for navigation use the arrow-keys). It was held at the project meeting of the Technical Faculty in H8.

The first revision of the Cell Editor is finished. The presentation took place in C5-151at 12 c.t..

We presented a first review paper of the Cm2.1 project at the Bioinformatics Research and Education workshop in Bielefeld.

The newest topic of CELLmicrocosmos is the Pathway Integration: Metabolic pathways should be integrated into a cell environment, using and modifying the Cm3 software and creating a new tool. The project preview has been at 14:00 c.t. at C5-151.

Sebastian, a participant of the Cm2.1 project, developed a plug-in interface for the integration of lipid distribution algorithms into the MembraneEditor. In addition, he added a powerfull Simulated Annealing algorithm, which shows already the high potential of this tool.

In the lecture of Prof. Ralf Hofestädt and Benjamin Kormeier dealing with metabolic pathways we presented an overview of the actual state of work. You can find the german presentation here.

For the last half year, Marion created a tool using C++ and VTK to visualize a combination of PDB and VRML models. It is the first approach to create an alternative to the comercial amira software from Mercury. She already implemented a side-by-side stereo and a membrane mapping function.

At 13:00 c.t. the final version of the Cm3 project will be presented in D5-113. To find out more about the Celleditor, which has been built in Java3D, have a look at this site, to find out more about the project talks, enter the aim page.

The end of the Cm3 cell editor project is near - and still there are so many new ideas which are waiting for their implementation. The first meeting of the new project will be in C5-151 at 14:00 c.t.. Infos about Cm3 you can get here.

First planned as an update of the Cm2 MembraneEditor, now a completely built from scratch version of the Cm2.1 MembraneEditor will be presented at 11 o'clock in D5-113 during the ag bi meeting. [more]

The introduction of the new project for the SS2007 will take place in C5-151 at 10 o'clock. The primary aim will be the generation of a simple cell model. Find out more in the introduction!

Five months after the presentation of CELLmicrocosmos II the first lesson oft the Cm2.1 project took place in C5-151 and we are still looking for some more participants. Just have a look at the introduction!

The master-thesis has to be finished at this date. Soon there will be some presentations concerning the project. If you are interested, just send an email to This email address is being protected from spambots. You need JavaScript enabled to view it. .

At his date there has been a presentation of the actual state of the master-project in C5-151 as a part of the seminar Arbeitsgemeinschaft Bioinformatik. If you want to have a look at the presentation, please refer to the master-thesis-page.

The presentation of our CELLmicrocosmos II project took place in C5-151 and we showed our MembraneEditor during the seminar Arbeitsgemeinschaft Bioinformatik.

To get a first glance at some of our results, you should have a look at our Cm2-page.