news

Site Updates and Fixes

01.11.2023

Due to an Hacker attack some time ago, the CELLmicrocosmos website had to be restored from a backup. In the process, the links to the software MembraneEditor and CellExplorer were broken. Those were fixed now.

Moreover, the poster pages did not work anymore correctly, they are also fixed now. Here is an example.

In addition, the APL@Voro website was updated.

Please note that the old forum had to be removed as the phpBB version was very old and seemed to have been the entry point for the original attack.

Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 29 October 2023; Hits: 767

Design X Bioinformatics

09.09.2022 London/Paris/Fukuoka, 1-5 pm (UK time)

With this initiative, we are intending to bring together Bioinformaticians from various fields, and designers, design researchers, as well as medical and scientific illustrators to discuss future challenges in the context of Bioinformatics and Design. Being an area which often combines abstract and spatial data, and often taking standardisation approaches into account, Bioinformatics provides a number of opportunities for future designers. In addition, we want to contextualise Design X Bioinformatics towards the newly emerging field of BioDesign, which uses the biological affordances of organisms to address some user needs, e.g. in terms of material development, applications of synthetic biology, or the creation of bio-digital hybrid systems.

http://desxbioinf.i2d.uk/

This workshop will take place hybrid: at London and Paris, in-person events will be planned!

Bioinformatics is an area which is applying computer science-related approaches to biological data analysis. It is widely known for providing genomics-based analytical approaches which were supporting, e.g., the 1000 Genomes Project. But it also relates to many other fields, such as analysis of microscopic images (e.g. organelle location), molecular modelling (e.g. proteins, biological membranes), or biological network visualisation (e.g. protein-protein interaction networks, metabolism).

Design is a highly interdisciplinary field integrating aspects, such as aesthetic, economic, functional, philosophical and/or socio-political considerations, and is usually driven by context. Whereas visualisation plays a crucial role in Bioinformatics, reflected by a number of conferences and workshops in this field, design in particular is not so well investigated in bioinformatics-related research contexts.

Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 14 August 2022; Hits: 1789

A new version of APL@Voro is in preparation!

Beta testers welcome!

Check-out the new video!

Since a couple of months we are working on a new version of APL@Voro - one of our best-cited tools!

The new version 3.3.3 will come with a couple of new functionalities! Martin Kern, the current main developer, invested a lot of effort to stream-line the code and provide an extended functionality. The biggest change will be the option to load an compare a number of membrane simulations in parallel. And as always in APL@Voro: with LIVE view!

Also, a new short article is currently under review.

The new website is available from:

http://aplvoro.com/

The new website is also hosted on the CELLmicrocosmos server!

Details: Written by bjoern

Immersive Exploration of Cell Localization Scenarios Using VR, Spatialized Video Communication, and Integrative Bioinformatics

We published a new book chapter in the Springer book: "Integrative Bioinformatics"!

The cell models we used as the base in this chapter were created with the Cm 4.2 PathwayIntegration!

Bjorn Sommer, Ayn Sayuti, Chang Hee Lee, Zidong Lin, Jenny Hu & Ashley Hall

Integrating spatially localized molecular networks into virtual cell environments is an approach which is only provided by a very small number of tools. As this task requires the combination of a set of Biotechnology/Bioinformatics-related information sources, it can be seen as an appropriate example for Integrative Bioinformatics research. Here, we want to show new immersive perspectives for cytological pathway integration by combining recent explorative technologies with the software CELLmicrocosmos 4 PathwayIntegration. A mesoscopic-localized metabolic pathway—i.e. the citrate cycle and the glycolysis—is localized based on database entries onto an abstract cell environment of Arabidopsis thaliana. The created cell model is used in three different contexts providing different degrees of immersion:

Web-based 2D exploration of 3D Scenarios (using Gather.town),
Exploration and Annotation in a VR Design Application (using Gravity Sketch), and
Large-Scale VR Visualization and Navigation (using the CAVE2 and zSpace).

All these examples promise to be very useful in the context of Integrative Bioinformatics-related education as well as communication.

https://doi.org/10.1007/978-981-16-6795-4_14

Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 16 April 2022; Hits: 1594

EUROVIS 2021 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

4th Workshop at the EUROVIS 2021  !ONLINE!

For the 4th time, the MolVA 2021 - Workshop on Molecular Graphics and Visual Analysis of Molecular Data is taking place in the context of the EuroVis 2021. The workshop will run from 8:00 am to 11:40 UK time and will virtually take place this year in Zurich, Switzerland.

The whole program can be found here!

The participation in the whole prestigious EuroVis2021 conference will be this year for free! If you would like to join for some of the talks, please register here.

Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 June 2021; Hits: 1464

EUROVIS 2020 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

Workshop at the EUROVIS 2021 

The workshop will be held in Zurich, Switzerland, June 14, 2021 as part of EuroVis 2021.

Molecular visualization is one of the oldest branches of scientific visualization, which has been developing for over 50 years. Nevertheless, it is still a very active research area mainly due to the continuous advances in computational biology and computer graphics techniques. Not only the ever-increasing dataset sizes yield a constant challenge for visual analysis, but also new technologies like advances in web-based graphics or augmented and virtual reality open new possibilities.

This multidisciplinary workshop – which is held in conjunction with EuroVis for the fourth time – brings together visualization and computer graphics researchers working with molecular data.

This year the MolVA Workshop teamed up with Computer and Graphics journal and we are happy to announce that the submitted papers will be accepted either as journal publications or conference-only publications. The journal publications will be published directly in Computers and Graphics Journal (C&G) Special Section on Molecular Graphics and Visual Analysis of Molecular Data, while the conference-only papers will be published in EG Digital Library. Moreover, the conference-only publications will be offered to submit an extended version that will undergo another peer-reviewed process and can be still accepted as a journal publication after the workshop.

We invite short papers as well as full papers (2-4 pages for short and up to 8 pages for full papers, both with an additional page reserved for references). Note that short papers are not eligible for journal publication but can be extended after the workshop to full-papers and submitted in the second round.All submissions will be fully peer-reviewed by at least three experts according to the standards of Computers and Graphics Journal. You can find the complete author guidelines at: https://www.elsevier.com/journals/computers-and-graphics/0097-8493/guide-for-authors.

All accepted papers will be presented at MolVA 2021 Workshop which will be co-located with EuroVis 2021 in Zurich, Switzerland. Therefore, at least one of the authors of an accepted paper will have to register and attend the workshop.We hope that MolVA 2021 can be held as an in-person conference but depending on the pandemic situation next year, we may adhere to some preventive measures. We will follow the scheme that will be put in place by EuroVis conference.

Suggested topics for papers include, but are not limited to:

Molecular Graphics & Rendering
Web-based Molecular Graphics & Visualization
Immersive Analytics approaches using, e.g., VR/AR technologies
Visual Analysis of Molecular Data (e.g., molecular structures, biological networks and pathways, or omics data)
Visualization of Dynamic Molecular Data & Large Molecular Systems
Machine-learning approaches for analysis of molecular data
Tools papers describing new molecular visualization tools or novel features in existing tools

Please find more info here: http://decibel.fi.muni.cz/~xbyska/molva

Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 03 November 2020; Hits: 4392

Bio Visualization with Blender and MembraneEditor - An Introduction

The workshop will be virtually held via Zoom, September 10th, 2020, 13:00 - 15:00 UTC (15:00 - 17:00 CEST, 2 - 4 pm UK), as satellite event of the GMDS conference.

Conferences like VizBi or BioVis show that biomedical visualization is crucial in many fields. In this mini workshop we will introduce methods using different software packages to visualize molecular data without the need of complex background knowledge. This mini workshop will come with a brief introduction talk to the field of bio visualization, an overview of the relevant software packages and resources, as well as life demos of how to use these software packages. Topics will be covered from creating membranes and building vesicles with the MembraneEditor, over design of biology-related 3D models with Blender. We will also give a short outlook regarding molecular simulations based on the models created.

The workshop will take place via Zoom. Follow-up workshops are planned with hands-on sessions for the different tools - interested participants can register for this purpose afterwards.

Attendance is free - please register here and you will get the link to join the Zoom Webinar:

https://rca-ac.zoom.us/webinar/register/WN_ggy0MoOGSOWFVTIWSKjVmg

Please also have a look at the original GMDS & CEN-IBS 2020 conference website and the other satellite sessions - there are a number of other exciting events available:

https://www.gmds-cen-2020.de/satellite-session

Tutor:
Dr. Bjorn Sommer
CELLmicrocosmos project lead
Research Tutor/Year 1 Lead, Innovation Design Engineering, Royal College of Art

Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 September 2020; Hits: 3234

Vesicle Builder 1.11 and MembraneEditor 2.2.2_3_beta02 Release at the

EUROVIS 2020 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

The workshop will be virtually held in Norrköping, Sweden, May 25th, 2020 as part of EuroVis 2020.

We will present the Vesicle Builder for the first time at a conference and will launch our brand new MembraneEditor beta relase!

Please follow the Start button until you find the download for:

BETA Test@MolVA2020: MembraneEditor 2.2.2_3beta02

https://www.cellmicrocosmos.org/index.php/cm2-project

More Info regarding the MolVA2020 Workshop and the exciting program:

http://decibel.fi.muni.cz/~xbyska/molva

To join the conference, please find here the regarding links:

https://weber.itn.liu.se/~marfa45/egev2020/

Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 25 May 2020; Hits: 2838

EUROVIS 2020 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

Workshop at the EUROVIS 2020

The workshop will be held in Norrköping, Sweden, May 25th, 2020 as part of EuroVis 2020.

Deadline extended until February 29, 2020.

Molecular visualization and graphics is one of the oldest branches of scientific visualization, which has been developing for over 50 years. Due to the continuous advances in both computational biology and computer graphics techniques, molecular graphics and visualization are very active areas of research. Not only the ever-increasing dataset sizes yield a constant challenge for visual analysis, but also new technologies like advances in web-based graphics or augmented and virtual reality open new possibilities. This half-day multidisciplinary workshop - which is held in conjunction with EuroVis for the third time and with Eurographics for the first time - brings together visualization and computer graphics researchers working with molecular data.

Suggested topics include, but are not limited to:

Molecular Graphics & Rendering
Web-based Molecular Graphics & Visualization
Immersive Analytics approaches using, e.g., VR/AR technologies
Visual Analysis of Molecular Data (e.g., molecular structures, biological networks, and pathways, or omics data)
Visualization of Dynamic Molecular Data & Large Molecular Systems
Tools papers describing new molecular visualization tools or novel features in existing tools

Please find more info here:

http://decibel.fi.muni.cz/~xbyska/molva

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 10 January 2020; Hits: 2856

EUROVIS 2019 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

Workshop at the EUROVIS 2019
The workshop will be held in Porto, Portogal, June 3th, 2019 as part of EuroVis 2019.

Molecular visualization is one of the oldest branches of scientific visualization, which has been developing for over 50 years. Due to the continuous advances in both computational biology and computer graphics techniques, molecular graphics and visualization are still very active areas of research. Not only the ever-increasing dataset sizes yield a constant challenge for visual analysis, but also new technologies like advances in web-based graphics or augmented and virtual reality open new possibilities. In this half-day workshop, which is held for the second time in conjunction with EuroVis, we would like to initiate a multidisciplinary meeting which brings visualization researchers together working with molecular data.

Whereas molecular graphics is an established topic since many years, the hybrid-dimensional visual analysis of molecular structures is still a quite new research field with a lot of potential. We would like to encourage submissions especially using new technologies, such as immersive analytics-related approaches.

Please find the full program here:

http://decibel.fi.muni.cz/~xbyska/molva

Organizers and Contact

Jan Byska, University of Bergen, Norway

Michael Krone, University of Tübingen, Germany

Björn Sommer, University of Konstanz, Germany (Sadly, I cannot be there this time)

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 May 2019; Hits: 3071

Visualizing Biological Data (VIZBI 2019)

10 years of Visualizing Biological Data will be celebrated this year in Heidelberg at the EMBL. An amazing program with Janet Iwasa, Hadley Wickham, Moritz Stefaner as keynote speakers will bring you the new trends in bio visualization.

At the molecular level their will be a session on "Proteins" with Marc Baaden, David Sehnal, and Peijun Zhang as speakers.

Please check out the full program here:

https://vizbi.org/2019/Program/

Also, make sure to do not miss the Art & Biology event on Thursday evening - exciting things will be shown there!

See you in Heidelberg!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 27 February 2019; Hits: 3173

Hand-on in Konstanz: Bio Visualization with Blender and MembraneEditor

In the context of the Konstanz Research School Chemical Biology (KoRS-CB), Mehmood Ghaffar (IPK Gatersleben) and Bjorn Sommer (University of Konstanz) will give a hands-on workshop on how to use Blender and the MembraneEditor.

It will take place at the University of Konstanz in on 25-26 February, 9-18 h, in M 631.

The visualisation of biological mesoscopic and molecular structures – such as cells and 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.

This two-day hands-on workshop will introduce to basic modelling and visualisation techniques with Blender and CELLmicrocosmos MembraneEditor on the first day. The second day will be devoted towards the use of web technologies in combination with Blender and Virtual Reality-related technologies to communicate the 3D models.

https://www.chembiol.uni-konstanz.de/training/scientific-courses/

Please find the corresponding software here:

Please find the corresponding forum entries here:

https://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=63&t=8172

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 February 2019; Hits: 3124

EUROVIS 2019 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

Call For Papers
Workshop at the EUROVIS 2019
The workshop will be held in Porto, Portogal, June 3th, 2019 as part of EuroVis 2019.

!Deadline extended to March 8, 2019!

We invite short papers as well as full papers (2-4 pages for short and up to 8 pages for full papers, both with an additional page reserved for references). All papers will undergo a single-stage, double-blind peer review process. Accepted papers will be published in the EG digital library. The workshop will be held in Porto, Portugal, June 3th, 2019 as part of EuroVis 2019.

Suggested topics include, but are not limited to:

Molecular Graphics
Visual Analysis of Molecular Data (e.g., molecular structures, biological networks and pathways, or omics data)
Visualization of Dynamic Molecular Data
Visualization of Large Molecular Systems
Web-based Molecular Graphics and Visualization
Immersive Analytics approaches using, e.g., VR/AR technologies
Tools papers describing new molecular visualization tools or novel features in existing tools

More info here:

http://decibel.fi.muni.cz/~xbyska/molva

Important Dates

Paper Submission Deadline: ~~February 28, 2019~~ !Deadline extended to March 8, 2019!

Notification of Acceptance: April 5, 2019

Camera-ready Deadline: April 15, 2019

Workshop Date: June 3, 2019

Organizers and Contact

Jan Byska, University of Bergen, Norway

Michael Krone, University of Tübingen, Germany

Björn Sommer, University of Konstanz, Germany

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 22 November 2018; Hits: 3230

BDVA 2018 Workshop on Immersive Molecular Modelling Workshop - ImmMolMod

In the context of the BDVA 2018 conference which we are organizing at the University of Konstanz (17.-19.10.2018) we will present a workshop on Immersive Molecular Modelling (ImmMolMod, nice abbreviation, right? ;-) .

In contrast to many other biochemical research areas where the applicability of immersive visualization and analysis still has to be proven, molecular data profits from spatial visualization since many years.

In this workshop, a number of tools will be presented which fall into the area of molecular modelling, docking and simulation.

http://bdva.net/2018/index.php/immersive-molecular-modelling-workshop/

This workshop is intended as a kind of hands-on extension of the MolVA workshop organized at the EUROVIS 2018 conference in Brno together with Jan Byška and Michael Krone:

http://decibel.fi.muni.cz/~xbyska/molva

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 07 August 2018; Hits: 3708

Presentation at VINCI 2018

Ath VINCI 2018 conference in Växjö, Sweden, Mehmood Ghaffar will present his work on membrane modeling with Blender:

https://vinci-conf.org/program.html#session3

Mehmood Ghaffar, Niklas Biere, Daniel Jäger, Karsten Klein, Falk Schreiber, Olaf Kruse and Björn Sommer
3D Modelling and Visualisation of Heterogeneous Cell Membranes in Blender

After publication, the ACM paper will be available here:

https://dl.acm.org/citation.cfm?doid=3231622.3231639&preflayout=flat

In the context of his Master thesis, Mehmood developed a Blender plugin which can be used to generate membrane models which can be animated in the following steps. His work was used to improve the 3D-stereoscopic Chlamydomonas visualization found at YouTube:

https://www.youtube.com/watch?v=qXJ2IYpB-5g

More information as well as the Blender plugin can be found at our new Cell Visualization web site:

http://Cm5.CELLmicrocosmos.org

The PDF of a related poster is available from here:

http://cellmicrocosmos.org/index.php/cm5-project/cm5-project-posters

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 06 August 2018; Hits: 3707

Konstanz Sino-German Mini Workshop on Bioinformatics and Bio Visualization

Friday, 10.08.2018, University of Konstanz, PZ1001

14:00
- Keynote: Non-coding RNAs and their intertwining networks
- Prof. Ming Chen, Group of Bioinformatics, Zhejiang University
  Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to non-coding RNA (ncRNA) study. We investigated plant transcriptome to characterize non-coding RNAs including microRNAs, siRNAs, lncRNAs, ceRNAs and cirRNAs. They are emerging as key players in gene regulatory networks by interacting with other biomolecules (DNA, RNA or protein). We developed several bioinformatics databases and pipelines to facilitate better understanding of the regulation of non-coding RNAs. An overview of ncRNA repertoire and highlight recent discoveries of their versatile interactions is introduced.
14:40
- Mini Workshop Welcome and Program
- Björn Sommer, Computational Life Sciences, University of Konstanz
14:45
- Introduction of Zhejiang University and team members
- Junshen She, Group of Bioinformatics, Zhejiang University
15:00
- Introduction to University of Konstanz and team members
- Björn Sommer, Computational Life Sciences, University of Konstanz
15:15
- 3DLAP: Lysine Acetylation Site Prediction Tools
- Sida Li, Group of Bioinformatics, Zhejiang University
15:30
- Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition
- Sabrina Jaeger, Computational Life Sciences, University of Konstanz

Coffee Break

The Application of Bioinformatics in Lung Cancer
Yang Shen, Group of Bioinformatics, Zhejiang University

16:30
- Network Analysis for Collective Behaviour
- Michael Aichem, Computational Life Sciences, University of Konstanz
16:45
- Benchmark of single cell RNA-seq clustering methods
- Tianyang Zheng, Group of Bioinformatics, Zhejiang University
17:00
- Visual analytics of biological networks using VANTED and its SBGN-ED add-on
- Hanna Borlinghaus, Computational Life Sciences, University of Konstanz
17:15
- POI Clustering and Prediction based on Human Mobility Data
- Yunlong Wang, Human-Computer-Interaction, University of Konstanz
17:30
- Discussion & Closing Remarks
17:45
- Computational Life Sciences Demo Session in the Immersive Lab
18:30
- Leaving for Dinner
19:00
- Mini Workshop Dinner
- If you would like to join, please contact the organizer, we have to reserve places.

Organizer: Björn Sommer

Co-Organizers: Stefan Brütsch, Sabrina Jaeger, Michael Aichem

With the kind support from Christine Agorastos

Financial support by Falk Schreiber, Computational Life Sciences, University of Konstanz

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 05 August 2018; Hits: 5780

Finally! Project 5 is online! Cell Visualization!

After already presenting a number of preliminary Cell Visualization videos at conferences, we finally present our "Chlamydomonas 3D - From Biological Cells to Biofuels" animation! And of course, in stereoscopic 3D!

Together with this animation, the publication discussing the visualization process was published. Find it here at the Journal of Integrative Bioinformatics: "Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell".

Just go on to our new website hosting all Cell Visualization videos released in the context of this project.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 12 July 2018; Hits: 3625

Integrative Bioinformatics 2018 conference

This time, our Integrative Bioinformatics conference will take place very close to London, at Harpenden/Rothamsted Research. We will also present a talk there with the title: "Immersive Analytics in Integrative Bioinformatics".

More info here:

https://agbi.techfak.uni-bielefeld.de/imbio/ib2018/

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 03 May 2018; Hits: 3347

EUROVIS 2018 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

At the EUROVIS 2018 conference, we will present together with Jan Byška and Michael Krone the MolVA Workshop - Molecular Graphics and Visual Analysis of Molecular Data. Two leading scientists in the molecular visualization community will give keynotes: Séan O'Donoghue and John E. Stone. They will talk about "Visualizing Biomolecular Structures for Research and Outreach" and "Visualization Challenges and Opportunities Posed by Petascale Molecular Dynamics Simulations", respectively. 5 paper presentations will complete the program.

More info here:

http://decibel.fi.muni.cz/~xbyska/molva

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 May 2018; Hits: 5575

From Virtual Reality to Immersive Analytics in Bioinformatics

The registration for our special session and the corresponding Stereoscopic Displays & Applications 2018 conference is open now!

http://www.imaging.org/site/IST/IST/Conferences/EI/EI_2018/Registration.aspx

More info regarding the special session you can find here:

http://vr2iainbioinf.immersive-analytics.org

Please join us: 28 January - 1 February, 2018 in Burlingame, California USA

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 January 2018; Hits: 4007

Applied Bioinformatics Winter School in Canazei

Please join us to the Winter School organized by Verona University. A few places for PhD students and PostDocs are still left!

There will be a number of exciting talks, with a focus on molecular modeling. During this winter school the participants will learn about:

Bioinformatics as a science
Designing bioinformatic studies
Resources for bioinformatics

We will give a talk on Cell Visualization.

https://www.winterschoolbiotech2018.com

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 28 December 2017; Hits: 3848

EUROVIS 2018 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

Call For Papers
Workshop at the EUROVIS 2018
The workshop will be held in Brno, Czech Republic, June 4th, 2018 as part of EuroVis 2018.

Molecular visualization is one of the oldest branches of scientific visualization. Due to the continuous advances in both computational biology and computer graphics techniques, molecular graphics and visualization are still very active areas of research. Not only the ever-increasing dataset sizes yield a constant challenge for visual analysis, but also new technologies like advances in web-based graphics or augmented and virtual reality open new possibilities. In this half-day workshop, which is held for the first time in conjunction with EuroVis, we would like to initiate a multidisciplinary meeting which brings visualization researchers together working with molecular data.

Potential topics include:

Molecular Graphics
Visual Analysis of Molecular Data
Visualization of Dynamic Molecular Data
Visualization of Large Molecular Systems
Web-based Molecular Graphics and Visualization
Immersive Analytics approaches

More info here:

http://decibel.fi.muni.cz/~xbyska/molva

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 December 2017; Hits: 4033

Talk at the Konservatorium of the TU Wien

CELLmicrocosmos visits the group of Meister Eduard Gröller at the TU Wien in Vienna! We will give a presentation with the topic: Multiscale Modeling and Visualization of Cells and their Membranes. More info here:

https://www.cg.tuwien.ac.at/courses/konversatorium/2017-11-10

Thanks a lot for the kind invitation!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 November 2017; Hits: 3712

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 August 2017; Hits: 4090

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 August 2017; Hits: 4075

@cellmicrocosmos joins the Twitter family

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

Follow @cellmicrocosmos

Or just have a look to:

https://twitter.com/cellmicrocosmos

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 August 2017; Hits: 4488

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 08 May 2017; Hits: 4795

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 07 May 2017; Hits: 4944

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 05 January 2017; Hits: 5377

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 30 August 2016; Hits: 4681

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 08 August 2016; Hits: 7222

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 August 2016; Hits: 4505

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 25 July 2016; Hits: 4516

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!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 16 June 2016; Hits: 4571

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 24 January 2016; Hits: 5904

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 24 January 2016; Hits: 4846

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 23 January 2016; Hits: 6250

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.

NUESTRAS MARCAS

Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 09 September 2015; Hits: 4774

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 04 September 2015; Hits: 5298

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 31 August 2015; Hits: 6672

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 June 2015; Hits: 5204

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 May 2015; Hits: 5642

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 April 2015; Hits: 4645

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?

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 31 March 2015; Hits: 4692

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]

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 20 February 2015; Hits: 5246

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 05 January 2015; Hits: 7683

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

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

CELLmicrosomos neXt proceedings
Björn Sommer (Ed.)(DOI: 10.2390/biecoll-next2014-0)

CELLmicrosomos X
Björn Sommer (DOI: 10.2390/biecoll-next2014-1)

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)

Evaluation and Visualization of Pathway Efficiency based on Subcellular Protein Localizations
Olga Popik, Björn Sommer, Ralf Hofestädt, Vladimir A. Ivanisenko (DOI: 10.2390/biecoll-next2014-3)

Top-down Systems Biology Approaches for -omics-based Tissue and Biofluid Analytics
Kirill Veselkov (DOI: 10.2390/biecoll-next2014-4)

Web-based Visualization with D3
Ahmet R. Öztürk (DOI: 10.2390/biecoll-next2014-5)

Towards a web-based Viewer for the PathwayIntegration
Gökhan Kovanci, Björn Sommer (DOI: 10.2390/biecoll-next2014-6)

Web-based MD Simulations using MoSGrid
Jens Krüger (DOI: 10.2390/biecoll-next2014-7)

Towards Pathway Prediction and Subcellular Localization by using FraMeTex
Thorben Wallmeyer, Björn Sommer, Benjamin Kormeier (DOI: 10.2390/biecoll-next2014-8)

A novel Lecture Program in Bioinformatics: Interdisciplinary Cell Visualization and Modeling
Björn Sommer and Ming Chen (DOI: 10.2390/biecoll-next2014-9)

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 11 November 2014; Hits: 5447

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

http://neXt.CELLmicrocosmos.org

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 14 July 2014; Hits: 5905

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 13 July 2014; Hits: 5746

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 13 July 2014; Hits: 5823

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/

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 28 May 2014; Hits: 5661

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/

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 17 May 2014; Hits: 5543

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!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 April 2014; Hits: 5636

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!!!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 April 2014; Hits: 7123

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 17 March 2014; Hits: 5076

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 05 March 2014; Hits: 5493

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!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 February 2014; Hits: 7311

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!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 February 2014; Hits: 5882

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!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 28 January 2014; Hits: 5694

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!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 November 2013; Hits: 5157

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!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 November 2013; Hits: 5663

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 28 October 2013; Hits: 5592

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 March 2013; Hits: 6086

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 20 February 2013; Hits: 11707

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:

Lecture: Interdisziplinäre ZellVisualisierung (3CP, SS2013)
Seminar: Cell Visualization (2 CP, SS2013)
Project: CELLmicrocosmos Cell Modelling (5 CP, SS2013 or WS2013-14)

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

Watch the 3D Intro at YouTube!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 20 February 2013; Hits: 7428

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!

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 18 February 2013; Hits: 6298

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 February 2013; Hits: 6037

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 February 2013; Hits: 6246

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 January 2013; Hits: 6344

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 November 2012; Hits: 6661

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).

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 July 2012; Hits: 6085

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 ...

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 July 2012; Hits: 6952

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 ...

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 June 2012; Hits: 6163

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 March 2012; Hits: 6315

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:

Lecture: Interdisziplinäre ZellVisualisierung (3CP, SS2012)
Seminar: Cell Visualization (2 CP, SS2012)
Project: CELLmicrocosmos Cell Modelling (5 CP, SS2012 or WS2012-13)

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 March 2012; Hits: 6183

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 24 November 2011; Hits: 6756

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 November 2011; Hits: 5693

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 July 2011; Hits: 6295

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 June 2011; Hits: 6522

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 24 May 2011; Hits: 6309

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 20 April 2011; Hits: 7463

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 March 2011; Hits: 6074

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 12 November 2010; Hits: 5575

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).

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 November 2010; Hits: 7408

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).

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 August 2010; Hits: 6052

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 May 2010; Hits: 6279

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 03 January 2010; Hits: 5824

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 January 2010; Hits: 5966

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 November 2009; Hits: 5927

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 03 September 2009; Hits: 6014

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 September 2009; Hits: 6086

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 September 2009; Hits: 5049

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 September 2009; Hits: 5812

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 04 August 2009; Hits: 5325

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 August 2009; Hits: 7086

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]

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 April 2009; Hits: 4902

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. .

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 April 2009; Hits: 4910

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 November 2008; Hits: 4743

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

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 November 2008; Hits: 5280

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

Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 01 October 2008; Hits: 4481

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.

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Details: Written by bjoern; Category: CELLmicrocosmos NEWS; Published: 02 September 2008; Hits: 4863

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Site Updates and Fixes

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Design X Bioinformatics

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Beta testers welcome!

Check-out the new video!

Immersive Exploration of Cell Localization Scenarios Using VR, Spatialized Video Communication, and Integrative Bioinformatics

EUROVIS 2021 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

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EUROVIS 2020 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

Workshop at the EUROVIS 2021

Konstanz Sino-German Mini Workshop on Bioinformatics and Bio Visualization

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

1.11.2013 Back in Black

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