Immersive Cell Exploration and Membrane Modeling

10.10.2015, Bjorn Sommer, Immersive Analytics Initiative, Monash University

2/401. Immersive Analytics

1. Immersive Analytics

3/401.1 Immersive Analytics | The Initiative

Immersive Analytics Initiative, Monash University

Lead by

Prof. Dr. Kim MariottProf. Dr. Falk SchreiberDr. Tim Dwyer

https://immersive-analytics.infotech.monash.edu

4/401.2 Immersive Analytics | Definition

Immersive Analytics

is “the science of analytical reasoning facilitated by interactive visual interfaces”

Thomas, J. J.; Cook, K. A., Eds., „Illuminating the path: The research and development agenda for visual analytics.“ IEEE Computer Society Press, 2005.

New Horizons BuildingMonash University, Clayton Campus

CAVE2 in New Horizons

5/402. Cell Visualization

2. Cell Visuali-zation

6/402.1 Cell Visualization | Granularity Levels

Granularity Levels

Light Microscopy

Confocal Microscopy

Electron Microscopy

High Resolution Techniques

Mesoscopic Level

Molecular Level

(MolecularLevel)

[NaNe06] [Arbo08][KKWZ08][Mpi11,BWFG00]

7/402.2 Cell Visualization | CELLmicrocosmos

CELLmicrocosmos

virtual cell modeling

Systems Biology approach

static approach; no internal simulation

visual approachfollows the Bauhaus idea

8/402.3 Cell Visualization | CELLmicrocosmos Projects

CELLmicrocosmos Projects

CmCX: CellExplorer

CmME: MembraneEditor

CmCE: CellEditor

CmPI: PathwayIntegration

Mesoscopic Level

Molecular LevelFunctional Level

based onJava/Java3D/JOGL

9/402.4 Cell Visualization | Workflow

Cell Modeling Workflow

10/403. Mesoscopic Level

3. Cell Modeling at the Mesoscopic Level

11/403.1 Mesoscopic Level | Abstraction Levels

Abstraction Levels

AL0. Ideal Value: a realistic copy (Clone)

AL1. 3D microscopy-/spectroscopy-based models (Image)

AL2. Interpretative Models (Allegory)

AL3. Abstract Models (Abstraction)

[UdKo82]

[MGWQ02]

12/403.6 Mesoscopic Level | Layers

Layer-dependent Modeling/Mapping

5 mitochondrial layersdatabase BRENDA CmPI→

13/404. Functional Level

3. Cell Modeling at the Functional Level

14/404.1 Functional Level | 2D Visualization

3.1 2D Visualizationin CmPI of the Citrate Cycle

KEGG by DAWIS-M.D.

pathway hsa00020

Also supports

SBMLGraphML

15/404.2 Functional Level | CmPI Workflow

CmPI Workflow

CELLmicrocosmos PathwayIntegration

CmPI Workflow

web: http://Cm4.CELLmicrocosmos.org

CmPI Workflow

DAWIS-M.D.[HKT+10]

based on BioDWH

contains a number of metabolic disease-related databases

applied subset

Brenda Gene Ontology (GO) ReactomeUniProt

CmPI Workflow

ANDCell[POSS08]

commercial database PBSoft Ltd.

applied database

PubMed abstractstext mining-based associations cell component/proteinassociations

16/404.3 Functional Level | Localization Charts

3.4 Localization Charts and the Citrate Cycle

The same method can be applied to

Glycolysis Cytosol→Cytological Disease Mapping

Sommer, B.; Kormeier, B.; Demenkov P. S.;et al.: Subcellular Localization Charts: A new visual methodology for the semi-automatic localisation of protein-related data sets. Journal of Bioinformatics and ComputationalBiology 11 (2013), no. 1, pp. 1340005, 2013

17/404.4 Functional Level | 2D Visualization

3.3 The Node Mapping Process

18/404.5 Classic 3D Navigation | Examples

Mesoscopic and Functional Level

Cytological Network Exploration (Demo)

Sommer, B.; Künsemöller, J.; Sand, N.; Husemann, A.; Rumming, M.; Kormeier, B.: CELLmicrocosmos 4.1: an interactive approach to integrating spatially localized metabolic networks into a virtual 3D cell environment. In: BIOSTEC BIOINFORMATICS 2010 Proceedings, pp. 90–95

19/405. Immersive Cell Exploration

4. Immersive Cell Exploration

20/405.1 Immersive Cell Visualization | Hybrid-dimensional Visualization

Hybrid-dimensional Visualization

Semi-immersive

3D Canvas + 2D Canvas = Hybrid-dimensional

21/405.2 Immersive Cell Visualization | Hybrid-dimensional Interaction

Hybrid-dimensional Interaction

2D Interaction 2-3DOF

Movement along X/Y AxisOptionally Rotation (Z Axis)

3D Interaction

6DOFMovement along X/Y/Z AxisRotation along X/Y/Z Axis (roll, yaw, pitch)

?

22/405.3 Immersive Cell Visualization | Hardware

Hardware

Objective: 2D plus 3D Working environment for long-term use

For 3D Visualization and Interaction

ZSpace 200with stylus pen half-immersive display

Hands-on Demo later!

23/405.4 Immersive Cell Visualization | Results

Summary: Classic vs. Advanced 3D Navigation

Floating Mode (FOM)

Flight Mode (FIM)Object-Bound Mode (OBM)

Navigation Modes Navigation 6DOF

Typesb Modes XT YT ZT XR YR ZR

C3DNAV

FOM X X X

FIM X X X

OBM X (X) X X

A3DNAV

FOM X X X X X

OBM X X X X

Björn Sommer, Stephen Jia Wang, Lifeng Xu, Ming Chen, Falk Schreiber, „Hybrid-Dimensional Visualization and Interaction – Integrating 2D and 3D Visualization with Semi-Immersive Navigation Techniques, IEEE Computer Society Press, in print 2015.

24/405.5 Immersive Cell Visualization | CAVE2 and zSpace

CAVE2 Integration: 3D Navigation and Large Scale Vis.

25/40

5. Membrane Modeling

6. Membrane Modeling

26/406.1 Membrane Modeling | Membrane Modeling Methods

Membrane Modeling Methods

Simulation: Self-Assembly

Very time-consumingUsually requires expert knowledgeNearly unpredictable results

Generation by Scripts

Requires scripting skills and mathematical thinkingOnly applicable for simple membranes

Packing Algorithms

Abstraction to shape-based distributionsRelatively fastThe result can be exactly defined

27/406.2 Membrane Modeling | Membrane Composition

Membrane Composition

R. Hovius, H. Lambrechts, K. Nicolay, and B. de Kruijff. „Improved methods to isolate and subfractionate rat liver mitochondria. Lipid composition of the inner and outer membrane“. Biochimica et Biophysica Acta (BBA)-Biomembranes 1021, Nr. 2 (1990): 217–226.

Sommer, B.; Dingersen, T.; Gamroth, C.; Schneider, S. E.; Rubert, S.; Krüger, J.; Dietz, K. J.: CELLmicrocosmos 2.2 MembraneEditor: a modular interactive shape-based software approach to solve heterogeneous Membrane Packing Problems. In: Journal of Chemical Information and Modeling 5 (2011), no. 51, pp. 1165–1182.

28/406.3 Membrane Modeling | Lipid Packing

Lipid Packing (The Wanderer algorithm)

29/406.4 Membrane Modeling | Protein Placement

Protein Placement (based on OPM database)

30/406.5 Membrane Modeling | Membrane Simulation

Membrane Simulation

heterogeneousmembrane Modeling: CmME

Simulation:GROMACS

Cooperationwith Jens Krüger

6 students overca. 3 years

31/406.6 Membrane Modeling | Vesicle Builder

Vesicle Builder

MembraneEditorPluginCreation of Vesicles

Based on EllipsoidFormula

32/406.7 Membrane Modeling | New Vesicle Builder

New Vesicle Builder

Version 1.11coming soon!

Create complex shapescontaining differentelements

33/406.7 Membrane Modeling | New Vesicle Builder

New Vesicle Builder

Create complex shapes: Multilammenar Vesicles

34/406.7 Membrane Modeling | New Vesicle Builder

New Vesicle Builder

Merged MembraneModels

35/407. Summary & Outlook

6. Summary & Outlook

36/407.1 Summary & Outlook | Summary

Summary

Use CELLmicrocosmos to Mesoscopic level:create different shape-based cell modelsFunctional Level:to analyze and visualize intracellular protein localizationMolecular Level:to model membrane/vesicle models and/or prepare models for MD simulations3D Interaction and Stereoscopic 3D Visualization for

educational purposes (teach cell structure) andscientific purposes (Human-Computer-Interaction)

37/407.2 Summary & Outlook | Outlook: VANTED

Outlook: VANTED

VANTED Integration

CmPI Addon for VANTEDVANTED 2.5.3 just released(Hi, Christian! ;-)

38/407.3 Summary & Outlook | Outlook: Post-mesoscopic level

Outlook: Post-mesoscopic level

Example: Visualization of final state of a Plant Simulation

39/408. Acknowledgements

7. Acknowledgements

40/408. Acknowledgements

7. Acknowledgements

Colleagues and Collaborators, e.g.Alejandro Giorgetti, Verona University, Verona

Benjamin Kormeier, Bielefeld University, Bielefeld

Falk Schreiber, Monash University, Melbourne

Jens Krüger, Tübingen University, Tübingen

Lifeng Xu, Zhejiang University of Technology, Hangzhou

Ming Chen, Zhejiang University, Hangzhou

Ralf Hofestädt, Bielefeld University, Bielefeld

Stephen Jia Wang, MADA, Melbourne

Vladimir Ivanisenko, Institute of Cytology and Genetics, Novosibirsk

All our Students!!! http://team.CELLmicrocosmos.org