Immersive Cell Exploration and Membrane Modeling - BTU · PDF fileImmersive Cell Exploration...
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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