Transcript Virtual Cell and CellML

Virtual Cell and CellML
The Virtual Cell Group
Center for Cell Analysis and Modeling
University of Connecticut Health Center
Farmington, CT – USA.
Outline
Virtual Cell – a brief introduction
 Current CellML support in VCell
 Issues
 Possibility of using CellML API
 Requirements for libCellML …
 Acknowledgements
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The Virtual Cell
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What is it?
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What can it do?
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Java and an Internet connection (it runs over the web)
It is free but you must register
Where can you find more info or get help?
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At http://www.vcell.org
What do you need to run it?
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Modeling reactions, diffusion, membrane transport, flow, electrical potential and currents
Compartmental or spatial simulations (1D, 2D, 3D) on analytical or image-based geometries
Collaborative work (shared database) and interoperability (SBML, CellML, data formats)
Where can you get it?
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It is a tool to build models and run simulations of cellular processes
Email [email protected]
The website (user guide, tutorials, technical info, examples)
What new features are expected in the near future?
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Standalone, grid-based, resource-sharing versions
Stochastics and brownian motion
Filaments and structures
Open source and plug-in architecture
Components as web services
Modeling the experiment… and much, much more!
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VCell Modeling Process
External Resources
• pathway databases
Physiological Model
Extracellular
• existing literature
Cytosol
Nucleus
ER
A+B
C
Experiment
D
Fluxes
Species
Reactions
Structures
Currents
Structures Map reactions,
fluxes, and
mapped to
currents
Subdomains
Init Condn
Boundary Condn
Diffusion
protocols
Model Application
(maps to experimental context)
Subdomains
(Image Regions)
Geometry
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Modeling &
Analysis
Math
Mapping
Math
Description
•Equations
•Domains
Simulation (job)
•Model Parameters
•Mesh
•Solver options
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Sim Results
•time response
•sensitivities
•steady state
Solver
Services
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Physiology
Molecular Species
Compartment Topology
Reactions and Fluxes
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Applications
Applications
Applications
Geometry,
Topology
Topology
Geometry,
Initial Conditions,
Boundary
Geometry,
Conditions, Diffusion
Initial Conditions,
Coefficients,
Pseudo-steady,
Initial
Conditions,
Boundary
Conditions,
Enable/Disable
Reactions
Boundary
Conditions,
Diffusion
Coefficients,
Electrophysiology
Protocols
Diffusion
Coefficients,
Pseudo-steady,
Pseudo-steady,
Enable/Disable
Enable/Disable
Reactions
Reactions
Math Description
Math Description
Math Description
Topology
Images
Images
Images
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VCMDL
Simulations
Simulations
Simulations
Timestep,
Timestep,
Mesh
Timestep,
Mesh
Size,
Mesh
Size,
Parameter
Size,
Parameter
Searches,
Parameter
Searches,
Sensitivity
Searches,
Sensitivity
Sensitivity
Results
Results
Results
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What can we simulate?
Math and Physics
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Fi   Di Ci  Ci Vi  zi i Ci ,
k1
A+B 
k 1
  B 
C , R  k1 A
i
Di F
i=
RT
 
 k1 C
Ci
 divFi  Ri
t
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Current Scope and Future Plans
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Intended Users
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Modeling domain
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Biologists
Biophysicists/Mathematicians
Compartmental or 1D, 2D, 3D Geometry
Reaction/Diffusion/Membrane Transport
Electric Potential (electrophysiology)
Advection and Membrane Diffusion
Future
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Optimization & parameter scans
Protocols
Advection & Directed Transport
Stochastic Processes
Complexes
Constraints & Virtual Experiments
Stand-alone & grid-based versions
Cell motility
New architecture – plug-ins, modules, etc. (VCell OpenSource)
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Current support for CellML in
Virtual Cell
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Incomplete support for CellML
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Parsing of XML DOM object from CellML and
translating into appropriate VCell equivalent object
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Export non-spatial biomodels and non-spatial math models to
CellML1.0
Hasn’t been actively maintained
Cumbersome process
Can be inconsistent
Does not export electrophysiological models
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Issues to consider
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New Physics-oriented layer in VCell
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All modeling assumptions made explicit and mathematically
complete (e.g. lumped vs distributed parameter model for the
same mechanism)
Components described by equations, connected to form a
system (causality may be left unspecified)
Compatible with CellML after determining causality
(identify solvable form of equations and all state
variables)
VCell Geometry
VCell Physiology
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New Physics Layer
VCell
Application
VCell Math Layer
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Solvers
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Using the CellML API
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Using the .idl files in the CellML API package,
generated the Java interface stubs
Seems to provide the necessary functionality to
create a CellML document
Problem :
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Implementation of the Java interfaces and client
necessary!
Possible, but time-consuming
Non-CORBA JNI (Java) Binding will be extremely
helpful !!
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What do we need? ….
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Simple library to read, write, manipulate CellML models
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similar to libSBML
we will have our own internal CellML compatible
representation
With Java bindings, supporting Windows, Linux, Mac platforms
Simple methods to add/extract CellML model constructs transparency from XML syntax
Looking forward to the release of the non-CORBA JNI
(Java) Binding for CellML-API (soon??) !!
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Acknowledgements
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We would like to thank CellML consortium
for providing this opportunity to present our
computational cell biology tool to the CellML
community
Our sincere thanks to David Nickerson for
making the presentation on our behalf
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