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Virtual Cell and CellML

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... for Cell Analysis and Modeling. University of Connecticut Health ... Modeling reactions, diffusion, membrane transport, flow, electrical potential and currents ... – PowerPoint PPT presentation

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Title: Virtual Cell and CellML


1
Virtual Cell and CellML
  • The Virtual Cell Group
  • Center for Cell Analysis and Modeling
  • University of Connecticut Health Center
  • Farmington, CT USA.

2
Outline
  • Virtual Cell a brief introduction
  • Current CellML support in VCell
  • Issues
  • Possibility of using CellML API
  • Requirements for libCellML
  • Acknowledgements

3
The Virtual Cell
  • What is it?
  • It is a tool to build models and run simulations
    of cellular processes
  • What can it do?
  • 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?
  • At http//www.vcell.org
  • What do you need to run it?
  • 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?
  • Email vcell_support_at_uchc.edu
  • The website (user guide, tutorials, technical
    info, examples)
  • What new features are expected in the near
    future?
  • Standalone, grid-based, resource-sharing versions
  • Stochastics and brownian motion
  • Filaments and structures
  • Open source and plug-in architecture

4
VCell Modeling Process
5
(No Transcript)
6
What can we simulate?
Math and Physics
7
Current Scope and Future Plans
  • Intended Users
  • Biologists
  • Biophysicists/Mathematicians
  • Modeling domain
  • Compartmental or 1D, 2D, 3D Geometry
  • Reaction/Diffusion/Membrane Transport
  • Electric Potential (electrophysiology)
  • Advection and Membrane Diffusion
  • Future
  • 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)

8
Current support for CellML in Virtual Cell
  • Incomplete support for CellML
  • Export non-spatial biomodels and non-spatial math
    models to CellML1.0
  • Hasnt been actively maintained
  • Parsing of XML DOM object from CellML and
    translating into appropriate VCell equivalent
    object
  • Cumbersome process
  • Can be inconsistent
  • Does not export electrophysiological models

9
Issues to consider
  • New Physics-oriented layer in VCell
  • 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)

10
Using the CellML API
  • 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
  • Implementation of the Java interfaces and client
    necessary!
  • Possible, but time-consuming
  • Non-CORBA JNI (Java) Binding will be extremely
    helpful !!

11
What do we need? .
  • Simple library to read, write, manipulate CellML
    models
  • 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??) !!

12
Acknowledgements
  • 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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