Virtual Cell and CellML

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Virtual Cell and CellML

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

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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

• 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

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VCell Modeling Process
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What can we simulate?
Math and Physics
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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)

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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

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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)

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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 !!

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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??) !!

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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