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E-Cell System Version 4

The next generation of E-Cell simulation technology is currently in the design phase. This project is led by Koichi Takahashi, The Molecular Sciences Institute.

E-Cell 4 simulation engine planned features

Main focuses in this new version will include:

  1. Generic representation of space
    • Support for particle, lattice, and compartment space representations.
    • Mixed uses of different spatial representations in a model.
  2. Dynamic model structure
    • Creation and deletion of objects during the simulation.
    • Integrating Moleculizer technology for efficient modeling of pathways involving multi-protein complexes.
  3. Support for large-scale parallel computation

E-Cell 4 planned technical changes

The following changes in software architecture, used components and coding styles are currently planned. This list will grow as time goes.

  • New object model for space.
    • Support for array data type, and a good memory manager.
    • Rename System to Entity?
  • New Logging architecture.
  • GUI: pyGtk to wxPython? Two reasons; a) portability, b) 3D visualization through VTK widgets.
  • PyEcs: from flat, functional API to object-orientation. This is related to adding support for dynamic model structure to the core. (also: Do we still need libemc layer?)
  • Slight changes in the coding standards.
Document Actions

DNA

Posted by Chris Caston at Jan 19, 2007 08:52 AM

Does or will e-cell support building cells using the contents of FASTA files?

DNA

Posted by Koichi Takahashi at Jan 19, 2007 08:52 AM
From DNA sequence -- that is the ultimate goal of
E-Cell Project in the long term, but E-Cell 4 won't
do it.

pyGtk to wxPython

Posted by Laurent Gautier at Jan 19, 2007 08:52 AM

The wxPython library does have good support for windows, but pyGTK can also be used on other platforms than linux as well.

pyGTK can work on windows when GTK-runtime is installed (there are reports that it works on MacOS X whenever an X11 server is around, but I did not test it personally).

Regarding 3D visualization, I have seen mentionned that pyGTK and VTK can play together.

If I look biased, this might be because I found GUI writting with GTK rather nice (compared to other experiences I had).

GUI toolkit

Posted by Koichi Takahashi at Jan 19, 2007 08:52 AM
Thanks for the comment. I have actually been viewing
wxWidgets as a primary candidate. As for 3D, I've been
trying out vtk a bit, too, with a lesser confidence about
its suitability in real-time visualization. We might
end up with vtk, we might not. Don't know at this moment.