E-Cell 4 Development

This page describes the development efforts for E-Cell 4.

E-Cell 4 seeks to extend E-Cell 3 by adding several new features, notably dynamic model structure and spatial representation.

Development Schedule 2007

1st Quarter?

2nd Quarter

Proposed Logger Architecture

3rd Quarter?

4th Quarter?

Feature Proposals

Front End Logging

Template for new feature proposals

Etc.

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.
  • see http://sourceforge.net/mailarchive/message.php?msg_id=16577227
• 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.