GENESIS 3 Development Plans

The GENESIS simulator is undergoing a major redevelopment effort that will result in GENESIS version 3.

The diagram below shows the components of GENESIS 2, as seen by the GENESIS user. Although GENESIS and its scripting language produce modular object-oriented simulations that are easy to modify and extend, this is not the case with the source code for GENESIS 2. The core modules of GENESIS were written in the late 1980's in C, and the modules are much more tightly coupled than the diagram would suggest. Although the simulation code is very efficient, it is difficult to add more modern Java-based graphical interfaces, alternate script parsers, and interfaces via the WWW.

In order to provide greater interoperability with other neuroscience software tools, databases, and modeling environments, we are modularizing the GENESIS architecture, as indicated by the dashed lines in the figure above. There are two ongoing projects that are developing a GENESIS-compatible replacement for the GENESIS core.

Upinder Bhalla (NCBS Bangalore), who wrote the X Windows XODUS GUI interface for GENESIS and did much of the initial GENESIS development, has been rewriting the GENESIS base code in C++, as MOOSE. This reimplementation in an object-oriented language makes it simple to "unbundle" the components of GENESIS.

The following outline summarizes MOOSE. More information may be found at http://moose.sourceforge.net/.

The Messaging Object Oriented Simulation Environment (MOOSE) provides:

• Improved Messaging between GENESIS objects
• Faster, smaller, cleaner implementation
• Portability to MS Windows and non-UNIX platforms
• Improved equation solvers, with specialized solvers for biochemical kinetics modeling
• Ability to use multiple script parsers and user interfaces

Hugo Cornelis (Bower lab, UT San Antonio), who programmed many of the advanced features of the GENESIS hsolve object, is developing Neurospaces and its compartmental model solver Heccer. This promises to be extremely efficient for the solution of large compartmental neuron models. For more information about Neurospaces and Heccer, see http://www.neurospaces.org.

GENESIS 3 will add:

• A modern graphical user interface
• XML representation of models
• Backwards compatibility with GENESIS 2
• Tutorials and educational applications

The last figure shows the multiple external interfaces to GENESIS 3 that will be allowed with the new architecture.

The first priorities for GENESIS 3 development are to:

• Reimplement the functionaliity of the X Windows graphical user interface of GENESIS in Java. This will allow the use of more modern user-friendly interfaces, and allow GENESIS to be used on non-UNIX platform such as Windows. A Java GUI for GENESIS will also allow tutorial simulations to be run over the internet from a GENESIS server. This work is in progress now, and will be followed with the addition of more advanced display and visualization capabilities.

• Develop XML-based representations of channel, cell, and network models. Although the present GENESIS cell parameter file format will continue to be supported for backwards compatibility with existing simulations, we plan to use a standard simulator-independent XML model description to import models into GENESIS. This will make it possible for modelers to more easily exchange simulations and simulation components, regardless of the simulator used. For more information about the NeuroML project and related efforts, see http://www.neuroml.org/, and the recently established SourceForge development website for NeuroML at http://sourceforge.net/projects/neuroml. For information about a prototype XML-based channel model database, see http://www.genesis-sim.org/hbp/channeldb/ChannelDB.html.