Modelers Workspace Channel Database

The links on this page describe a prototype MySQL database and Java-based GUI for a database of ionic conductance models. This work was performed under the 'GENESIS Neural Database and Modeler's Workspace' project, which was funded under the NIH Human Brain Project between 1995 and 2002 (http://www.genesis-sim.org/hbp). More recent developments in the representation for conductance models have been carried out under the ongoing NeuroML collaborative effort (http://www.neuroml.org), which involves several other groups and institutions in addition to the GENESIS group.

Our work during the period 1999 - 2001 was directed towards the detailed design for the Modelers Workspace GUI and the simulator-independent representation scheme for neural models in XML. This led to a collaboration with the HBP work of Nigel Goddard, in which our representation was incorporated into the jointly-developed NeuroML language for model specification (for details, see http://www.neuroml.org).

We are now in the phase of implementing the core components of the Modelers Workspace (MWS). The first of these is ChannelDB, an implementation of a database of ionic conductance models stored in simulator-independent NeuroML format.

At present, ChannelDB is implemented as a stand-alone module, with its own graphical user interface to the database, which is implemented with MySQL. After further development, the ChannelDB GUI will be merged into the MWS.

The NeuroML development kit parser (from http://www.neuroml.org/ndk.html) is used to create Java objects from the NeuroML format XML files stored in the database. These are then accessed with Java software to create simulation scripts for the particular simulator. Our first implementation of a parser to create simulation scripts is (of course) for GENESIS.

• A diagram of the ChannelDB design

• Screen capture of the ChannelDB GUI

• Paper describing the ChannelDB representation

  D. Beeman and J. M. Bower, "Simulator-independent representation of ionic conductance models with ChannelDB", Neurocomputing 58-60: 1085-1090 (2004). (PDF preprint of CNS*2003 paper)

• Sample NeuroML representations of channels

  [ XML version ] (Not viewable without XML-enabled browser)
  [ Text version ] (Should be viewable)

• Read the ChannelDB documentation

• Download the ChannelDB software.

  This will allow you to access the channel database and to create your own database to which you can add your own channel models and share them with others.

Go to the GENESIS Home Page at http://www.genesis-sim.org/GENESIS