The GENESIS Neural Database and Modeler's Workspace

Project Vision: Develop an easy-to-use tool for computational neuroscientists that facilitates the following tasks: creating, editing and visualizing models and other objects; interacting with neuronal databases; interacting with simulation systems such as GENESIS; and collaborating with other modelers using simultaneous shared editing and visualization.

The links on this page describe work performed under the 'GENESIS Neural Database and Modeler's Workspace' project, which was funded under the NIH Human Brain Project between 1995 and 2002.

The principal accomplishments during this period that continue to be relevant today are:

1. We designed a next-generation interface for collaborative neural simulations. Elements of this design are being incorporated into interfaces for GENESIS version 3 ( http://www.genesis-sim.org/GENESIS/G3).

2. We developed a simulator-independent XML-based representation of biologically realistic neural models that later became the basis for the NeuroML project (http://www.neuroml.org).

3. We implemented a prototype MySQL database and Java-based GUI for a database of ionic conductance models stored in simulator-independent NeuroML format, with a parser to convert the representation into GENESIS simulation scripts. ( http://www.genesis-sim.org/hbp/channeldb/).

Recent Developments - The Modelers Workspace Channel Database

Description of the project

Design Documents

• An Overview of the Modeler's Workspace [HTML] [PS]
• The Modeler's Workspace Database Organization and Interaction
• The Modeler's Workspace Representation of Models [HTML]
• The Modeler's Workspace User Interface

Posters and Presentations

• Experimental Biology Meeting (San Diego, April 15-18, 2000)
• May 1998 HBP Principal Investigators Meeting

History and Evolution of the Modeler's Workspace

Collaborations

Publications

Principal Investigator

James M. Bower, Research Imaging Center, University of Texas Health Science Center, San Antonio and Cajal Neuroscience Research Center, University of Texas, San Antonio

Other participants

David Beeman, Department of Electrical and Computer Engineering, University of Colorado, Boulder

Michael Hucka, Department of Biology, Caltech

Kavita Shankar, Department of Biology, Caltech

Sara Emardson, Department of Biology, Caltech

Jenny Forss, Department of Biology, Caltech

Participants during the first year

Jason Leigh and Thomas A. DeFanti, Electronic Visualization Lab, University of Illinois at Chicago

Some other relevant links

GENESIS Home Page

Human Brain Project Home Page