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GENESIS Neural Database and Modelers Workspace

Software system to assist computational neuroscientists in interacting with databases of models and with neural simulation packages such as GENESIS. There are three components in the system: a user interface, a database server, and a global registry and repository. The collection of software tools with a graphical user interface enables users to interact over the WWW with databases of models and data. It provides facilities for searching multiple remote databases for model components based on various criteria; visualizing the characteristics of the components retrieved; creating new components, either from scratch or derived from existing models; combining components into new models; linking models to experimental data as well as online publications; and interacting with simulation packages such as GENESIS to simulate the new constructs. Although the initial version uses GENESIS as the simulator, the design permits the use of multiple simulation systems, with or without the use of a database. This allows modeling at multiple levels of scale from the molecular level, through the subcellular (e.g. ion channel), single cell, and network levels, to the systems level (e.g. relating models to fMRI studies). The system is intended to help users create and organize models and to interact with databases of models and neuronal simulation software. More specifically, the Modeler''''s Workspace is designed to provide the following: * Search and retrieval facilities for interacting with databases of models and other information; * Facilities for creating, editing and visualizing the characteristics of models; * Facilities for combining model components together and translating them into formats suitable for simulation systems such as GENESIS and NEURON; * Facilities for managing a personal database where a user can collect models and other objects; and * Collaboration facilities for connecting one or more users together, to allow them to simultaneously edit objects in a shared database and communicate with each other using real-time chat. The Modeler''''s Workspace is written in Java for portability and extensibility. It is modular in design and uses pluggable components for supporting different data formats, which means that new data types can be supported by loading an appropriate plug-in. To increase the probability that the Modeler''''s Workspace will be compatible with future databases and tools, they are using the eXtensible Markup Language (XML) as the interchange format for communicating with databases.

URL: http://www.genesis-sim.org/hbp/

Resource ID: nif-0000-21168     Resource Type: Resource     Version: Latest Version


channel, ion, model, neuron, simulation, visualization, xml, neural model, neural simulation, data sharing, database, neuronal cell, voltage-gated channel, data repository, registry

Funding Information

Human Brain Project, Sun Microsystems Inc., Academic Equipment, #EDUD-7824-000127-US


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Related To

NeuroML, GENESIS,General Neural SImulation System


Modeler''''s Workspace, Modelers Workspace

Parent Organization


GENESIS Neural Database and Modeler''''s Workspace

Additional Resource Types

Software Resource, Service Resource

Old URLs


Original Submitter


Version Status


Submitted On

12:00am December 2, 2011

Originated From


Changes from Previous Version

    No Changes

    Version 4

    Created 2 weeks ago by Christie Wang

    Version 3

    Created 3 weeks ago by Christie Wang

    Version 2

    Created 3 weeks ago by Christie Wang

    Version 1

    Created 4 years ago by Anonymous