arrow

From NeuroLex

Jump to: navigation, search



Resource:GENESIS Neural Database and Modelers Workspace

Name: Resource:GENESIS Neural Database and Modelers Workspace
Description: 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.
Other Name(s): GENESIS Neural Database and Modeler's Workspace
Abbreviation: Modeler's Workspace, Modelers Workspace
Parent Organization: University of Texas at San Antonio; Texas; USA
Supporting Agency: Resource:Human Brain Project, Sun Microsystems Inc., (Academic Equipment)
Grant: #EDUD-7824-000127-US
Resource Type(s): Software resource, Service resource
Resource: Resource
URL: http://www.genesis-sim.org/hbp/
*Id: nif-0000-21168
Related to: Resource:Neuro-Markup Language, Resource:GEneral NEural SImulation System
Availability: The community can contribute to this resource
Keywords: channel, ion, model, neuron, simulation, visualization, XML, neural model, neural simulation, data sharing, Database, Neuronal cell, Voltage-gated channel, Data repository, Registry
Link to OWL / RDF: Download this content as OWL/RDF

Categories related to Resource:GENESIS Neural Database and Modelers Workspace

Resource:NSG Portal - The Neuroscience Gateway

Parts of Resource:GENESIS Neural Database and Modelers Workspace

Curation status: Uncurated

This resource will be curated within 7 days.

For Resource Owners:
After the resource is curated, you may create a sitemap, which will help keep your registry description up-to-date and inform search engines about your resource.

Note: For a new resource, the website's URL must first be verified by a NIF curator before you may proceed.

Learn more about what NIF can do for your resource.
Proudly proclaim your inclusion in NIF by displaying the "Registered with NIF" button on your site. Please login to create the sitemap. (top right)

Notes

This page uses this default form:Resource

Old URL: http://www.modelersworkspace.org/

Contributors

Aarnaud, Zaidaziz



bookmark

*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.

Facts about Resource:GENESIS Neural Database and Modelers WorkspaceRDF feed
AbbrevModeler's Workspace, Modelers Workspace  +
AvailabilityThe community can contribute to this resource  +
CurationStatuscurated  +
DefiningCitationhttp://www.genesis-sim.org/hbp/  +
DefinitionSoftware system to assist computational ne 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.
at for communicating with databases.
EditorialNoteI don't see how one would get the software...
GrantCategory:#EDUD-7824-000127-US   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleSoftware resource  +, and Service resource  +
Idnif-0000-21168  +
Is part ofUniversity of Texas at San Antonio; Texas; USA  +
KeywordsChannel  +, Ion  +, Model  +, Neuron  +, Simulation  +, Visualization  +, XML  +, Neural model  +, Neural simulation  +, Data sharing  +, Database  +, Neuron  +, Voltage-gated channel  +, Data repository  +, and Catalog  +
LabelResource:GENESIS Neural Database and Modelers Workspace  +
ModifiedDate25 July 2014  +
OldURLhttp://www.modelersworkspace.org/  +
Page has default formThis property is a special property in this wiki.Resource  +
RelatedToResource:NeuroML  +, and Resource:GENESIS  +
SuperCategoryResource  +
Supporting AgencyResource:Human Brain Project  +, Sun Microsystems Inc.  +, and (Academic Equipment)  +
SynonymGENESIS Neural Database and Modeler's Workspace  +