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General purpose simulation platform developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models. As such, GENESIS, and its version for parallel and networked computers (PGENESIS) was the first broad scale modeling system in computational biology to encourage modelers to develop and share model features and components. User contributed GENESIS models and simulations are available. You may to contribute a model or simulation. Educational tutorials for instruction in both neurobiology and computational methods have been developed. These tutorials and GENESIS are now being widely used in graduate and undergraduate instruction. These uses include full semester courses in computational neuroscience or neural modeling, short intensive courses or workshops, an option for a course project, and short units on computational neuroscience within courses on artificial neural nets. They also have a repository of user-contributed tutorials and materials for use in neuroscience education. If you have course descriptions, syllabi, exercises, tutorials, or short HOWTO documents, please upload them to Education.
Proper citation: General Neural Simulation System (RRID:SCR_006316) Copy
Public research university in San Antonio, Texas.
Proper citation: University of Texas at San Antonio; Texas; USA (RRID:SCR_011719) Copy
http://www.genesis-sim.org/hbp/channeldb/
Implementation of a database of ionic conductance models stored in simulator-independent NeuroML format, with a parser to convert the representation into GENESIS simulation scripts. It was developed as a means of sharing channel models between different neural simulators. It is also one of the first core components of the Modelers Workspace (MWS). 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. The first implementation of a parser to create simulation scripts is for GENESIS. The files in this package will let you * Search a small remote database of ion channel models to retrieve and view their descriptions and NeuroML representations, and generate simulator scripts from the model representation. * Set up your own database of ion channel models * Extend ChannelDB with the addition of parsers for other simulators, and with Java classes to cover other types of channels.
Proper citation: ChannelDB (RRID:SCR_007089) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
