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http://genesis-sim.org/

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   

•   Source: SciCrunch Registry

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

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.

Proper citation: GENESIS Neural Database and Modelers Workspace (RRID:SCR_002357) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry