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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/GENESIS/bog/bog.html
Book with a downloadable version of the second edition of a practical introduction to the interdisciplinary field of computational neuroscience through the use of the GENESIS simulator. It is designed to be a step-by-step tutorial for professionals, researchers and students working in fields ranging from neuroscience to bioengineering, medicine, artificial neural networks and the cognitive sciences. Part I of the book teaches concepts in neuroscience and neural modeling by means of interactive computer tutorials on subjects ranging from neuronal membrane properties to cortical networks. These chapters, written by several contributors, allow the student to perform realistic simulations and experiments on model neural systems and provide the necessary background for understanding and using the tutorials. The simulations are user-friendly with on-line help and may be used without any prior knowledge of the GENESIS simulator or computer programming. Part II is intended to teach the use of the GENESIS script language for the construction of one's own simulations. This part will be useful for self-study by researchers who wish to do neural modeling, as well as students. It follows approximately the same sequence of topics as Part II, and uses parts of the tutorial simulations as examples of GENESIS programming. Several of these are based on recent research simulations which have been published in the neuroscience literature, but which have not been previously available for use outside the laboratories of the original researchers. Thus, the reader may modify these simulations and use them as a starting point for the development of original simulations. In addition to many revisions and additions to existing chapters, this second edition includes two new chapters on the modeling of biochemical signaling pathways and on the use of GENESIS on parallel computers and networks of workstations. Other new additions include a section describing ways to implement synaptic modification (learning), a section describing uses of a new method for modeling of a wide variety of voltage and ionic concentration dependent channels, a description of improvements in the procedure for implementing fast implicit numerical methods in GENESIS simulations, and descriptions of many new GENESIS commands and simulation components.
Proper citation: The Book of GENESIS (RRID:SCR_001657) Copy
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
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
http://www.nitrc.org/projects/topographica/
A software package for computational modeling of neural maps developed as part of the NIMH Human Brain Project. Topographica focuses on the large-scale structure and function that is visible only when many thousands of such neurons are connected into topographic maps containing millions of connections. The software package provides a general-purpose framework for building models at this level, at an appropriate level of detail and complexity, as determined by the available computing power, phenomena of interest, and amount of biological data available for validation. It is intended to complement low-level neuron simulators that are available, such as General Neural Simulation System and NEURON.
Proper citation: Topographica (RRID:SCR_014174) Copy
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