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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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General Neural Simulation System Resource Report Resource Website 100+ mentions |
General Neural Simulation System (RRID:SCR_006316) | GENESIS | data or information resource, narrative resource, data set, software library, software toolkit, source code, training material, simulation software, software resource, software application | 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. | electrophysiology, computer, in silico, model, modeling, simulation, neural system, network, neurobiology, computational neuroscience, neural modeling, subcellular, biochemical reaction, neuron, channel, cell, FASEB list |
is related to: GENESIS Neural Database and Modelers Workspace is related to: ChannelDB is related to: Topographica has parent organization: University of Texas at San Antonio; Texas; USA is parent organization of: The Book of GENESIS |
The community can contribute to this resource | nif-0000-00091 | http://www.nitrc.org/projects/genesis http://genesis-sim.org/GENESIS/ | SCR_006316 | GENESIS, GENESIS Simulator, GEneral NEural SImulation System | 2026-08-19 10:45:15 | 459 | ||||||
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University of Texas at San Antonio; Texas; USA Resource Report Resource Website 1+ mentions |
University of Texas at San Antonio; Texas; USA (RRID:SCR_011719) | UTSA | university | Public research university in San Antonio, Texas. |
is parent organization of: UTSA Engineering Core is parent organization of: GENESIS Neural Database and Modelers Workspace is parent organization of: Neuroscientists Talk Shop is parent organization of: General Neural Simulation System is parent organization of: GEneral NEural SImulation System: The Neurospaces Project is parent organization of: University of Texas at San Antonio Laboratory of Professor Brenda Claiborne is parent organization of: Computer-Assisted Information Retrieval Service System for Music is parent organization of: EEGVIS is parent organization of: UTSA Biophysics Facility is parent organization of: UTSA Cellular and Tissue Engineering Laboratory is parent organization of: UTSA Computational Biology Initiative is parent organization of: UTSA Kleberg Advanced Microscopy Laboratory is parent organization of: University of Texas San Antonio Cell Analysis Core Facility is parent organization of: UTSA RCMI Computational Systems Biology Core is parent organization of: UTSA RCMI Nanotechnology and Human Health Core is parent organization of: University of Texas San Antonio Mass Spectrometry and Proteomics Core Facility is parent organization of: UTSA SNRP Image Analysis Core is parent organization of: UTSA SNRP Neurostatistics Core is parent organization of: UTSA X-ray Crystallography Laboratory is parent organization of: BCmicrO is parent organization of: UTSA RCMI Proteomics and Protein Biomarkers Cores is parent organization of: University of Texas at San Antonio Labs and Facilities is parent organization of: ExomePeak is parent organization of: NeuroManager is parent organization of: University of Texas at San Antonio Stem Cell Core Facility |
Wikidata:Q183170, grid.215352.2, ISNI:121845633, Crossref funder ID:100008634, nlx_67879 | https://ror.org/01kd65564 | SCR_011719 | UTSA | 2026-08-15 11:24:21 | 3 | ||||||||
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The Book of GENESIS Resource Report Resource Website |
The Book of GENESIS (RRID:SCR_001657) | BoG | data or information resource, book, training material, narrative resource | 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. | computational neuroscience, neuroscience, bioengineering, medicine, artificial neural network, cognitive sciences, neural network, tutorial | has parent organization: General Neural Simulation System | Free, Available for download, Freely available | nlx_153938 | SCR_001657 | Book of GENESIS | 2026-08-19 10:43:28 | 0 | |||||||
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Topographica Resource Report Resource Website 1+ mentions |
Topographica (RRID:SCR_014174) | simulation software, software resource, software application | 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. | computational modeling, neural map, simulation software, neuron |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: General Neural Simulation System is related to: NEURON |
NIMH Human Brain Project 1R01-MH66991 | SCR_014174 | 2026-08-18 09:43:57 | 5 | ||||||||||
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ChannelDB Resource Report Resource Website |
ChannelDB (RRID:SCR_007089) | ChannelDB | data or information resource, source code, database, software resource | 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. | ion channel, conductance model, neural model, xml, simulation, data sharing, ion channel model, java, simulator script, model |
is related to: NeuroML is related to: General Neural Simulation System has parent organization: GENESIS Neural Database and Modelers Workspace |
nif-0000-00104 | http://www.modelersworkspace.org/channeldb/ChannelDB.html | SCR_007089 | Modeler''''s Workspace Channel Database, Modelers Workspace Channel Database, Channel Database | 2026-08-19 10:45:24 | 0 | |||||||
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GENESIS Neural Database and Modelers Workspace Resource Report Resource Website |
GENESIS Neural Database and Modelers Workspace (RRID:SCR_002357) | Modeler's Workspace, Modelers Workspace | service resource, software resource | 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. | channel, ion, model, neuron, simulation, visualization, xml, neural model, neural simulation, data sharing, database, neuronal cell, voltage-gated channel, data repository, registry |
is related to: NeuroML is related to: General Neural Simulation System is related to: Neuroscience Gateway has parent organization: University of Texas at San Antonio; Texas; USA is parent organization of: ChannelDB |
Human Brain Project ; Sun Microsystems Inc. ; Academic Equipment |
The community can contribute to this resource | nif-0000-21168 | http://www.modelersworkspace.org/ | SCR_002357 | GENESIS Neural Database and Modeler's Workspace | 2026-08-19 10:43:53 | 0 |
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