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https://neuron.yale.edu/neuron/

Software for computational neurophysiology. Simulation environment is used for building and using computational models of neurons and networks of neurons. NEURON Users Group can participate in collaborative development of documentation, tutorials, and software.

Proper citation: NEURON (RRID:SCR_017449) Copy   

•   Source: SciCrunch Registry

http://neuronvisio.org/

A Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections'''' properties and it offers easy integration with matplotlib for plotting the results. The geometry can be saved using NeuroML and the computational results in a customized and extensible HDF5 format; the results can then be reload in the software and analyzed in a later stage, without re-running the simulation. Featuring 3D visualization of the model with the possibility to change it runtime; creation of vectors to record any variables present in the section; pylab integration to plot directly the result of the simulation; exploration of the timecourse of any variable among time using a color coded scale; saving the results simulation for later analysis; automatic download and running of models in ModelDB.

Proper citation: NeuronVisio (RRID:SCR_006839) Copy   

•   Source: SciCrunch Registry

http://www.neuroconstruct.org/

Software for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface.

Proper citation: neuroConstruct (RRID:SCR_007197) Copy   

•   Source: SciCrunch Registry

http://www.nih.gov/science/brain/

Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts.

Proper citation: BRAIN Initiative (RRID:SCR_006770) Copy   

•   Source: SciCrunch Registry

http://www.nsgportal.org/

Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists.

Proper citation: Neuroscience Gateway (RRID:SCR_008915) Copy   

•   Source: SciCrunch Registry

http://lfpy.github.io

Python package for calculation of extracellular potentials from multicompartment neuron models. LFPy can be used to set up a model, run simulations, and calculate the extracellular potentials arising from activity in the given model neuron. It relies on the Python interface provided by the NEURON simulator.

Proper citation: LFPy (RRID:SCR_014805) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/

Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.

Proper citation: NeuroImaging Tools and Resources Collaboratory (NITRC) (RRID:SCR_003430) Copy   

•   Source: SciCrunch Registry

http://www.yale.edu/

Private Ivy League research university in New Haven, Connecticut. Founded in 1701 as the Collegiate School, it is the third-oldest institution of higher education in the United States and one of the nine Colonial Colleges chartered before the American Revolution.

Proper citation: Yale University; Connecticut; USA (RRID:SCR_006352) Copy   

•   Source: SciCrunch Registry

https://github.com/INCF/MUSIC

Software that allows large scale neuron simulators to communicate during runtime. It allows exchange of data among parallel applications in a cluster environment, interconnects large-scale neuronal network simulators with each other or with other tools, participates in multi-simulations, and is continuously developed and extended. Three simulators currently have MUSIC interfaces: Moose, NEURON and NEST. Three applications execute in parallel while exchanging data via MUSIC. The software interface promotes interoperability by allowing models written for different simulators to be simulated together in a larger system. It enables re-usability of models or tools by providing a standard interface. As data are distributed over a number of processors, it is non-trivial to coordinate data transfer so that it reaches the correct destination at the correct time. Current and future simulators can make use of MUSIC - compliant general purpose tools and participate in multi-simulations, for example when: * Different parts of a complex nervous system model are optimally implemented in different simulators, and need to communicate with each other. * Post-processing of generated data is needed, where the amounts of data are too large for intermediate storage, and requires the simulator to pass the data directly to the post-processing module. A standard interface enables straight-forward independent third-party development and community sharing of interoperable software tools for parallel processing. * Library and utilities are written in C++, uses MPI. * It is possible to add a MUSIC interface to existing simulators. * Works independently, no assumptions are made about other applications to facilitate development of general purpose tools. * Performance Data transport with high bandwidth and low latency.

Proper citation: MUlti SImulation Coordinator (RRID:SCR_001756) Copy   

•   Source: SciCrunch Registry

http://netpyne.org/

Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks.

Proper citation: NetPyNE (RRID:SCR_014758) Copy   

•   Source: SciCrunch Registry

http://icg.neurotheory.ox.ac.uk/

A database that provides a comprehensive and quantitative assay of ion channel models currently available in the neuroscientific modeling community. Specifically, it contains analyses of the ion channel models from NEURON. The database quantifies the similarity in kinetics between models using a series of standardized voltage clamp simulation protocols and subsequent cluster analysis. Citation links and duplications of channels, along with similarity of kinetics between channel models, are combined into genealogical trees and dendrograms that are searchable through the ICG web interface. ICG also experimentally recorded current traces and provides tools for uploading new channel models.

Proper citation: IonChannelGenealogy (RRID:SCR_014194) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/chlubba/PyPNS

Python based software module for the simulation of peripheral nerves. Used in the field of computational neuroscience.

Proper citation: PyPNS (RRID:SCR_016336) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/neuronpm/

Client/server application that makes parameter maps for neural simulations written in NEURON.

Proper citation: neuronPM (RRID:SCR_014768) Copy   

•   Source: SciCrunch Registry

http://mariannebezaire.com/simtracker/

MATLAB-based tool for use with NEURON network models. It supports the modeler with model design, organization, execution (including on supercomputers), analysis, and reproducibility.

Proper citation: SimTracker (RRID:SCR_014735) Copy   

•   Source: SciCrunch Registry