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http://senselab.med.yale.edu/modeldb/

Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions.

Proper citation: ModelDB (RRID:SCR_007271) Copy   

•   Source: SciCrunch Registry

http://flybrain.neurobio.arizona.edu/

An interactive database of the Drosophila melanogaster nervous system. It is used by the drosophila neuroscience community and by other researchers studying arthropod brain structure. Flybrain contains neuroanatomical peer reviewed descriptions of the central and peripheral nervous system of Drosophila melanogaster. It also contains an introductory hypertext tour guide to the basic structure of the nervous system, as well as more specific information concerning different anatomical structures, developmental stages, and visualization techniques for the Drosophila nervous system. Additionally, The site contains schematic representations, a 3D project, immunocytology stains, a library of golgi impregnations, and enhancer-trap images.

Proper citation: MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous System (RRID:SCR_007661) Copy   

•   Source: SciCrunch Registry

https://www.bi.mpg.de/borst

Merger of the Max Planck Institute of Neurobiology and the Max Planck Institute of Ornithology and has been renamed to Circuits - Computation – Models. Department devoted to the study of how the brain computes to understand neural information processing at the level of individual neurons and small neural circuits.

Proper citation: Max Planck Institute for Biological Intelligence Circuits - Computation – Models (RRID:SCR_008048) Copy   

•   Source: SciCrunch Registry

http://bellsouthpwp.net/c/a/capowski//NTSPublic.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A hardware and software package with which a scientist could trace the structure of neurons and other neuroscientific features directly from tissue sections or from a stack of their images into a computer. Then it also could edit, merge, filter, display in 3D, and make realistic plots of the structures. The NTS also includes a substantial statistical package that provided many, now standardized, mathematical and statistical summaries that described each neuron and compared one population to another. Additionally, NTS also provided an embryonic electrotonic modeler that simulates and displayes the electrical functioning of a cell. The NTS uses a special purpose graphics display processor called the VDP3 whose output is presented on a very high resolution CRT. During tracing, the VDP3 presents a variable-diameter cursor and other information directly in the microscope and enables tracing at a high spatial resolution and with measurement of process diameters limited only by the microscope''s optics. Control of tracing is done with a 3D joystick that allows easy control of five input variables: X,Y,Z position, cursor diameter, and a numeric tag. Finally, superb 3D interactive displays of completed cells are provided on the VDP3.

Proper citation: Eutectic NTS (RRID:SCR_008062) Copy   

•   Source: SciCrunch Registry

http://www.neurostruct.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A built-in toolbox for the tracing and analysis of neuroanatomy from nanoscale (high-resolution) imaging. It is a project under ongoing development. The name is originating by merging the words Neuron + reconstruct. The working concept is organized in filters applied successively on the image stack to be processed (pipeline). Currently, the focus of the software is the extraction of detailed neuroanatomical profiles from nanoscale imaging techniques, such as the Serial Block-Face Scanning Electron Microscopy (SBFSEM). The techniques applied, however, may be used to analyze data from various imaging methods and neuronal versatility. The underlying idea of Neurostruct is the use of slim interfaces/filters allowing an efficient use of new libraries and data streaming. The image processing follows in voxel pipelines by using the CUDA programming model and all filters are programmed in a datasize-independent fashion. Thus Neurostruct exploits efficiency and datasize-independence in an optimal way. Neurostruct is based on the following main principles: * Image processing in voxel pipelines using the general purpose graphics processing units (GPGPU) programming model. * Efficient implementation of these interfaces. Programming model and image streaming that guarantees a minimal performance penalty. * Datasize-independent programming model enabling independence from the processed image stack. * Management of the filters and IO data through shell scripts. The executables (filters) are currently managed through shell scripts. The application focuses currently in the tracing of single-biocytin filled cells using SBFSEM imaging. : * Extraction of neuroanatomical profiles: 3D reconstrution and 1D skeletons of the imaged neuronal structure. * Complete tracing: Recognition of the full neuronal structure using envelope techniques, thereby remedying the problem of spines with thin necks of an internal diameter approaching the SBFSEM resolution. * Separation (Coloring) of subcellular structures: Algorithms for the separation of spines from their root dendritic stem. * Evaluation and analysis of the imaged neuroanatomy: Calculation of the dendritic and spine membrane''s surface, spine density and variation, models of dendrites and spines

Proper citation: Neurostruct (RRID:SCR_008861) Copy   

•   Source: SciCrunch Registry

http://bmsr.usc.edu/software/eons/

Modeling platform to study the basic interactions between synaptic elements that allows the user to study qualitatively, and also quantitatively the relative contributions of diverse mechanisms underlying synaptic efficacy: the relevance of each and every element that comprises a synapse, the interactions between these components and their subcellular distribution, as well as the influence of synaptic geometry (presynaptic terminal, cleft and postsynaptic density). This platform consists of a graphical interface in which elements that comprise a single glutamatergic synapse (both pre- and post-synaptically), their behavior as well as the underlying synaptic geometry can be modified. For example, EONS offers the ability to study the effect of voltage-gated calcium channels density and distribution, the number and location of receptors and more. EONS is a parametric model of a generic glutamatergic synapse that takes into account pre-synaptic mechanisms, such as calcium buffering and diffusion, neurotransmitter release, diffusion and uptake in the cleft, and postsynaptic elements, such as ionotropic AMPA and NMDA receptors, their distribution and synaptic geometry, as well as metabotropic glutamate receptors. There are no complicated equations to write: all the models are predefined. This version is a great tool for first time users and students interested in learning about synapses, as well as for studying geometry and distribution hypotheses in a 2D rectangular geometry. System Requirements: EONS V1.2 is a Windows program but can be also successfully installed and run on Mac and Linux.

Proper citation: EONS (RRID:SCR_002979) Copy   

•   Source: SciCrunch Registry

http://www.nest-simulator.org/

Software tool as simulator for spiking neural network models that focuses on dynamics, size and structure of neural systems rather than on exact morphology of individual neurons. Used for any size spiking neurons networks including models of information processing, models of network activity dynamics, models of learning and plasticity.

Proper citation: NEST Simulator (RRID:SCR_002963) Copy   

•   Source: SciCrunch Registry

http://bluebrain.epfl.ch/

A Swiss-led project with the aim of reverse engineering the mammalian brain and achieving a complete virtual human brain. The researchers have demonstrated the validity of their method by developing a realistic model of a rat cortical column, consisting of about 10,000 neurons. The eventual goal is to simulate systems of millions and hundreds of millions of neurons. The virtual brain will be an exceptional tool giving neuroscientists a new understanding of the brain and a better understanding of neurological diseases. In five years of work, Henry Markram's team has perfected a facility that can create realistic models of one of the brain's essential building blocks. This process is entirely data driven and essentially automatically executed on the supercomputer. Meanwhile the generated models show a behavior already observed in years of neuroscientific experiments. These models will be basic building blocks for larger scale models leading towards a complete virtual brain.

Proper citation: Blue Brain Project (RRID:SCR_002994) Copy   

•   Source: SciCrunch Registry

http://pons.incf.org/

Program consisting of three Task Forces and one Working Group to promote data exchange and integration in the neurosciences by developing terminology standards and formal ontologies for neural structures. Closely linked to the Program on Digital Brain Atlasing, the Program aims to establish a structured lexicon for the translation and definition of terms describing neural structures at multiple levels of granularity. The three Task Forces and one Working Group involved in the PONS effort: * Structural lexicon * Neuron registry * Representation and deployment * KnowledgeSpace Working Group Structural lexicon, Neuron registry, Representation and deployment, and KnowledgeSpace Working Group.

Proper citation: Program on Ontologies of Neural Structures (RRID:SCR_003549) Copy   

•   Source: SciCrunch Registry

http://synapses.clm.utexas.edu

A portal into the 3D ultrastructure of the brain providing: Anatomy of astrocytes, axons, dendrites, hippocampus, organelles, synapses; procedures of 3D reconstruction and tissue preparation; as well as an atlas of ultrastructural neurocytology (by Josef Spacek), online aligned images, and reconstructed dendrites. Synapse Web hosts an ultrastructural atlas containing more than 500 electron micrographs (added to regularly) that identify unique ultrastructural and cellular components throughout the brain. Additionally, Synapse Web has raw images, reconstructions, and quantitative data along with tutorial instructions and numerous tools for investigating the functional structure of objects that have been serial thin sectioned for electron microscopy.

Proper citation: Synapse Web (RRID:SCR_003577) Copy   

•   Source: SciCrunch Registry

https://neurowiki.case.edu/

Curriculum materials for an Introduction to Neurobiology course for undergraduate and graduate students.

The course focuses on the analysis of neurons and neural circuits for behavior using the fundamental principles of neuroscience. From the online course syllabus, the 24 units that make up the course may be directly accessed. Each unit contains a reading, links to at least one simulation, and a problem set.

A list of all available simulations can be found here: https://neurowiki.case.edu/wiki/Simulations. * 25 simulations are written in JavaScript and will run in any browser.
Source code: https://github.com/CWRUChielLab/JSNeuroSim * Pre-compiled executables (Windows, Mac, Linux) are available for 1 desktop simulation, the Nernst Potential Simulator.
Source code: https://github.com/CWRUChielLab/Nernst Structure of the Course * Solving problems based on simulations of neuronal components, neurons, and simple circuits to understand how they work. * For advanced students, writing a neuroscience Wikipedia article, critical review, or grant, in stages.

Proper citation: NeuroWiki (RRID:SCR_004066) Copy   

•   Source: SciCrunch Registry

http://spike.g-node.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.This project attempts to establish a platform for spike sorting with two different goals: First, to provide a sophisticated benchmark data set which could be used for future publications on this topic. Second, to give researchers using spike sorting software the possibility to evaluate their data under different conditions and compare their results to other spike sorters. Extracellular recordings are a standard procedure to analyzing the activity of neurons. A problem with this kind of recording is the simultaneous recording of not a single neuron but a small local population of neurons. It is not straight-forward to reconstruct the single neuronal activities. To estimate the single neuron activity (the so called spike train) from this multi neuron activity, spike sorting is applied. Many different algorithms for spike sorting were proposed. However, despite many efforts to tackle this problem, it is still difficult to tell under which circumstances which spike sorting algorithm is the best. If you are interested in some basic reading about spike sorting please consult the following references. A review of methods for spike sorting: the detection and classification of neural action potentials M. S. Lewicki (1998), Network: Computation in Neural Systems, Vol. 9, No. 4. (1998), pp. 53-78 Towards reliable spike-train recordings from thousands of neurons with multielectrodes. Einevoll GT, Franke F, Hagen E, Pouzat C, Harris KD (2011), Curr Opin Neurobiol. 2011 Oct 22.

Proper citation: Spike Sorting Evaluation Project (RRID:SCR_004063) Copy   

•   Source: SciCrunch Registry

http://celltypes.org/

Central repository of information on neuronal cell types mainly accumulating information on: Genetically labeled cell types in mouse brain and genetically engineered mouse lines for cell type research. Mouse lines are annotated with * Atlas for examining transgene expression patterns * Information on construct used to generate transgene * Associated publications * Anatomical regions where transgene is expressed (based on Atlas) * Information on where to obtain the animals Currently, the mouse lines in the database are mostly generated at Cold Spring Harbor Lab, Scripps Research Institute, Baylor College of Medicine and Brandeis University with few other exceptions. In the future, they will incorporate more mouse lines useful for neuronal cell type research. Cell types are annotated with * Anatomical region * Properties (frequently used terms in neuroscience research) * Mouse line used to define the cell type * Genome wide transcriptome data (if available) * Specific (marker) genes (if available) * Marker immunostaining data (if available) * Associated publications * Electrophysiological characterizations (when available) * Morphological characterizations (when available)

Proper citation: celltypes.org (RRID:SCR_004545) Copy   

•   Source: SciCrunch Registry

http://connectomes.org/

Project mapping whole mouse brain connectivity using serial block face scanning electron microscopy (SBF-SEM) with a specially-designed whole-brain microtome (WBM). With any luck, the whole mouse brain will be mapped ultrastructurally in the near term, which will then open the door to more serious problems; reliable automated segmentation and circuit reconstruction. These will undoubtedly require advances in machine learning methods and their application. Connectomics Software and a Multiresolution Image Viewer (MIV) is also available.

Proper citation: Connectomes.org (RRID:SCR_002243) Copy   

•   Source: SciCrunch Registry

http://www.janelia.org/team-project/fly-em

A project producing datasets, software, and algorithms that is developing the technology to produce connectomes at the electron microscopic level of behaviorally-relevant neural circuits as well as the entire Drosophila nervous system. This technology will enable them to create a map of every neuron and synapse in the Drosophila nervous system, using novel approaches to electron microscopy (EM) as the foundation. In the same way that the fly genome paved the way for larger projects, including sequencing the human genome, Fly EM may ultimately contribute to our understanding of the human brain by establishing a fly "connectome" a map that shows how all neurons in the fly brain are connected to each other. They began their entry into EM reconstruction with the fly's adult visual system, where much is known about cell types from previous EM and histological studies, as well as ongoing studies in the Fly Light Project. In addition to establishing and publishing a fly connectome, Fly EM will make technology and methodology available that is needed to perform large-scale EM reconstructions. Fly EM will generally pursue an open policy with their datasets, software, and algorithms after relevant publications. When an EM reconstruction is published, the derived connectome and reconstructed neuronal skeletons will be made available online. The raw data and annotatations will be made available upon request as logistics dictate. To encourage further collaboration and scientific discovery, a small fraction of their raw data and corresponding segmentation will be made available independent of publication. Their goal is to enable others who wish to approach the many algorithmic challenges, but who do not have access to an EM facility, to have the data they need to support methods development, as well as their results to use as a benchmark. Fly EM emphasizes publication of supporting techniques and software approaches before major EM reconstruction releases to encourage rapid feedback from the community and adoption of their strategies. FlyEM maintains much of its software in the open-source repository GitHub:http://janelia-flyem.github.com. They will provide information on official release versions of these packages on git-hub when it reaches reasonable maturity.

Proper citation: Fly EM (RRID:SCR_002242) Copy   

•   Source: SciCrunch Registry

http://www.theearlab.org

A computationally oriented experimental laboratory interested in the encoding of auditory information in the cerebral cortex and brainstem, and in the mechanisms of tinnitus and the effect of various drugs (Lidocaine, steroids, anti-oxidants) in relieving noise trauma induced tinnitus. The ferret (Mustela putorius) and the rat serve as their system model. Through chronic implants, they obtain electrophysiological data from awake behaving animals in order to investigate the response properties and functional organization of the auditory system, both in health and after noise trauma that induces tinnitus in rats. Projects: * Response Modulation to Ongoing Broadband Sounds in Primary Auditory Cortex * Neuronal Response Characteristics in the Inferior Colliculus of the Awake Ferret and Rat * Spectro-Temporal Representation of Feature Onsets in Primary Auditory Cortex * Targeting the changes in inferior colliculus induced by tinnitus

Proper citation: Ear Lab (RRID:SCR_002531) Copy   

•   Source: SciCrunch Registry

http://neuinfo.org

Framework for identifying, locating, relating, accessing, integrating, and analyzing information from neuroscience research. Users can search for and add neuroscience-related resources at NIF portal and receive and RRID to track and cite resources within scientific manuscripts.

Proper citation: Neuroscience Information Framework (RRID:SCR_002894) Copy   

•   Source: SciCrunch Registry

http://www.wellesley.edu/Neuroscience/

Neuroscience was implemented as a new interdisciplinary major in 1999, replacing the Psychobiology Program and providing a base of experiences in biology, chemistry and psychology. Our students benefit from being able to work in small classes and to experience investigative lab experiences even in their introductory courses. Wellesley's neuroscience majors graduate with a liberal arts background coupled with sufficient concentration in this specialized field to be competitive among students coming from exclusively research-oriented institutions. The best proofs of the success of this approach are its products: * 60% of our graduates proceed to medical school; * 15% of our graduates continue on with graduate work in neuroscience, psychology, or neuropsychology; * 10% of our graduates pursue careers that intersect with neuroscience - for example, patent law or work in the biotech industry. Neuroscience is the study of the structure and function of neurons and how they are assembled to produce behaviors. This topic uses a multidisciplinary approach that extends from the molecular, through the cellular, and to the behavioral level.

Proper citation: Wellesley College Neuroscience (RRID:SCR_002734) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu/neurondb

Database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.

Proper citation: NeuronDB (RRID:SCR_003105) 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