An ecosystem of computational resources

ModelDB, and its closely related databases SimToolDB and NeuronDB, are key elements of an ecosystem of resources for computational neuroscience. These resources fall into two broad categories: portals and data resources with which we have had formal or informal collaborations, and simulators and simulation tools.

Neuroinfomatics portals and resources with which we have collaborated

• Neuroscience Information Framework "The Neuroscience Information Framework is a dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected to the Internet. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment."
• NeuroMorpho.org is a centrally curated inventory of digitally reconstructed neurons. NeuroMorpho.Org contains contributions from over two-dozen labs and is continuously updated as new morphological reconstructions are collected, published, and shared, with the goal of densely covering all available data. A related site is L-NEURON, a modeling tool for the efficient generation and parsimonious description of dendritic morphology.
• Neuroelectro "The goal of the NeuroElectro Project is to extract information about the electrophysiological properties (e.g. resting membrane potentials and membrane time constants) of diverse neuron types from the existing literature and place it into a centralized database."
• The Ion Channel Genealogy database provides a comprehensive and quantitative assay of ion channel models currently available in the neuroscientific modeling community, all browsable in interactive visualizations.
• The Open Source Brain repository (OSB) is a public repository for detailed neuronal models in standardised formats, with curated, stable releases which will evolve in line with new experimental findings, the latest modelling paradigms and simulator technology development. Anyone can contribute to any of the models on OSB, either through fixing a bug, adding new features or improving documentation for published models.
• NeuroML is intended as the home for markup language efforts for neuroscience. Source Forge hosts NeuroML development efforts This includes syntax and semantics for data, sites, other entities such as chemical species, methods, models, and references. A number of simulation tool developers are collaborating to define and use a common data model for describing neuroscience simulation models. Currently the levels of description covers models of ion channels, multicompartment cells and networks of neurons.
• The Simulation Platform (SimPF) provides a test environment of computational models via web.
• The Neuroscience Gateway (NSG portal) is a resource for the neuroscience community supported by the National Science Foundation. Through a simple web-based portal, the NSG provides an administratively and technologically streamlined environment for uploading models, specifying HPC job parameters, querying running job status, receiving job completion notices, and storing and retrieving output data. The NSG transparently distributes user's jobs to appropriate XSEDE HPC resources.

Simulators and Simulator Tools

• NEURON for empirically-based simulations of neurons and networks of neurons.
• GENESIS GEneral NEural SImulation System developed at Caltech to provide a standard and flexible means of constructing realistic simulations of biological neural systems. MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. ... MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. it is backwards-compatible with GENESIS, and forward compatible with Python and XML-based model definition standards like SBML and MorphML.
• SNNAP Simulator for Neural Networks and Action Potentials is a tool for the rapid development and simulation of realistic models of single neurons and small neural networks.
  
• MCell makes it possible to incorporate high resolution ultrastructure into models of ligand diffusion and signaling, and has evolved from experimental and theoretical work of the MCell group: Joel Stiles (deceased, formerly of Biomedical Applications, Pittsburgh Supercomputing Center), Miriam Salpeter (Neurobiology & Behavior, Cornell University), Edwin Salpeter (Department of Physics and Astronomy, Cornell University), and Thomas Bartol and Terrence Sejnowski (Computational Neurobiology Laboratory, Salk Institute).
  
• Virtual Cell Environment ... "The user can build complex models with a web-based Java interface to specify compartmental topology and geometry, molecular characteristics, and relevant interaction parameters. The Virtual Cell automatically converts the biological description into a corresponding mathematical system of ordinary and/or partial differential equations. Distinct biological and mathematical frameworks are encompassed within a single graphical interface. The mathematic-savy user may directly specify the complete mathematical description of the model, bypassing the schematic interface. The Virtual Cell will then solve the equations by applying numerical solvers and generate appropriate software code to perform and analyze simulations. Results can be displayed and analyzed on-line or downloaded to the users computer in a variety of formats." Published VCell models
• The Surf-Hippo neuron simulator is a public domain package written in Lisp for Unix workstations and PCs that is used to investigate morphometrically and biophysically detailed compartmental models of single neurons and networks of neurons. Surf-Hippo allows ready construction of cells and networks using built-in functions and various anatomical file formats (NTS, Rodney Douglas, and Rocky Nevin formats, using a modified version of the anatomy file conversion program ntscable by JC Wathey; Neurolucida).
  
• NEST - The Neural Simulation Technology Initiative is a collaborative effort to advance simulation technology for large, biologically realistic networks of spiking neurons. ...
  The main goals of the collaboration are: 1) development of new simulation methods and algorithms, 2) development of new analysis and visualization tools, as well as the 3) collection of information and resources related to neural simulations. These goals are expressed in the joint development of a simulation system for biologically realistic neuronal networks. This groups software was previously called BLISS and SYNOD.
  
• XPP-Aut X-windows phase plane analysis program by Bard Ermentrout. Designed to solve dynamical systems problems that take several different forms: (i) ordinary differential equations (ODEs); (ii) delay differential equations (DDEs); (iii) differential-algebraic equations (DAEs); (iv) Volterra integro-differential equations (IDEs); (v) discrete dynamical systems (MAPs); (vi) boundary value problems (BVP). Includes "locbif" (locate bifurcations), a phase plane analysis tool. Runs under Windows or Unix.
  
• Emergent (Formally PDP++) The PDP++ software is a neural-network simulation system written in C++. It represents the next generation of the PDP software originally released with the McClelland and Rumelhart "Explorations in Parallel Distributed Processing Handbook", MIT Press, 1987. It is easy enough for novice users, but very powerful and flexible for research use.
• "Brian is a new simulator for spiking neural networks available on almost all platforms. The motivation for this project is that a simulator should not only save the time of processors, but also the time of scientists. Brian is easy to learn and use, highly flexible and easily extensible. The Brian package itself and simulations using it are all written in the Python programming language, which is an easy, concise and highly developed language with many advanced features and development tools, excellent documentation and a large community of users providing support and extension packages. ..."
• "QUB is a software package for Markov analysis of single-molecule kinetics, especially ion channel records. With QuB's user-friendly graphical interfaces, you can * simulate single-channel currents for any model * calculate rate constants and voltage-dependence without fitting histograms * detect current transitions in the presence of noise * filter data, correct baseline, and select subintervals * test all possible model topologies * fit data to any function or system of ODEs * (more...)"