Brain and Cognitive Science

Related Sites





  • A Federated Design for a Neurobiological Simulation Engine: The CBI Federated Software Architecture, Cornelis, H., Coop, A.D., and Bower, J.M., PLoS ONE, 7(1), 2012.(link)
  • Encoding and Decoding Spikes for Dynamic Stimuli, R. Natarajan, Q. J. M. Huys, Neural Computation, 20:2325-2360, 2008.
  • Modeling Single-Neuron Dynamics and Computations: A Balance of Detail and Abstraction, A. V. M. Herz, T. Gollisch, C. K. Machens and D. Jaeger, Science, 314:80-5, 2006. (pdf)
  • Neuronal Computations with Stochastic Network States, A. Destexhe and D. Contreras, Science, 314:85-90, 2006. (pdf)
  • Biologically Based Computational Models of High-Level Cognition, R. C. O'Reilly, Science, 314:91-4, 2006. (pdf)
  • Neural Network Dynamics, T. P. Vogels, K. Rajan and L.F. Abbott, Annu. Rev. Neurosci., 28:357–76, 2005. (pdf)


  • EEG Processing & Brain-Computer Interface
    • EEGLAB: Matlab toolbox for EEG processing
    • OpenVibe: Software for brain-computer interfaces and real-time neurosciences
  • Mycrophysiological Modeling
    • Abstracted Protein Simulator
    • CalC (Ca2+ Calculator): Reaction/Diffusion Modeling Software
    • Copasi: complex pathway simulator for biochemical networks
    • MCell: A Monte Carlo Simulator of Cellular Microphysiology
    • Meredys: Mesoscopic Reaction Dynamics Simulator
    • NeuroRD: neuronal reaction diffusion simulator
    • pSICS: the Parallel Stochastic Ion Channel Simulator
    • STEPS: STochastic Engine for Pathway Simulation
    • VCell: Virtual Cell Modeling & Analysis Software
  • Compartmental Modeling
    • GENESIS: GEneral NEural SImulation System
    • NEURON: a simulation environment for modeling individual neurons and networks of neurons
    • CONICAL: C++ class library for the development of compartmental models and other neuroscience simulations
    • Maxsim: Analysis and simulation of multiple axonal arbors
    • MIEN: Model Interaction Environment for Neuroscience
    • MOOSE: Multiscale Object-Oriented Simulation Environment
    • NANS: Neuron and Network Simulator
    • NEURON (at Yale): a simulation environment for modeling individual neurons and networks of neurons
    • NeuronC: Neural Simulation Language
    • Nodus: a software package designed for simulation of the electrical behavior of neurons and small networks
    • PyDSTool: simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems)
    • simEngine: from Simatra Modeling Technologies
    • SNNAP: Simulation of Neural Networks and Action Potentials
    • Surf-Hippo Neuron Simulation System
    • XPP: Biophysical modeling of cells and membranes, as well as connectionist networks
  • Realistic Network Modeling
    • AnimatLab: biomechanical simulation and biologically realistic neural networks
    • Brian: a simulator for spiking neural network
    • Catacomb: A workbench for developing biologically plausible network models
    • CSIM: a tool for simulating heterogeneous networks composed of different classes of model neurons (analog/spiking) and synapses (Static/STDP)
    • MVASpike: a general purpose tool aimed at modeling and simulating large, complex networks of biological neural networks
    • NCS (NeoCortical Simulator): Allows large networks of many biologically realistic (Hodgkin-Huxley) neurons to be constructed
    • NENGO: a software package for simulating large-scale neural systems
    • The Neural Simulation Technology (NEST): a simulation system for large networks of biologically realistic (spiking) neurons
    • NSL: Neural Simulation Language
    • NeuroDragon: Neural circuit simulations tied to behavioral level visualization
    • :
    • ReMoto: a web-based simulator of the spinal cord and innervated muscles of the human leg
    • SpikeNet: a neural simulator for modeling large networks of integrate and fire neurons
    • Topographica: a software package for computational modeling of neural maps
    • XNBC: neurobiology simulation tool
  • Interoperability
    • BrainML: a developing initiative to provide a standard XML metaformat for exchanging neuroscience data
    • MUSIC: MUlti-SImulation Coordinator
    • neuroConstruct: Software for developing biologically realistic 3D neural networks
    • NeuroML: Model Descriptions for Computational Neuroscience
    • NineML: An XML based Markup Language for describing spiking neuronal network models
    • PyNN: a Python package for simulator-independent specification of neuronal network models

Research Centers

Leading Laboratories

Laboratory Principal Investigator Location
Andersen Lab Richard Andersen Caltech
Andreas Herz Research Group Andreas Herz LMU - Munich
Antwerp Theoretical Neurobiology Eric DeSchutter U. Antwerpen
Biologically Inspired Neural & Dynamical Systems (BINDS) Laboratory Hava Siegelmann U. Massachusetts, Amherst
Brain Engineering Laboratory Richard Granger Dartmouth
Butera Group Robert Butera Georgia Tech
Computational Neurobiology Group Nicolas Le Novère European Bioinf. Inst.
Computational Neurobiology Lab Gal Chechik Bar Ilan U.
Computational Neurobiology Laboratory Terrence Sejnowski Salk Institute
Computational Neuroscience Group John Taylor KCL
Computational Neuroscience Laboratory Ernst Niebur Johns Hopkins U.
Computational Neuroscience Unit Erik De Schutter OIST
Computational Sensorimotor Systems Laboratory (CSSL) Timothy Horiuchi & Jonathan Simon U. Maryland - College Park
Computational | Systems | Neuroscience Group Rolf Kötter HHU - Düsseldorf
Dendrites Michael Hausser UCL
Faisal Lab Aldo Faisal Imperial Coll. London
Fiete Lab Ila Fiete U. Texas - Austin
Gribble Lab Paul Gribble U. Western Ontario
Institute for Brain and Neural Systems Leon Cooper Brown
Katz Lab Paul Katz Georga State U.
Kauer Laboratory John Kauer Tufts U.
Kay Lab Leslie Kay U. Chicago
Koch Lab Christof Koch Caltech
Körding Lab: Home Konrad Körding Northwestern U.
Kreiman Lab Gabriel Kreiman TCH, Harvard Med. Sch.
Laboratory for Neural Computation Bartlett Mel USC
Marder Lab Eve Marder Brandeis
Methods Group (theoretical and neurobiology) Karl Friston U. College London
Neural Information Processing Group Klaus Obermeyer TU-Berlin
Neural Systems Group Rajesh Rao U. of Washington
Neurophysics Laboratory Mayank Mehta Brown
Nicolelis Lab Miguel Nicolelis Duke
Quantitative Neuroscience Laboratory Ken Harris Imperial Coll. London
Redish Lab David Redish U. Minnesota
Reinagel Lab Pam Reinagel UCSD
Rolls Lab Edmund Rolls Oxford
Shepherd-Willhite Laboratory Gordon Shepherd & David Willhite Yale
Urban Lab Nathan Urban CMU
Van Essen Lab David Van Essen Washington U. St. Louis
W. J. Freeman Neurophysiology Lab WWW Server Walter Freeman UC Berkeley
Wang Lab Xiao-Jing Wang Yale
Zach Mainen - CNP Zach Mainen IGC Portugal

This page is maintained by Chung-Yeon Lee (
Last update: January 10, 2012.