• BIOSIG project
• Catacomb: Components And Tools for Accessible COmputer Modeling in (neuro)Biology
• ChannelLab: Simulation and analysis of ion channel kinetics
• CVapp including a NeuroLucida to GENESIS/NEURON converter
• GENESIS GEneral NEural SImulation System
• GENESIS Users group BABEL
• GEPASI: Biochemical kinetics simulator
• Graph theory methods for the analysis of neural connectivity patterns
• HHsim: Matlab-based educational software illustrating Hodgkin-Huxley equations
• IATR: Image analysis tools registry
• Internet Analysis Tools Registry
• IQR421 for large scale heterogeneous neuronal systems
• KlustaKwik: Fast automatic clustering using a mixture of Gaussians model
• Lissom: Hierarchical laterally connected self-organizing maps
• Madonna: General purpose differential equation solver
• Mathematica
• Mathematica Journal
• Mathematica Information Center
• MATLAB
• MAXSIM for axonal arbors
• MCell: General monte carlo simulator of cellular microphysiology
• MDP: Modular toolkit for Data Processing
• NANS: Neuron And Network Simulator
• NCS3: NeoCorticalSimulator
• NEOSIM: Neural Open Simulation
• NEST: The Neural Simulation Technology Initiative
• Neural Network simulators list
• Neural Simulation Language (NSL)
• NEURON home page
• NEURON tutorial
• NeuronMesher: Eutectics/NeuroLucida to GENESIS/NEURON converter
• NeuroScholar Software
• NeuroScope: advanced viewer for electrophysiological and behavioral data
• NeuroSpec: Multivariate Fourier Analysis of Neural Data
• NEV2lkit: a tool for handling neuronal event files
• Nodus for Macintosh computers
• PDP++
• PhasePlane & Auto (XPP, WinPP)
• SNNAP: Simulator for Neural Networks and Action Potentials
• SPM Anatomy Toolbox
• Statistics Software List
• SURF-HIPPO neuron simulator system
• Synthesis - Complex Systems Simulator
• Thyrix - an agent/environment simulator for artificial intelligence and artificial life research
• Topographica: Computational modeling of cortical maps
• Virtual Cell
• VMD: Visual Molecular Dynamics
• XNBC: a workstation for biological neural network simulation

Jaap Murre's list of Simulation Tools