Neural models

Computer code for models of individual neurons and networks of neurons are increasingly being made available in public repositories.

The GENESIS site hosts a number of example models built and run in GENESIS.
Izhikevich IF:
Izhikevich has some very simple MATLAB implementations of his IF model, including network simulations, on his website at:
A well-supported repository for published neural models, hosted by Yale University. Most entries have been developed in the NEURON simulator, but other codes are also represented, including GENESIS, XPPAUT and others.

Cell morphologies

There are repositories of morphological reconstructions of biological neurons that are suitable for use in modelling studies.

Claiborne Lab:
Database of reconstructed cells from hippocampus.
Hippocampal Neuronal Morphology:
Duke-Southampton archive of reconstructed hippocampal cells. Comes with morphology editing and viewing software, cvapp.
Large database (over 5000 cells) of digitally reconstructed neurons.
Virtual Neuromorphology Electronic Database. Collection of reconstructed cells and model-generated cells of many different types.

Cell signalling

Repositories of cell signalling pathway models are available. Certain data relevant to the specification of parameter values in such models are also available. Protein interaction databases are useful for developing signalling schemes. Typically little reaction rate data is available. Enzymatic kinetics are generally more readily available.
Published cell signalling models for a variety of simulation environments. Links to associated data sources are provided. Models can be run online via the simulation environment JWS Online (
BJP Guide to Receptors and Channels:
An overview of receptors and channels with bibliographies for each channel subfamily.
The Database of Quantitative Cellular Signalling contains models of signalling pathways, largely built using GENESIS and Kinetikit. It includes reaction schemes, concentrations and rate constants.
IUPHAR Databases:
The IUPHAR Database of G-Protein-Coupled Receptors and the IUPHAR Database of Voltage-Gated and Ligand-Gated Ion Channels contain information about the gene sequences, structural and functional characteristics and pharmacology of ion channels. They are available from the database of the IUPHAR Committee on Receptor Nomenclature and Drug Classification.

Data analysis

Colquhoun's analysis programs:
A suite of programs, developed by David Colquhoun and coworkers , which analyse single channel data to determine opening and closing times, and then find the maximum likelihood fit of the kinetic scheme to the open and close time distributions.
An alternative suite of programs to the Colquhoun programs, which use a different algorithm to infer kinetic scheme parameters from single channel data.