Using a highly abstracted view of protein structure, allows Monte-Carlo
simulations of relatively large systems to be carried out on single PCs.
Written in Java and Java3D.
Provides for biophysical modeling of intracellular calcium dynamics.
It allows the inclusion of mobile and/or fixed calcium buffers, as well as
various diffusion barriers. Written in C++. Tested on Linux, SGI, SUN and
Windows. See
manual
for details.
EONS provides a modeling platform to study the basic molecular mechanisms
that occur at the synaptic junction, both pre- and postsynapticly, as well
as the impact of synaptic geometry (2D).
MCell
Monte Carlo Similator of Cellular Microphysiology
Incorporates high resolution cellular ultrastructure into models of ligand
diffusion and signal transduction.
One can address questions at the level of molecular interactions and
signal transduction in biological systems, where local concentration
effects and the geometry of interactions are important. Input files are
formatted in NeuroML.
Modigliani is a stochastic simulation software framework for modelling
cell signalling at a biophysically realistic level, especially in the
nervous system. It can be thought of as filling a gap between packages
like MCell and Neuron. Modigliani simulates discrete, stochastic ion
channels in spatially extended neuronal membranes.
pSICS
the Parallel Stochastic Ion Channel Simulator
pSICS computes the behavior of neurons taking account of the stochastic
nature of ion channel gating.
The biologically oriented user interface allows experimentalists to
create models, define cellular geometry, specify simulations and analyze
the simulation results. The solver is transparent to the average user,
but is accessible to the theorist. SBML import/export.
GENESIS is a general purpose simulation platform which was developed to
support the simulation of neural systems ranging from complex models of
single neurons to simulations of large networks made up of more abstract
neuronal components. XODUS, the graphic front end, requires the X Window
System. PGENESIS (Parallel GENESIS) depends on PVM. The most recent
development efforts can now be followed at
SourceForge.
Versions of Parallel GENESIS rewritten for MPI are available
through the GENESIS users group, BABEL. Of these,
mpgenesis
can also be obtained directly from the developer, Christo Panchev.
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.
NEURON is a simulation environment for modeling individual neurons and
networks of neurons. It provides tools for conveniently building,
managing, and using models in a way that is numerically sound and
computationally efficient. It is particularly well-suited to problems
that are closely linked to experimental data, especially those that
involve cells with complex anatomical and biophysical properties. Python
can now be used as alternative command line interpreter, and NeuroML
model descriptions can be imported.
Neural simulation language used to build biophysically-based models.
Converts branched cables to compartments. Details channel conductances,
synapses and gap junctions.
Neurospaces is a middle-ware data container for large and complex
neuronal models. It is used as an abstraction layer on top of a simulator
and deals with biological entities and end-user concepts instead of
mathematical equations. This allows for optimization the numerical core
separately from the modeling package.
PyDSTool is related to DSTool (see
Differential Equation Solvers
below), but this new simulation, modeling, and analysis package contains
additional toolkits and features for computational neuroscience. It
includes: a model development environment, with templates for
compartmental models; data analysis tools, including conversion tools for
use with DSSRT (see
Time Series Data
below); and built-in tools for continuation / bifurcation analysis.
SNNAP
- Simulation of Neural Networks and Action Potentials
Rapid simulation of single neurons (including ion channels and second
messenger concentrations) and small networks of neurons.
Surf-Hippo allows construction of morphometrically and biophysically
detailed models of single neurons and networks of neurons. Written in
Lisp for both Unix and PC installations. It can accept anatomical data in
Neurolucida, NTS, Rodney Douglas, and Rocky Nevin formats. Built-in
functions also allow user developed anatomical descriptions to be
processed.
Biophysical modeling of cells and membranes, as well as connectionist
networks. Phaseplane analysis. Takes advantage of a variety of numerical
methods.
Older version still available at
CMU.
Brian is a simulator for spiking neural networks. Both integrate-and-fire
models and Hodgkin-Huxley type models can be used. Brian is useful for
models with a few compartments, but not with reconstructed dendritic
trees. Written in Python, it will run on Windows, Unix/Linux and OS X.
CSIM is a tool for simulating heterogeneous networks composed of different
classes of model neurons (analog/spiking) and synapses (Static/STDP).
The simulator is written in C++ with a Matlab user interface.
A simulation system for large networks of biologically realistic (spiking)
neurons. It is best suited for the simulation of large networks of spiking
point-neuron models. The internal dynamics of these models may be
arbitrarily complex.
Software to ease the development of large 3D networks for the NEURON and
GENESIS Simulators. Imports cell morphology files from these simulators as
well as from .swc format files. Implemented in Java.
A system for the simulation of very large networks of biologically
accurate neurons on parallel computers (Beowulf clusters, and networks
of workstations).
The project provides a standardized software interface for communication
between disparate parallel applications for large-scale modeling. Built
on top of MPI.
An XML based Markup Language for models in neuroscience. It allows for
specification of neuronal morphology, the distribution of ion channels on
cell membranes, descriptions of the channel mechanisms and of neuronal
connectivity. Current development activity can be followed at
SourceForge.
Allows for controlling up to 4 neurons in real time, dynamic clamp mode.
Written in C++ for Windows 95/98/2000/NT using the DIGIDATA 1200A board
from Axon Instruments
Simulates ionic currents in real time (up to 50kHz). Can be used to:
(i) artificially insert ion channels into a neuron,
(ii) connect in vitro neurons with simulated synapses, or
(iii) connect simulated neurons to in vitro neurons.
Runs on Linux with the RTLinux kernel extention.
A modification of DynClamp2 (see above) to include the following features:
(i) a spike generator, (ii) hidden parameter panels, (iii) data displays
for debugging, (iv) saving and loading of parameter settings, (v) spike
timing dependent plasticity, and (vi) experimental automatization and
scripting.
Java 1.1 application/applet converts Neurolucida morphology files
to GENESIS or NEURON format. It was developed as a morphology
viewer/editor to validate cells contributed to the Duke/Southampton
Cell Morphology Archive. A
modified version
is available that will handle remeshing of structures for Genesis.
is a software package for the generation and description of
dendritic morphology. Virtual neurons are created by the stochastic
implementation of neuroanatomical rules. Statistical distributions
of parameters used can be measured from computer files of
reconstructed neurons in several commonly used formats. Generated
neurons can be saved as compartmental files compatible with the
GENESIS and NEURON simulators.
A Generator for realistic Neurons in 3D. NeuGen is made for the
generation of dendritic and axonal morphology of realistic neurons
and neuroal networks in 3D. It directly supports geometry formats
for using the NEURON simulation software.
A plug-in for
ImageJ
that allows one to measure the coordinates
and the diameter of a section of a neuron together with other
information that can be used to reconstruct neuron morphology.
Outputs .swc format files.
An automated system for digitization, 3D reconstruction and
geometric analysis of detailed neuronal morphology. Scales from
spine geometry through multi neuron networks.
Tailored for use in computational neuroscience, DSSRT analyzes
simulation data to determine time intervals within which different
"inputs" to a differential equation (e.g. currents crossing a cell
membrane) are most dominant. DSSRT indicates the temporal pattern
of changing strengths of influence of each current on a cell.
This can be useful in reducing detailed biophysical equations, or
identifying parts of the cell's dynamics which are either robust or
sensitive to perturbations or variability. Matlab package with GUI.
Designed to asist neurophysiologists with both manual and automatic
spike sorting/cluster cutting. Visualization tools include waveform
displays and auto- and cross-correlograms.
A Matlab toolbox which enables a user to perform manual clustering
on single-electrode, stereotrode, and tetrode recordings taken with
the DataWave and Cheetah recording systems. The toolbox is
free-ware, but you will need Matlab 5.2 or higher to run it. Tested
on Windows and Solaris.
neurALC is an open-source cross-platform software for the analysis
of multi-electrode recordings. It also offers analysis functions
like population activity estimation, single electrode/unit PSTH, ISI
& instant firing rate calculation, correlation/autocorrelation,
spectrum, delay, mutual information, recurrence plots, among others.
Visualization of the recordings can be done in 2D and 3D.
Transforms a simple description of the geometry and activity of a
network of neurons and transforms it to a 3D animation.
C++ with the addition of the OpenGL extension of QT. Tested on
Fedora II with QT 3.3.
The NeuroScholar system is a knowledge management system for the
neuroscientific literature, allowing users to build an organized library
of PDF files and then make and manage free-form notes based on the
articles.
Though not itself a differential equation solver,
DSSRT further analyzes simulation data numerically computed using
tools such as those built into Bard Ermentrout's XPP software, or any
other fixed time-step ODE solver. (See fuller description under
Time Series Data
above).
Very good for phaseplane analysis.
Patched
versions
for Redhat linux are available.
For current development efforts providing expanded capabilities as a full
modeling package see PyDSTool (under
Compartmental Modeling
above).
This page is maintained by Jim Perlewitz
(
perlewitz@earthlink.net
)
Please send reports of errors, updates, omissions, or suggestions.
Last updated Aug. 26, 2008.
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