Brain Emulation Software
Heath Matlock
various degrees, would like to see others add to the list. I skipped
over topology agnostic network simulators, stimulation
analysis/simulation, protein folding, and non-biologically inspired
AGI software. Not that I don't care for that software, but the list is
large enough as it is. But I suppose if someone wants to mention such
software, I'm not stopping you.
So here's the list (no guarantees as to the quality of the software):
http://sourceforge.net/projects/genesis-sim/
GENESIS (GEneral NEural SImulation System) is a software platform for
the simulation of neural systems ranging from subcellular components
and biochemical reactions to complex models of single neurons, large
networks, and systems-level processes.
http://sourceforge.net/projects/pysces/
Pysces is the Python Simulator of Cellular Systems. For a network of
coupled reactions it does a stoichiometric matrix analysis, calculates
the time course and steady state, and does a complete control
analysis.
http://sourceforge.net/projects/synbioss/
Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for
biochemical kinetic constants, a graphical interface for simulating
synthetic biological pathways, and a simulator that runs on either a
desktop or supercomputer.
http://www.neuron.yale.edu/neuron/
NEURON is a flexible and powerful simulator of neurons and networks.
http://synaptic-modeling.com/
EONS is a tool to study the basic interactions between synaptic elements.
http://www.ra.cs.uni-tuebingen.de/SNNS/
SNNS (Stuttgart Neural Network Simulator) is a software simulator for
neural networks on Unix workstations developed at the Institute for
Parallel and Distributed High Performance Systems (IPVR) at the
University of Stuttgart. The goal of the SNNS project is to create an
efficient and flexible simulation environment for research on and
application of neural nets.
http://leenissen.dk/fann/
Fast Artificial Neural Network Library is a free open source neural
network library, which implements multilayer artificial neural
networks in C with support for both fully connected and sparsely
connected networks. Cross-platform execution in both fixed and
floating point are supported. It includes a framework for easy
handling of training data sets. It is easy to use, versatile, well
documented, and fast. PHP, C++, .NET, Ada, Python, Delphi, Octave,
Ruby, Prolog Pure Data and Mathematica bindings are available.
http://sourceforge.net/projects/brian/
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.
http://sourceforge.net/projects/stochsim/
STOCHSIM is a stochastic simulator for biochemical reactions. The
particles are represented as individual software objects which react
according to probabilities derived from concentrations and rate
constants. Simple spatial structures can be built.
http://sourceforge.net/projects/neurofitter/
Neurofitter is a parameter tuning package for electrophysiological
neuron models. For more information please take a look at
http://neurofitter.sourceforge.net
http://sourceforge.net/projects/pcsim/
PCSIM is a tool for distributed simulation of heterogeneous networks
composed of different model neurons and synapses. The development of
PCSIM is supported by the FACETS EU project.
http://sourceforge.net/projects/spikestream/
SpikeStream is a fast, flexible simulator of spiking neural networks.
Easy to use graphical user interface with comprehensive monitoring
facilities. Runs in parallel across an arbitrary number of machines
and dynamically loads neuron and synapse classes.
http://sourceforge.net/projects/snaiu/
SNAIU is a simulator for large neuronal networks using leaky INF as
its basic element. Simple few line scripts will enable rapid creation
of large networks with different connectivities. Aimed at researchers
interested in quickly testing large networks of neurons.
http://sourceforge.net/projects/tezeract/
Tezeract Neural Network Simulator is an Open Source neural network simulator
http://sourceforge.net/projects/cervelletto/
Cervelletto is a neural network simulator. It uses a new neural model
based on biological, neurological and psychological studies.
http://sourceforge.net/projects/neuralsyns/
NeuralSyns is a neural simulator for large spiking networks. New
neuron and synapse dynamics can be added, and complex network models
can be easily built using the included tool NetBuilder. OpenGL is used
to show the network's architecture and activity.
http://sourceforge.net/projects/isns/
iSNS is an interactive neural network simulator written in
Java/Java3D. The program is intended to be used in lessons of Neural
Networks. The program was developed by students as the software
project at Charles University in Prague.
http://topographica.org
Topographica is a neural modeling package developed in a Human Brain
Project grant from NIH. Topographica helps neuroscientists and
computational scientists simulate and understand how topographic maps
contribute to brain function
http://sourceforge.net/projects/elysia/
http://elysia.sourceforge.net/
Elysia is an attempt to study the complex process behind decision
making in neural systems. An evolved entity approach is used to
converge on an 'intelligence' solution through genetic algorithms as
well as adaptable models of distributed 'thinking'.
http://sourceforge.net/projects/barney/
Barney, a primitive brain simulator for medical research. It uses the
background of massive complex networks to evaluate the brain behavior
through low level neuron modeling. The source code and comments are
written in Brazilian Portuguese.
http://sourceforge.net/projects/opengenetics/
This is an open source genetics simulator. The simulator is based on
the crossing of fruit flies and the different attributes of these
fruit flies.
http://sourceforge.net/projects/techiebrain/
Techiebrain: this is a step by me to see how can we develop something
which does the functionality much like a brain
http://sourceforge.net/projects/lifeform/
LifeForm: Artificial Intelligence project aimed at integrating into
modern operating environments to achive increased productivity,
interactivity, and perhaps something we cannot predict at this time.
Based on theory of emulating the human brain.
http://sourceforge.net/projects/bbrain/
BBrain project aims to develop an innovative Neural Network design
based on the new findings in Neuroscience and Biology. The ultimate
goal is to emulate a complete and self-conscious "brain" based on
theories in Dennet's school of thought.
http://sourceforge.net/projects/bdv-cell/
Brain Derived Vision on IBM CELL: a high-level model of the cortex
region of the brain in C. The code has been optimized to run on IBM
CELL processor for high performance computation
http://sourceforge.net/projects/becca/
BECCA is a Brain-Emulating Cognition and Control Architecture. It is a
general unsupervised learning and control approach based on
neuroscientific and psychological models of humans.
http://sourceforge.net/projects/cycells/
CyCells is a 3D, discrete-time simulator for studying intracellular
interactions using individual cells and extracellular molecular
concentrations. Model definition input files allow simulation of
multiple systems without recompiling.
http://sourceforge.net/projects/geneusim/
A small simulator for Mendelian genetics, genetic drift, natural
selection and random mutations, built on matplotlib and wxpython. A
graph will be generated that traces the distribution of genotypes at
successive generations.
http://sourceforge.net/projects/synapsenn/
SynapseNN is a simulator for artificial neuronal networks. It can be
used to solve concrete problems. Use it as a standalone-application or
as a library from your own applications.
http://sourceforge.net/projects/four-dices/
4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid
(stochastic and deterministic) modeling and simulation of (whole) cell
environments in 4D. The framework may incorporate any reaction and
diffusion algorithms applicable in a 4D grid layout.
http://sourceforge.net/projects/ecmojo/
ECMOjo is a simulator and trainer for extracorporeal membrane
oxygenation (ECMO). ECMOjo consists of a graphical user interface to
allow interaction and train ECMO practitioners.
http://sourceforge.net/projects/brams/
BRAHMS is a Biomembrane Reduced-ApproacH Molecular Simulator.
http://sourceforge.net/projects/gensim/
Gene-Environment iNteraction Simulator (GENS) is a novel method to
simulate full-controllable case-control studies for complex diseases
where gene-environment interactions determine the disease risk.
http://sourceforge.net/projects/steps/
Stochastic simulator for signaling pathways occuring in biological
cells. Handles reaction-diffusion processes in 3D tetrahedral meshes.
http://sourceforge.net/projects/gnuvallesfam/
GNUValles FAM is an open source C++ simulator of Fuzzy ARTMAP Neural
Networks, with learning propouse. The project is developed by CUValles
researchers and students, all at the University of Guadalajara.
http://sourceforge.net/projects/spikingneurons/
The Spiking Neurons software is intended to implement faithfully
currently available models of neuron spiking behaviour. It is intended
to be of use in teaching and learning.
http://sourceforge.net/projects/bgneuron/
Bgneuron is a lightweight C++ neuron simulator to simulate networks
of spiking neurons in the basal ganglia and the cortex.
http://sourceforge.net/projects/brainlab/
Brainlab is a Python toolkit to aid in the design, simulation, and
analysis of spiking neural networks with the NeoCortical Simulator
(NCS).
http://sourceforge.net/projects/pybrainsim/
PyBrainSim - The Brain Phantom Project is an interactive tool for the
simulation and visualization of the electromagnetic activity of the
brain.
--
Heath Matlock
+1 256 274 4225
Heath Matlock
http://home.earthlink.net/~perlewitz/sftwr.html
Also... forgot to look into membrane potentials last message. But
here's some more software:
http://netmorph.org/
NETMORPH is a simulation environment for the developmental generation
of 3D large-scale neuronal networks with realistic neuron
morphologies. In NETMORPH, neuronal morphogenesis is simulated from
the perspective of the individual growth cone. For each growth cone in
a growing axonal or dendritic tree, its actions of elongation,
branching and turning are described in a stochastic, phenomenological
manner. In this way, neurons with realistic axonal and dendritic
morphologies, including neurite curvature, can be generated. Synapses
are formed as neurons grow out and axonal and dendritic branches come
in close proximity of each other. NETMORPH is a flexible tool that can
be applied to a wide variety of research questions regarding
morphology and connectivity. Research applications include the
formation of synaptic connectivity during development and the complex
relationship between neuronal morphology and global patterns of
synaptic connectivity.
http://nerve.bsd.uchicago.edu/nerve1.html
NERVE, this program simulates the generation and propagation of the
action potential by solving the Hodgkin and Huxley (HH) model for the
space-clamped (membrane AP) or the partial differential equations of
the simple core conductor cable with membrane characteristics based on
the HH equations, for the propagated action potential
http://snnap.uth.tmc.edu/
SNNAP (Simulator for Neural Networks and Action Potentials) is a tool
for rapid development and simulation of realistic models of single
neurons and neural networks. It includes mathematical descriptions of
ion currents and intracellular second messengers and ions. In
addition, you can simulate current flow in multicompartment models of
neurons by using the equations describing electric coupling.
SNNAP also includes mathematical descriptions of intracellular second
messengers and ions, and simulate the modulation of membrane currents
and synaptic transmission, , either enhancement or inhibition.