Computational neuroscience

From Biohack

See also computational biology in general. Still need to run additional searches for calcium ion channel simulators. And apparently there are no bookmarks available re: computational fluid dynamics and the solvers. Oops. -- Kanzure 10:14, 15 March 2008 (CDT)

PSICS - the Parallel Stochastic Ion Channel Simulator
GENESIS
MCell - A Monte Carlo Simulator of Cellular Microphysiology
BioMOCA - Transport Monte Carlo simulation of conduction in biological Ionic Channels. (seems to only be on that website .. so.)
Tons of computational neuroscience software packages -- must read.
Cell modeling and simulation resources
Abstracted Protein Simulator
- from neurogems.org - neuroinformatics software
NEURON @ yale - [1]
StochSim - a stochastic simulator of (bio)chemical reactions
- Systems Biology Markup Language (SBML)

1 More Software
2 Conferences
3 Projects
4 See also

[edit]

More Software

Genesis, a general neural simulation system
Neuron, a neural network simulator
NEST, a simulation tool for large neuronal systems.
Neuroconstruct, software for developing biologically realistic 3D neural networks.
Neurofitter, a parameter tuning package for electrophysiological neuron models.
Neurojet, a neural network simulator specialized for the hippocampus
HHsim, a neuronal membrane simulator
MCell, A Monte Carlo Simulator of Cellular Microphysiology
Emergent, neural simulation software
Python tools : http://neuralensemble.org/
- pyNN
CHARMM (thanks Endos127)
BioSpice - Biological Simulation Program for Intra- and Inter-Cellular Evaluation
2008-03-15: I get it. coolzach19's distributedneuron project could use one of the distributed computing projects from Berkeley, and then use some of the models that are already out there in computational neurobiology, and just package together these different programs and basically do the equivalent of the Blue Gene project except over p2p (and much, much more slowly). -- Kanzure 08:39, 15 March 2008 (CDT)