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Software

Neurofitter

Neurofitter is a parameter tuning package for electrophysiological neuron models.

Neurofitter : Information on Neurofitter.

More questions or suggestions about Neurofitter?
Email us : Wernerattnb.ua.ac.be.


Steps

STEPS (STochastic Engine for Pathway Simulation) is the name of our reaction kinetics simulator package. Its core simulation algorithm is a voxel-based variation of Gillespie's SSA, modified to handle combined reaction-diffusion systems. Molecules are able to diffuse within arbitrarily complex 3-dimensional reconstructions of cellular morphology. STEPS not only provides support for reactions between soluble ligands, but also for membrane-bound reactions and transmembrane fluxes, making it a very general simulation tool.

STEPS is particularly useful in the field of neuroscience. Relevant spatial features of neuronal morphology start well below the sub-micron scale for spines and organelles, but can span up to several hundreds of microns for the entire dendritic tree. To allow simulation of models that exhibit such a wide range of spatial detail, STEPS uses unstructured meshes to discretize space. These meshes adapt the spatial resolution of the simulation to the local level of detail, meaning that small voxels are used in areas with fine features, whereas larger voxels are used elsewhere. STEPS also provides solvers for simulating a reaction system in the absence of spatial detail and diffusion.

Every step in the cycle of designing and simulating models in STEPS is controllable from within the Python scripting language. This includes specifying the reaction rules and diffusion constants, defining the cellular morphology and generating a mesh, running a simulation, manipulating its internal state and generating output. The computational routines however are still written in C++, eliminating any overhead that might result from scripting.

Download at Sourceforge.


Review

review : Review of single neuron simulation software.

overview : Overview of neural simulation software.


Nodus software

Nodus (copyright E. De Schutter) is a user-friendly software package for simulation of neurons and small networks on Apple Macintosh computers.

Note: on OSX Nodus will only work in Classic mode.

Information : Information on Nodus.

System : Nodus system requirements.

Publications : Nodus related publications.

Obtain Nodus : The Nodus software is freely available for downloading

More questions or suggestions about Nodus? E-mail me at Erikattnb.ua.ac.be


GENESIS software

GENESIS is used to simulate large neuronal models and realistic neural networks on unix and parallel platforms. GENESIS was originally developed by Matt Wilson at the California Institute of Technology. GENESIS 2.0 was the result of an intensive collaboration between multiple centers, including the Theoretical Neurobiology unit at the University of Antwerp.

GENESIS : Information on GENESIS.


Other popular packages

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