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NeuroRD - latest version: Computationally efficient, neuronal reaction-diffusion stochastic simulator (pronounced NeurRDS). Java program which runs on any platform. The algorithm is based on Gillespie's tau-leap reaction algorithm, and the stochastic diffusion algorithm of Blackwell. It uses XML-based model specifications. README with instructions for creating models. An example to get you started will be helpful, and additional examples to explain branching if you are ambitious. More complicated simulation files are available either from modelDB or associated with specific publications
Programs (in Python and c++) used to process the output data Postprocessing

Chemesis2.4 is available for the Unix operating systems. It can be compiled on any unix OS that has GENESIS (I hope:). It's been tested on Fedora 19. The main difference between 2.4 and previous versions is the addition of unit fields to allow using SI or any other units.

To download click here. After downloading and extracting, editing the makefile for your OS, then type make. Or you can install a pre-compiled version following the directions from here. Email me if you want Chemesis2.1, which was used to run all the published Hermissenda simulations.

Computationally efficient, stochastic diffusion algorithm. C program used to generate figures in Blackwell 2006 J Neuroscience Methods. It runs under unix, and probably also under windows (no graphical interface).

To download click here. Compilation instructions are in the first line of diftest*.c. An output file is provided for verification.


Free Online Tutorials
How do I model biochemical reactions and diffusion?

What else can you do with the chemesis software?

This software was developed under the generous support of the National Institute of Mental Health under grant K21-MH01141, the National Science Foundation under grant IBN 0077509, the CRCNS program under grants R01 AA16022 and AA18066, and HFSP.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation.

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