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 get the rpm.
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.
How do I use the chemesis software?
- An explanation of how to use chemesis is in Neuroscience Databases: A Practical Guide, Ed. R. Kotter. Kluwer Academic Publishers, Norwell, MA (2002). The chapter is called Modeling the dynamics of second messenger pathways by Blackwell K.T. and Hellgren Kotaleski J. PDF file
- Tutorial (in PowerPoint) on modeling calcium dynamics and second messenger pathways. The first part presents the theory; the second part explains Chemesis, Kinetikit, and Genesis objects to implement the such models:
- Tutorial (with more words) published in Brains, Minds, Media, BMM 224
- Scripts implementing second messenger reactions and calcium dynamic models illustrated in presentation. The second messenger reactions are implemented in XPPAUT, Kinetikit, and Chemesis; the calcium dynamics are solely in Chemesis.
What else can you do with the chemesis software?
- Genesis simulation illustrating Donnan Equilibrium. This simulation uses Chemesis objects to help explain Figure 2.2 in Foundations of Cellular Neurophysiology by Johnston and Wu, MIT Press. The graphical interface allows students to explore the effects of concentration changes.
Chemesis scripts used for simulations in "Paired Turbulence and Light do not Produce a Supralinear Calcium Increase in Hermissenda." J Computational Neuroscience 2004 Jul-Aug;17(1):79-97
GENESIS scripts used for simulations in "Using potassium currents to solve signal-to-noise problems in inhibitory feedforward networks of the striatum." J Neurophysiology 2006 95: 331-41
Chemesis scripts used for simulations in "Ionic currents underlying difference in light response between type A and type B photoreceptors." J Neurophysiology 2006 95: 3060-3072
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.
12/2013 - Avrama Blackwell