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?
- 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 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 models. The Scripts2014 below are updated versions of the scripts linked from the article and work with Chemesis 2.4.
- Powerpoint Tutorial on Biochemical Reactions. Updated from the Brains, Mind, Media article
- Powerpoint Tutorial on Calcium. Updated from the Brains, Mind, Media article. Includes information on using standard genesis objects to model calcium
- Powerpoint Tutorial on NeuroRD. Use in conjunction with example files (with reactions implemented in NeuroRD, chemesis and xppaut) and the README above
- Scripts2014 to teach how to develop models of second messenger reactions and calcium dynamics. The second messenger reactions are implemented in XPPAUT, Kinetikit, and Chemesis; the calcium dynamics in both Chemesis and Genesis.
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