Commit 0406c9b8 authored by Urban BEZELJAK's avatar Urban BEZELJAK


parent 7d7683b5
......@@ -9,16 +9,16 @@ The basic model was implemented with [Smoldyn]( stochast
[Smoldyn]( is a particle based stochastic simulator, which alows detailed spatial simulations of reaction-diffusion systems. Smoldyn was created by Steve Andrews (Seattle University). You can find out more in:
* Andrews, S.S., Addy, N.J., Brent, R., and Arkin, A.P. (2010). Detailed simulations of cell biology with Smoldyn 2.1. PLoS Comput. Biol. 6, e1000705.
**Instalation and running models**
### Instalation and running models
To install Smoldyn:
**To install Smoldyn:**
1. Download pre-compiled install package from the [website](
2. Extract the zip file to the desired location.
3. Open “Command Prompt” as administrator.
4. Change directories to the newly extracted Smoldyn directory (e.g. type `cd C:\Users\username\Downloads\smoldyn-2.xx-windows)`.
5. Type “install”. This copies all of the Smoldyn executable files to a Smoldyn subdirectory inside your “C:\Program Files” directory.
To run Smoldyn:
**To run Smoldyn:**
1. Navigate Command prompt to Smoldyn instalation folder (e.g. \Program Files\Smoldyn)
2. run with `smoldyn "model_filepath.txt"`
......@@ -55,3 +55,7 @@ Smoldyn uses parameters in micrometer and second units, which have to be recalcu
| k_rab | / | 10 um s-1 |
| k_rr_on | / | 0.01 um s-1 |
| k_rr_off | / | 1 s-1 |
### Model configuration files
### Python script for parameter scans
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