Commit 7d7683b5 authored by Urban BEZELJAK's avatar Urban BEZELJAK

Update README.md

parent 61cbf468
......@@ -10,6 +10,7 @@ The basic model was implemented with [Smoldyn](http://www.smoldyn.org/) stochast
* 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**
To install Smoldyn:
1. Download pre-compiled install package from the [website](http://www.smoldyn.org/download.html).
2. Extract the zip file to the desired location.
......@@ -21,6 +22,9 @@ To run Smoldyn:
1. Navigate Command prompt to Smoldyn instalation folder (e.g. \Program Files\Smoldyn)
2. run with `smoldyn "model_filepath.txt"`
By far the best resource is the Smoldyn User Manual and Examples, which are included in the installation zip folder.
## Model
The basic model includes the following reactions:
......@@ -35,3 +39,19 @@ reaction rxn_4_1 Rab5GTP(front) + RR(fsoln) <-> Rab5GTP:RR(front) k_5 k_6
reaction rxn_4_2 Rab5GTP(front) + RR(front) <-> Rab5GTP:RR(front) k_5 k_6
reaction rxn_5_2 Rab5GTP:RR(front) + Rab5GDP(front) -> Rab5GTP:RR(front) + Rab5GTP(front) k_7
```
Smoldyn uses parameters in micrometer and second units, which have to be recalculated from the estimated values according to the User Manual.
| Parameter | Estimated value | Smoldyn value |
| ------------- |:-------------:| -----:|
| k1 | 0.01 s-1 | 0.01 s-1 |
| k2 | 40000 M-1 s-1 | 0.00007 um3 s-1 |
| k3 | 5.00E-04 s-1 | 5.00E-04 s-1 |
| k4 | 2000 M-1 s-1 | 0.000003 um3 s-1 |
| k5 | 20000 M-1 s-1| 0.00003 um3 s-1 |
| k6 | 0.1 s-1 | 0.1 s-1 |
| k7 | 6000000 M-1 s-1 | 0.01 um3 s-1 |
| k8 | 8.00E+04 M-1 s-1 | 0.00015 um3 s-1 |
| k_rab | / | 10 um s-1 |
| k_rr_on | / | 0.01 um s-1 |
| k_rr_off | / | 1 s-1 |
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