Dynafit Simulation automation
Jagan
Use Igor to run and import simulated data from Dynafit.
Particularly useful if you want to generate progress curve in Dynafit based on enzymatic reactions and use IGOR to fit the data.
Scripts reads the Dyanfit scripts and allows you change values of the Dynafit script constants on the fly, simulate it and import the data.
The simulated data can be fit and individual observed rates are extracted and plotted onto a new graph*.
*Works for exponential and linear fit!
Edit:
Let me know if you are planning to use it for publications or would like to see any improvements?
Example Script File for testing purposes:
[task]
task = simulate
data = progress
;approximation = none
[mechanism]
Hx <==> H : k-H k+H
H + HA <==> HHA : k2 k-2
Hx + HHA --> P + P + NH3 : k31
[constants]
k-H = 80
k+H = 100
k2 = 20
k-2 = 5 * k2
k31 = 100000
[concentrations]
[responses]
P = 100
[data]
directory ./IGOR_Dynadata
extension igxt
mesh from 0.005 to 1 step 0.0001
monitor Hx, H
file HA-50
equilibrate Hx = 0.01 ,dilute 1
concentration HA = .05
file HA-250
equilibrate Hx = 0.01 ,dilute 1
concentration HA = .25
file HA-5000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = .5
file HA-1000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 1
file HA-2000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 2
file HA-3000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 3
file HA-4000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 4
file HA-5000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 5
file HA-10000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 10
file HA-15000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 15
file HA-20000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 20
file HA-30000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 30
file HA-40000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 40
file HA-50000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 50
[output]
directory ./Scripts/Simulation_HA_rxn/Progress_curve
[end]
View All Releases
Particularly useful if you want to generate progress curve in Dynafit based on enzymatic reactions and use IGOR to fit the data.
Scripts reads the Dyanfit scripts and allows you change values of the Dynafit script constants on the fly, simulate it and import the data.
The simulated data can be fit and individual observed rates are extracted and plotted onto a new graph*.
*Works for exponential and linear fit!
Edit:
Let me know if you are planning to use it for publications or would like to see any improvements?
Example Script File for testing purposes:
[task]
task = simulate
data = progress
;approximation = none
[mechanism]
Hx <==> H : k-H k+H
H + HA <==> HHA : k2 k-2
Hx + HHA --> P + P + NH3 : k31
[constants]
k-H = 80
k+H = 100
k2 = 20
k-2 = 5 * k2
k31 = 100000
[concentrations]
[responses]
P = 100
[data]
directory ./IGOR_Dynadata
extension igxt
mesh from 0.005 to 1 step 0.0001
monitor Hx, H
file HA-50
equilibrate Hx = 0.01 ,dilute 1
concentration HA = .05
file HA-250
equilibrate Hx = 0.01 ,dilute 1
concentration HA = .25
file HA-5000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = .5
file HA-1000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 1
file HA-2000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 2
file HA-3000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 3
file HA-4000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 4
file HA-5000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 5
file HA-10000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 10
file HA-15000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 15
file HA-20000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 20
file HA-30000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 30
file HA-40000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 40
file HA-50000
equilibrate Hx = 0.01 ,dilute 1
concentration HA = 50
[output]
directory ./Scripts/Simulation_HA_rxn/Progress_curve
[end]
Project Details
Current Project Release
Dynafit Simulation automation IGOR.6.30.x-2.2-beta1
| Release File: | Dynafit_SCript_winV2_Loc.ipf (41.56 KB) |
| Version: | IGOR.6.30.x-2.2-beta1 |
| Version Date: | |
| Version Major: | 2 |
| Version Extra: | beta1 |
| Version Patch Level: | 2 |
| OS Compatibility: | Mac-Intel Windows |
| Release Notes: |
Fix: Dynafit location can be updated even if script file is not in folder containing Dynafit. SOP 1) Use open Dynafit script under DynafitHook menu items to open a Dynafit script file. (After compiling the procedure file) 1a) For best result make sure the script is under a subfolder in a parent folder named DyanfitX (X refers to version no) containing DynafitC executable file 2) Once the script file is loaded you can look/modify the constants displayed in a new table 3) Select appropriate options in the panel that is created (Like how to fit the imported data) and hit run 4) Panel show current graph and table prefix and counter number. 5) Each run creates a new script file, unless overwrite script file option is selected. |
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