//genesis
//mglu-ip3-kkit.txt

//need to be in kinetikit script directory; Fabulous tutorial accessed by clicking "help"
cd genesis/Scripts/kinetikit
genesis Kinetikit

/* Same reactions implemented in Chemesis
 * Parameters are from param.g

 Glu-mGLuR + G <-> G-Glu-mGluR -> aG + Glu-mGluR (uses Vmax2 Km2)
 aG + PLC <-> aPLC-aG (uses G2)
 aPLC + PIP2 <-> aPLC-PIP2 -> aPLC +IP3+ DAG (uses Vmax1 Km1)
 */

/* Create pools of molecules.  One element is required for each molecule.
No difference in creating conserve pools or reaction pools */

/*To make kpool creation easier, click on Units, then set default diameter=12.8
However, if you want to run it faster, set default diameter =1.28, and then you
can use a dt of 1e-5 */

click and drag kpool
CoInit=0, color=14, name=Glu_mGluR, Diam=12.8 uM

click and drag kpool
CoInit=25, color=26, name=Gtot, Diam=12.8 uM

click and drag kpool
CoInit=5, color=62, name=PLCtot, Diam=12.8 uM

click and drag kpool
CoInit=160, color=4, name=PIP2tot, Diam=12.8 uM

click and drag kpool
CoInit=0.0007, color=27, name=aG, Diam=12.8 uM

click and drag kpool
CoInit=0.0035, color=46, name=aPLC_aG, Diam=12.8 uM

click and drag kpool
CoInit=0.1, color=3, name=IP3, Diam=12.8 uM

/*To set up the conserve pools as such, place mouse over other pools, and 
drag to the conserve pools.  But don't do this in this simulation.
1. Click aG, drag to Gtot
2. Click aPLC_aG, drag to Gtot
3. Click aPLC_aG, drag to PLCtot
4. Click IP3, drag to PIP2tot
*/

/* Now create the reactions that will increase or decrease various molecules*/
/*First, enzyme reaction */

Click and drag kenz onto Glu_mGluR
Vmax=1.8, Km=0.6, name=GGlu_mGLuR
drag from Gtot to GGlu_mGLuR (substrate)
drag from GGlu_mGluR to aG (product)

/* Next, create bimolecular reaction */
click and drag kreac
kf=100, kb=100, name=PLC_rxn

drag aG to PLC_rxn (substrate)
drag PLCtot to PLC_rxn (substrate)
drag PLC_rxn to aPLC_aG (product)

/* Then, create second enzyme reaction */
Click and drag kenz to aPLC_aG
k1=0.83, k2=0.1, k3=0.58, name=pip2ip3

drag PIP2tot to pip2ip3 (substrate)
drag pip2ip3 to IP3 (product)

/* Blue arrows indicate conserved reactions
 * Red arrows indicate enzyme reactions
 * green arrows indicate bimolecular reactions
 * try to move around your pools to minimize arrow crossing */

Now, need to plot some values

drag aG to Concs1 graph
drag aPLC_aG to Concs1 graph
drag IP3 to concs2 graph
drag Gtot to concs2 graph
drag PLCtot to concs2 graph

Click Options, set clock dt for simultion =1e-8
set clock dt for plots = 1e-6
click options again to hide

set runtime=0.1
reset
start
set CoComplex=0 (of GG_mGLuR)
start
Runtime = 0.9
Start

// To verify your reactions
ce kinetics
le
showfield Gtot, Ga
showmsg PIP2tot, IP3

!!!!!!!!!!!!Warning!!!!!!!!!!!
The above didn't work for me. I.e., I don't get the same values as XPP and Chemesis