From 566e6046ff34d438a765a733e38fbae138755f48 Mon Sep 17 00:00:00 2001
From: Rui Ribeiro <rui.ribeiro@icloud.com>
Date: Wed, 9 Mar 2022 18:16:25 +0100
Subject: [PATCH] pre-release
---
SI/Gi_parameters.csv | 68 +++++++++++
SI/Gi_pathway_parameters.md | 39 -------
...athway_parameters.csv => Gi_reactions.csv} | 42 +++----
SI/Gq_parameters.csv | 40 +++++++
SI/Gq_reactions.csv | 2 +
SI/Gs_parameters.csv | 106 +++++++++++-------
SI/Gs_reactions.csv | 38 +++++++
src/lib/pathways/Gi_parameters.csv | 40 +++----
src/lib/pathways/Gi_reactions.csv | 40 +++----
src/lib/pathways/Gs_parameters.csv | 40 +++----
src/lib/pathways/Gs_reactions.csv | 42 +++----
11 files changed, 318 insertions(+), 179 deletions(-)
create mode 100644 SI/Gi_parameters.csv
delete mode 100644 SI/Gi_pathway_parameters.md
rename SI/{Gi_pathway_parameters.csv => Gi_reactions.csv} (63%)
create mode 100644 SI/Gq_parameters.csv
create mode 100644 SI/Gq_reactions.csv
create mode 100644 SI/Gs_reactions.csv
diff --git a/SI/Gi_parameters.csv b/SI/Gi_parameters.csv
new file mode 100644
index 0000000..c0602dd
--- /dev/null
+++ b/SI/Gi_parameters.csv
@@ -0,0 +1,68 @@
+Parameter,Value,Unit
+time_in,0,s
+time_out,0,s
+L_init,0.01,uM
+R_init,2,uM
+Gi_init,3,uM
+AC5_init,0.7,uM
+Ca_cytos_free,0.06,uM
+ATP_init,5000,uM
+PDE4_init,2,uM
+PDE10_init,1,uM
+PKA_init,1.2,uM
+RL_kon,100.0,uM-1*s-1
+RL_koff,200,s-1
+RL_Gi_kon,6600.0,uM-1*s-1
+RL_Gi_koff,200,s-1
+RL_Gi_decay,60,s-1
+GaiGTP_decay,30,s-1
+Gi_formation,100,s-1
+AC5_ATP_kon,0.1,uM-1*s-1
+AC5_ATP_koff,1,s-1
+AC5_basal,1,uM-1*s-1
+AC5_reverse_basal,0.0004,
+AC5_Ca_kon,1.0,uM-1*s-1
+AC5_Ca_koff,0.9,s-1
+AC5_Ca_ATP_kon,0.075,uM-1*s-1
+AC5_Ca_ATP_koff,1,s-1
+AC5_Ca_ATP_to_cAMP,0.5,uM-1*s-1
+AC5_Ca_ATP_to_cAMP_reverse,0.00015,
+AC5_ATP_Ca_kon,1.0,uM-1*s-1
+AC5_ATP_Ca_koff,0.9,s-1
+AC5_GaiGTP_kon,50000,uM-1*s-1
+AC5_GaiGTP_koff,5,s-1
+AC5_GaiGTP_ATP_kon,0.0625,uM-1*s-1
+AC5_GaiGTP_ATP_koff,1,s-1
+AC5_ATP_GaiGTP_kon,50000,uM-1*s-1
+AC5_ATP_GaiGTP_koff,5,s-1
+AC5_GaiGTP_ATP_to_cAMP,0.25,uM-1*s-1
+AC5_GaiGTP_ATP_to_cAMP_reverse,0.00105,
+AC5_GaiGTP_decay,30,s-1
+AC5_GaiGTP_decay_koff,30,s-1
+AC5_Ca_GaiGTP_kon,50000,uM-1*s-1
+AC5_Ca_GaiGTP_koff,5,s-1
+AC5_Ca_GaiGTP_ATP_kon,0.0563,uM-1*s-1
+AC5_Ca_GaiGTP_ATP_koff,1,s-1
+AC5_Ca_ATP_GaiGTP_kon,50000,uM-1*s-1
+AC5_Ca_ATP_GaiGTP_koff,5,s-1
+AC5_Ca_GaiGTP_ATP_to_cAMP,0.125,uM-1*s-1
+AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,2.81E-5,s-1
+AC5_Ca_GaiGTP_decay,30,s-1
+AC5_Ca_GaiGTP_ATP_decay,30,s-1
+PDE4_cAMP_kon,10.0,uM-1*s-1
+PDE4_cAMP_koff,1,s-1
+PDE4_cAMP_to_AMP,2,s-1
+PDE10_2cAMP_kon,0.001,uM-1*s-1
+PDE10_2cAMP_koff,9,s-1
+PDE10_cAMP_kon,100.0,uM-1*s-1
+PDE10_cAMP_koff,2,s-1
+PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1
+PDE10_2cAMP_cAMP_koff,2,s-1
+PDE10_cAMP_decay,3,s-1
+PDE10_2cAMP_cAMP_decay,10,s-1
+PKA_cAMP2_kon,0.26,uM-1*s-1
+PKA_cAMP2_koff,1,s-1
+PKA_cAMP4_kon,0.346,uM-1*s-1
+PKA_cAMP4_koff,1,s-1
+PKA_activation,10000.0,uM-1*s-1
+PKA_activation_reverse,0.025,s-1
diff --git a/SI/Gi_pathway_parameters.md b/SI/Gi_pathway_parameters.md
deleted file mode 100644
index 4f213af..0000000
--- a/SI/Gi_pathway_parameters.md
+++ /dev/null
@@ -1,39 +0,0 @@
-| Reaction number | Reaction | Foward parameters names | Reverse parameters names | Foward default values (1/(nM*s)) | Reverse default values (1/s) |
-|:---------------:|:------------------------------------------:|:------------------------:|:---------------------------------:|:--------------------------------:|:----------------------------:|
-| 1 | DA + D2R <-> D2RDA | RL_kon | RL_koff | 0.1 | 200 |
-| 3 | D2RDA + Gi <-> D2RDAGi | RL_Gi_kon | RL_Gi_koff | 6.6 | 200 |
-| 9 | D2RDAGi -> GaiGTP + D2RDA + Gbgi | | RL_Gi_decay | | 60 |
-| 13 | GaolfGTP -> GaolfGDP | | GaiGTP_decay | | 30 |
-| 14 | GaolfGDP + Gbgolf -> Golf | | Gi_formation | | 100 |
-| 16 | AC5 + Ca <-> AC5Ca | AC5_Ca_kon | AC5_Ca_koff | 0.001 | 0.9 |
-| 21 | AC5 + ATP <-> [AC5*ATP] | AC5_ATP_kon | AC5_ATP_koff | 0.0001 | 1 |
-| 22 | [AC5*ATP] -> cAMP + AC5 | | AC5_basal | | 1 |
-| 23 | cAMP + AC5 -> [AC5*ATP] | | AC5_reverse_basal | | 0.0004 |
-| 24 | AC5Ca + ATP <-> [AC5Ca*ATP] | AC5_Ca_ATP_kon | AC5_Ca_ATP_koff | 7.50E-05 | 1 |
-| 25 | [AC5Ca*ATP] -> cAMP + AC5Ca | | AC5_Ca_ATP_to_cAMP | | 0.5 |
-| 26 | cAMP + AC5Ca -> [AC5Ca*ATP] | | AC5_Ca_ATP_to_cAMP_reverse | | 0.00015 |
-| 30 | Ca + [AC5*ATP] <-> [AC5Ca*ATP] | AC5_ATP_Ca_kon | AC5_ATP_Ca_koff | 0.001 | 0.9 |
-| 37 | GaiGTP + AC5 <-> AC5GaiGTP | AC5_GaiGTP_kon | AC5_GaiGTP_koff | 50 | 5 |
-| 38 | ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP] | AC5_GaiGTP_ATP_kon | AC5_GaiGTP_ATP_koff | 6.25E-05 | 1 |
-| 39 | [AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP] | AC5_ATP_GaiGTP_kon | AC5_ATP_GaiGTP_koff | 50 | 5 |
-| 40 | [AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP | | AC5_GaiGTP_ATP_to_cAMP | | 0.25 |
-| 41 | cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP] | | AC5_GaiGTP_ATP_to_cAMP_reverse | | 0.00105 |
-| 42 | AC5GaiGTP -> AC5 + GaiGDP | | AC5_GaiGTP_decay | | 30 |
-| 43 | [AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP | | AC5_GaiGTP_decay_koff | | 30 |
-| 55 | GaiGTP + AC5Ca <-> AC5CaGaiGTP | AC5_Ca_GaiGTP_kon | AC5_Ca_GaiGTP_koff | 50 | 5 |
-| 56 | AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP] | AC5_Ca_GaiGTP_ATP_kon | AC5_Ca_GaiGTP_ATP_koff | 5.63E-05 | 1 |
-| 57 | [AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP] | AC5_Ca_ATP_GaiGTP_kon | AC5_Ca_ATP_GaiGTP_koff | 50 | 5 |
-| 58 | [AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP | | AC5_Ca_GaiGTP_ATP_to_cAMP | | 0.125 |
-| 59 | cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP] | | AC5_Ca_GaiGTP_ATP_to_cAMP_reverse | | 2.81E-05 |
-| 60 | AC5CaGaiGTP -> AC5Ca + GaiGDP | | AC5_Ca_GaiGTP_decay | | 30 |
-| 61 | [AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP | | AC5_Ca_GaiGTP_ATP_decay | | 30 |
-| 73 | cAMP + PDE4 <-> [PDE4*cAMP] | PDE104_cAMP_kon | PDE4_cAMP_koff | 0.01 | 1 |
-| 74 | PDE10 + 2 cAMP <-> PDE10c | PDE10_2cAMP_kon | PDE10_2cAMP_koff | 1.00E-06 | 9 |
-| 75 | [PDE4*cAMP] -> PDE4 + AMP | | PDE4_cAMP_to_AMP | | 2 |
-| 76 | cAMP + PDE10 <-> [PDE10*cAMP] | PDE10_cAMP_kon | PDE10_cAMP_koff | 0.1 | 2 |
-| 77 | cAMP + PDE10c <-> [PDE10c*cAMP] | PDE10_2cAMP_cAMP_kon | PDE10_2cAMP_cAMP_koff | 0.13 | 2 |
-| 78 | [PDE10*cAMP] -> PDE10 + AMP | | PDE10_cAMP_decay | | 3 |
-| 79 | [PDE10c*cAMP] -> PDE10c + AMP | | PDE10_2cAMP_cAMP_decay | | 10 |
-| 80 | cAMP + PKA <-> PKAcAMP2 | PKA_cAMP2_kon | PKA_cAMP2_koff | 0.00026 | 1 |
-| 81 | cAMP + PKAcAMP2 <-> PKAcAMP4 | PKA_cAMP4_kon | PKA_cAMP4_koff | 0.000346 | 1 |
-| 82 | PKAcAMP4 <-> PKAc + PKAreg | PKA_activation | PKA_activation_reverse | 10 | 0.025 |
diff --git a/SI/Gi_pathway_parameters.csv b/SI/Gi_reactions.csv
similarity index 63%
rename from SI/Gi_pathway_parameters.csv
rename to SI/Gi_reactions.csv
index 373b031..4e04782 100644
--- a/SI/Gi_pathway_parameters.csv
+++ b/SI/Gi_reactions.csv
@@ -1,38 +1,38 @@
-Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(nM*s)),Reverse default values (1/s)
-1,DA + D2R <-> D2RDA,RL_kon,RL_koff,0.1,200
-3,D2RDA + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6.6,200
-9,D2RDAGi -> GaiGTP + D2RDA + Gbgi,,RL_Gi_decay,,60
+Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(uM*s)),Reverse default values (1/s)
+1,L + R <-> LR,RL_kon,RL_koff,100.0,200
+3,LR + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6600.0,200
+9,LRGi -> GaiGTP + LR + Gbgi,,RL_Gi_decay,,60
13,GaolfGTP -> GaolfGDP,,GaiGTP_decay,,30
14,GaolfGDP + Gbgolf -> Golf,,Gi_formation,,100
-16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,0.001,0.9
-21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1
+16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,1.0,0.9
+21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1
22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1
23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004
-24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1
+24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1
25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5
26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015
-30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9
-37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,50,5
-38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,6.25E-05,1
-39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50,5
+30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9
+37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,5000,5
+38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,0.0625,1
+39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50000,5
40,[AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP,,AC5_GaiGTP_ATP_to_cAMP,,0.25
41,cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP],,AC5_GaiGTP_ATP_to_cAMP_reverse,,0.00105
42,AC5GaiGTP -> AC5 + GaiGDP,,AC5_GaiGTP_decay,,30
43,[AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP,,AC5_GaiGTP_decay_koff,,30
-55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50,5
-56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,5.63E-05,1
-57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50,5
+55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50000,5
+56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,0.0563,1
+57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50000,5
58,[AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP,,AC5_Ca_GaiGTP_ATP_to_cAMP,,0.125
59,cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP],,AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,,2.81E-05
60,AC5CaGaiGTP -> AC5Ca + GaiGDP,,AC5_Ca_GaiGTP_decay,,30
61,[AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP,,AC5_Ca_GaiGTP_ATP_decay,,30
-73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,0.01,1
-74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9
+73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,10.0,1
+74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9
75,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2
-76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2
-77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2
+76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2
+77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2
78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3
79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10
-80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1
-81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1
-82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.025
+80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1
+81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1
+82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.025
diff --git a/SI/Gq_parameters.csv b/SI/Gq_parameters.csv
new file mode 100644
index 0000000..8f1b5a1
--- /dev/null
+++ b/SI/Gq_parameters.csv
@@ -0,0 +1,40 @@
+Parameter,Value,Unit
+time_in,0,s
+time_out,0,s
+Gq_a_GDP_init:0.0027739,uM
+Gq_a_GDP_init:6.4172E-4,uM
+Gq_bg_init:0.0037173,uM
+RGS4_init:0.019994,uM
+RGS4_Gq_a_GTP_init:6.4168E-6,uM
+Ca_init:0.1,uM
+PLCb_init:0.090022,uM
+PLCb_Gq_a_GTP_init:1.4492E-4,uM
+PLCb_Ca_init:0.0093825,uM
+PLCb_Ca_Gq_a_GTP_init:1.5038E-4,uM
+PIP2_init:2.6578,uM
+IP3_init:0.21952,uM
+DAG_init:0.055555,uM
+R_Gq_trimer_init:0,uM
+R_L_Gq_trimer_init:0,uM
+Gq_trimer_init:0.61869,uM
+RL_kon:1.00,uM-1*s-1
+RL_koff:0.0046,s-1
+Gqa_Gqbg_kon:6.0,uM-1*s-1
+Gqa_Gqbg_koff:0.0001,s-1
+RL_Gq_decay:0.04,s-1
+RGS4_Gq_a_GTP_kon:20.83,uM-1*s-1
+RGS4_Gq_a_GTP_koff:33.32,s-1
+RGS4_Gq_a_GTP_decay:8.33,s-1
+Gq_a_GTP_decay:0.01,s-1
+Gq_a_GTP_PLCb_kon:2.52,uM-1*s-1
+Gq_a_GTP_PLCb_off:1.00,s-1
+Gq_a_GTP_PLCb_Ca_kon:30.0,uM-1*s-1
+Gq_a_GTP_PLCb_Ca_koff:1.00,s-1
+Gq_a_GTP_PLCb_Ca_decay:0.013,s-1
+PLCb_Ca_kon:3.00,uM-1*s-1
+PLCb_Ca_koff:1.00,s-1
+PLCb_Ca_Gq_a_GTP_kon:25.2,uM-1*s-1
+PLCb_Ca_Gq_a_GTP_koff:1.00,s-1
+DAG_decay:0.15,s-1
+
+
diff --git a/SI/Gq_reactions.csv b/SI/Gq_reactions.csv
new file mode 100644
index 0000000..0f6d4a7
--- /dev/null
+++ b/SI/Gq_reactions.csv
@@ -0,0 +1,2 @@
+Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(nM*s)),Reverse default (1/s)
+
diff --git a/SI/Gs_parameters.csv b/SI/Gs_parameters.csv
index fb28a2f..9606930 100644
--- a/SI/Gs_parameters.csv
+++ b/SI/Gs_parameters.csv
@@ -1,38 +1,68 @@
-Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(nM*s)), Reverse default (1/s)
-1,D1R + DA <-> D1RDA,RL_kon,RL_koff,0.005,5
-3,D1RDA + Golf <-> D1RDAGolf,RL_Golf_kon,RL_Golf_koff,0.003,5
-9,D1RDAGolf -> Gbgolf + D1RDA + GaolfGTP,,RL_Golf_decay,,15
-10,GaolfGTP -> GaolfGDP,,GaolfGTP_decay,,30
-11,GaolfGDP + Gbgolf -> Golf,,Golf_formation,,100
-15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,0.2,0.1
-16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,0.001,0.9
-17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,0.2,0.1
-18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,0.00105,1
-19,[AC5GaolfGTP*ATP] -> cAMP + AC5GaolfGTP,,cAMP_formation,,20
-20,cAMP + AC5GaolfGTP -> [AC5GaolfGTP*ATP],,cAMP_reverse,,0.084
-21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1
-22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1
-23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004
-24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1
-25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5
-26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015
-27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_koff,AC5_GaolfGTP_ATP_a_koff,0.2,0.1
-28,AC5GaolfGTP -> AC5 + GaolfGDP,,AC5_GaolfGTP_decay,,0.2
-29,[AC5GaolfGTP*ATP] -> [AC5*ATP] + GaolfGDP,,AC5_GaolfGTP_ATP_decay,,0.2
-30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9
-31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.00055,1
-32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,0.2,0.1
-33,[AC5CaGaolfGTP*ATP] -> cAMP + AC5CaGaolfGTP,,AC5_Ca_GaolfGTP_ATP_to_cAMP,,10
-34,cAMP + AC5CaGaolfGTP -> [AC5CaGaolfGTP*ATP],,AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,,0.022
-35,AC5CaGaolfGTP -> AC5Ca + GaolfGDP,,AC5_Ca_GaolfGTP_decay,,0.2
-36,[AC5CaGaolfGTP*ATP] -> [AC5Ca*ATP] + GaolfGDP,,AC5_Ca_GaolfGTP_ATP_decay,,0.2
-73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,0.01,1
-74,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2
-75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9
-76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2
-77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2
-78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3
-79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10
-80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1
-81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1
-82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.01
+Parameter,Value,Unit
+time_in,0,s
+time_out,0,s
+L_init,0.01,uM
+R_init,2,uM
+Golf_init,2,uM
+AC5_init,0.7,uM
+Ca_init,0.06,uM
+ATP_init,5000,uM
+PDE4_init,2,uM
+PDE10_init,0.7,uM
+PKA_init,1.2,uM
+RL_kon,5.0,uM-1*s-1
+RL_koff,5,s-1
+RL_Golf_kon,3.0,uM-1*s-1
+RL_Golf_koff,5.0,s-1
+RL_Golf_decay,15,s-1
+GaolfGTP_decay,30,s-1
+Golf_formation,100,s-1
+AC5_ATP_kon,0.1,uM-1*s-1
+AC5_ATP_koff,1,uM-1*s-1
+AC5_basal,1,s-1
+AC5_reverse_basal,0.0004,s-1
+AC5_Ca_kon,1.0,uM-1*s-1
+AC5_Ca_koff,0.9,s-1
+AC5_Ca_ATP_kon,0.075,uM-1*s-1
+AC5_Ca_ATP_koff,1,s-1
+AC5_Ca_ATP_to_cAMP,0.5,s-1
+AC5_Ca_ATP_to_cAMP_reverse,0.00015,s-1
+AC5_ATP_Ca_kon,1.0,uM-1*s-1
+AC5_ATP_Ca_koff,0.9,
+AC5_GaolfGTP_kon,200.0,uM-1*s-1
+AC5_GaolfGTP_koff,0.1,
+AC5_GaolfGTP_ATP_i_kon,1.05,uM-1*s-1
+AC5_GaolfGTP_ATP_i_koff,1,
+cAMP_formation,20,s-1
+cAMP_reverse,0.084,s-1
+AC5_GaolfGTP_ATP_a_kon,200.0,uM-1*s-1
+AC5_GaolfGTP_ATP_a_koff,0.1,
+AC5_GaolfGTP_decay,0.2,s-1
+AC5_GaolfGTP_ATP_decay,0.2,s-1
+AC5_Ca_GaolfGTP_kon,200.0,uM-1*s-1
+AC5_Ca_GaolfGTP_koff,0.1,s-1
+AC5_Ca_GaolfGTP_ATP_kon,0.55,uM-1*s-1
+AC5_Ca_GaolfGTP_ATP_koff,1,s-1
+AC5_CA_ATP_GaolfGTP_kon,200.0,uM-1*s-1
+AC5_CA_ATP_GaolfGTP_koff,0.1,s-1
+AC5_Ca_GaolfGTP_ATP_to_cAMP,10,s-1
+AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,0.022,s-1
+AC5_Ca_GaolfGTP_decay,0.2,s-1
+AC5_Ca_GaolfGTP_ATP_decay,0.2,s-1
+PDE4_cAMP_kon,10.0,uM-1*s-1
+PDE4_cAMP_koff,1,s-1
+PDE4_cAMP_to_AMP,2,s-1
+PDE10_2cAMP_kon,0.001,uM-1*s-1
+PDE10_2cAMP_koff,9,s-1
+PDE10_cAMP_kon,100.0,uM-1*s-1
+PDE10_cAMP_koff,2,s-1
+PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1
+PDE10_2cAMP_cAMP_koff,2,s-1
+PDE10_cAMP_decay,3,s-1
+PDE10_2cAMP_cAMP_decay,10,s-1
+PKA_cAMP2_kon,0.25999999999999995,uM-1*s-1
+PKA_cAMP2_koff,1,s-1
+PKA_cAMP4_kon,0.34600000000000003,uM-1*s-1
+PKA_cAMP4_koff,1,s-1
+PKA_activation,10000.0,uM-1*s-1
+PKA_activation_reverse,0.01,s-1
diff --git a/SI/Gs_reactions.csv b/SI/Gs_reactions.csv
new file mode 100644
index 0000000..af9bc90
--- /dev/null
+++ b/SI/Gs_reactions.csv
@@ -0,0 +1,38 @@
+Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(uM*s)),Reverse default (1/s)
+1,R + L <-> RL,RL_kon,RL_koff,5.0,5
+3,RL + Golf <-> RLGolf,RL_Golf_kon,RL_Golf_koff,3.0,5
+9,RLGolf -> Gbgolf + RL + GaolfGTP,,RL_Golf_decay,,15
+10,GaolfGTP -> GaolfGDP,,GaolfGTP_decay,,30
+11,GaolfGDP + Gbgolf -> Golf,,Golf_formation,,100
+15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,200.0,0.1
+16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,1.0,0.9
+17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,200.0,0.1
+18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,1.05,1
+19,[AC5GaolfGTP*ATP] -> cAMP + AC5GaolfGTP,,cAMP_formation,,20
+20,cAMP + AC5GaolfGTP -> [AC5GaolfGTP*ATP],,cAMP_reverse,,0.084
+21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1
+22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1
+23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004
+24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1
+25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5
+26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015
+27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_kon,AC5_GaolfGTP_ATP_a_koff,200.0,0.1
+28,AC5GaolfGTP -> AC5 + GaolfGDP,,AC5_GaolfGTP_decay,,0.2
+29,[AC5GaolfGTP*ATP] -> [AC5*ATP] + GaolfGDP,,AC5_GaolfGTP_ATP_decay,,0.2
+30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9
+31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.55,1
+32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,200.0,0.1
+33,[AC5CaGaolfGTP*ATP] -> cAMP + AC5CaGaolfGTP,,AC5_Ca_GaolfGTP_ATP_to_cAMP,,10
+34,cAMP + AC5CaGaolfGTP -> [AC5CaGaolfGTP*ATP],,AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,,0.022
+35,AC5CaGaolfGTP -> AC5Ca + GaolfGDP,,AC5_Ca_GaolfGTP_decay,,0.2
+36,[AC5CaGaolfGTP*ATP] -> [AC5Ca*ATP] + GaolfGDP,,AC5_Ca_GaolfGTP_ATP_decay,,0.2
+73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,10.0,1
+74,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2
+75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9
+76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2
+77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2
+78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3
+79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10
+80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1
+81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1
+82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.01
diff --git a/src/lib/pathways/Gi_parameters.csv b/src/lib/pathways/Gi_parameters.csv
index fac775f..c0602dd 100644
--- a/src/lib/pathways/Gi_parameters.csv
+++ b/src/lib/pathways/Gi_parameters.csv
@@ -10,59 +10,59 @@ ATP_init,5000,uM
PDE4_init,2,uM
PDE10_init,1,uM
PKA_init,1.2,uM
-RL_kon,0.1*1E3,uM-1*s-1
+RL_kon,100.0,uM-1*s-1
RL_koff,200,s-1
-RL_Gi_kon,6.6*1E3,uM-1*s-1
+RL_Gi_kon,6600.0,uM-1*s-1
RL_Gi_koff,200,s-1
RL_Gi_decay,60,s-1
GaiGTP_decay,30,s-1
Gi_formation,100,s-1
-AC5_ATP_kon,0.0001*1E3,uM-1*s-1
+AC5_ATP_kon,0.1,uM-1*s-1
AC5_ATP_koff,1,s-1
AC5_basal,1,uM-1*s-1
AC5_reverse_basal,0.0004,
-AC5_Ca_kon,0.001*1E3,uM-1*s-1
+AC5_Ca_kon,1.0,uM-1*s-1
AC5_Ca_koff,0.9,s-1
-AC5_Ca_ATP_kon,7.50E-5*1E3,uM-1*s-1
+AC5_Ca_ATP_kon,0.075,uM-1*s-1
AC5_Ca_ATP_koff,1,s-1
AC5_Ca_ATP_to_cAMP,0.5,uM-1*s-1
AC5_Ca_ATP_to_cAMP_reverse,0.00015,
-AC5_ATP_Ca_kon,0.001*1E3,uM-1*s-1
+AC5_ATP_Ca_kon,1.0,uM-1*s-1
AC5_ATP_Ca_koff,0.9,s-1
-AC5_GaiGTP_kon,50*1E3,uM-1*s-1
+AC5_GaiGTP_kon,50000,uM-1*s-1
AC5_GaiGTP_koff,5,s-1
-AC5_GaiGTP_ATP_kon,6.25E-5*1E3,uM-1*s-1
+AC5_GaiGTP_ATP_kon,0.0625,uM-1*s-1
AC5_GaiGTP_ATP_koff,1,s-1
-AC5_ATP_GaiGTP_kon,50*1E3,uM-1*s-1
+AC5_ATP_GaiGTP_kon,50000,uM-1*s-1
AC5_ATP_GaiGTP_koff,5,s-1
AC5_GaiGTP_ATP_to_cAMP,0.25,uM-1*s-1
AC5_GaiGTP_ATP_to_cAMP_reverse,0.00105,
AC5_GaiGTP_decay,30,s-1
AC5_GaiGTP_decay_koff,30,s-1
-AC5_Ca_GaiGTP_kon,50*1E3,uM-1*s-1
+AC5_Ca_GaiGTP_kon,50000,uM-1*s-1
AC5_Ca_GaiGTP_koff,5,s-1
-AC5_Ca_GaiGTP_ATP_kon,5.63E-5*1E3,uM-1*s-1
+AC5_Ca_GaiGTP_ATP_kon,0.0563,uM-1*s-1
AC5_Ca_GaiGTP_ATP_koff,1,s-1
-AC5_Ca_ATP_GaiGTP_kon,50*1E3,uM-1*s-1
+AC5_Ca_ATP_GaiGTP_kon,50000,uM-1*s-1
AC5_Ca_ATP_GaiGTP_koff,5,s-1
AC5_Ca_GaiGTP_ATP_to_cAMP,0.125,uM-1*s-1
-AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,2.81E-5,
+AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,2.81E-5,s-1
AC5_Ca_GaiGTP_decay,30,s-1
AC5_Ca_GaiGTP_ATP_decay,30,s-1
-PDE4_cAMP_kon,0.01*1E3,uM-1*s-1
+PDE4_cAMP_kon,10.0,uM-1*s-1
PDE4_cAMP_koff,1,s-1
PDE4_cAMP_to_AMP,2,s-1
-PDE10_2cAMP_kon,1.0E-6*1E3,
+PDE10_2cAMP_kon,0.001,uM-1*s-1
PDE10_2cAMP_koff,9,s-1
-PDE10_cAMP_kon,0.1*1E3,
+PDE10_cAMP_kon,100.0,uM-1*s-1
PDE10_cAMP_koff,2,s-1
-PDE10_2cAMP_cAMP_kon,0.13*1E3,
+PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1
PDE10_2cAMP_cAMP_koff,2,s-1
PDE10_cAMP_decay,3,s-1
PDE10_2cAMP_cAMP_decay,10,s-1
-PKA_cAMP2_kon,0.00026*1E3,uM-1*s-1
+PKA_cAMP2_kon,0.26,uM-1*s-1
PKA_cAMP2_koff,1,s-1
-PKA_cAMP4_kon,0.000346*1E3,uM-1*s-1
+PKA_cAMP4_kon,0.346,uM-1*s-1
PKA_cAMP4_koff,1,s-1
-PKA_activation,10*1E3,uM-1*s-1
+PKA_activation,10000.0,uM-1*s-1
PKA_activation_reverse,0.025,s-1
diff --git a/src/lib/pathways/Gi_reactions.csv b/src/lib/pathways/Gi_reactions.csv
index f7e994d..4e04782 100644
--- a/src/lib/pathways/Gi_reactions.csv
+++ b/src/lib/pathways/Gi_reactions.csv
@@ -1,38 +1,38 @@
-Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(nM*s)),Reverse default values (1/s)
-1,L + R <-> LR,RL_kon,RL_koff,0.1,200
-3,LR + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6.6,200
+Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(uM*s)),Reverse default values (1/s)
+1,L + R <-> LR,RL_kon,RL_koff,100.0,200
+3,LR + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6600.0,200
9,LRGi -> GaiGTP + LR + Gbgi,,RL_Gi_decay,,60
13,GaolfGTP -> GaolfGDP,,GaiGTP_decay,,30
14,GaolfGDP + Gbgolf -> Golf,,Gi_formation,,100
-16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,0.001,0.9
-21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1
+16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,1.0,0.9
+21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1
22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1
23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004
-24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1
+24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1
25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5
26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015
-30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9
-37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,50,5
-38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,6.25E-05,1
-39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50,5
+30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9
+37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,5000,5
+38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,0.0625,1
+39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50000,5
40,[AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP,,AC5_GaiGTP_ATP_to_cAMP,,0.25
41,cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP],,AC5_GaiGTP_ATP_to_cAMP_reverse,,0.00105
42,AC5GaiGTP -> AC5 + GaiGDP,,AC5_GaiGTP_decay,,30
43,[AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP,,AC5_GaiGTP_decay_koff,,30
-55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50,5
-56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,5.63E-05,1
-57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50,5
+55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50000,5
+56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,0.0563,1
+57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50000,5
58,[AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP,,AC5_Ca_GaiGTP_ATP_to_cAMP,,0.125
59,cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP],,AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,,2.81E-05
60,AC5CaGaiGTP -> AC5Ca + GaiGDP,,AC5_Ca_GaiGTP_decay,,30
61,[AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP,,AC5_Ca_GaiGTP_ATP_decay,,30
-73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,0.01,1
-74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9
+73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,10.0,1
+74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9
75,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2
-76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2
-77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2
+76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2
+77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2
78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3
79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10
-80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1
-81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1
-82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.025
+80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1
+81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1
+82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.025
diff --git a/src/lib/pathways/Gs_parameters.csv b/src/lib/pathways/Gs_parameters.csv
index 67a6110..9606930 100644
--- a/src/lib/pathways/Gs_parameters.csv
+++ b/src/lib/pathways/Gs_parameters.csv
@@ -10,59 +10,59 @@ ATP_init,5000,uM
PDE4_init,2,uM
PDE10_init,0.7,uM
PKA_init,1.2,uM
-RL_kon,5.0,nM-1*s-1
+RL_kon,5.0,uM-1*s-1
RL_koff,5,s-1
-RL_Golf_kon,3.0,nM-1*s-1
+RL_Golf_kon,3.0,uM-1*s-1
RL_Golf_koff,5.0,s-1
RL_Golf_decay,15,s-1
GaolfGTP_decay,30,s-1
Golf_formation,100,s-1
-AC5_ATP_kon,0.1,nM-1*s-1
-AC5_ATP_koff,1,nM-1*s-1
+AC5_ATP_kon,0.1,uM-1*s-1
+AC5_ATP_koff,1,uM-1*s-1
AC5_basal,1,s-1
AC5_reverse_basal,0.0004,s-1
-AC5_Ca_kon,1.0,nM-1*s-1
+AC5_Ca_kon,1.0,uM-1*s-1
AC5_Ca_koff,0.9,s-1
-AC5_Ca_ATP_kon,0.075,nM-1*s-1
+AC5_Ca_ATP_kon,0.075,uM-1*s-1
AC5_Ca_ATP_koff,1,s-1
AC5_Ca_ATP_to_cAMP,0.5,s-1
AC5_Ca_ATP_to_cAMP_reverse,0.00015,s-1
-AC5_ATP_Ca_kon,1.0,nM-1*s-1
+AC5_ATP_Ca_kon,1.0,uM-1*s-1
AC5_ATP_Ca_koff,0.9,
-AC5_GaolfGTP_kon,200.0,nM-1*s-1
+AC5_GaolfGTP_kon,200.0,uM-1*s-1
AC5_GaolfGTP_koff,0.1,
-AC5_GaolfGTP_ATP_i_kon,1.05,nM-1*s-1
+AC5_GaolfGTP_ATP_i_kon,1.05,uM-1*s-1
AC5_GaolfGTP_ATP_i_koff,1,
cAMP_formation,20,s-1
cAMP_reverse,0.084,s-1
-AC5_GaolfGTP_ATP_a_kon,200.0,nM-1*s-1
+AC5_GaolfGTP_ATP_a_kon,200.0,uM-1*s-1
AC5_GaolfGTP_ATP_a_koff,0.1,
AC5_GaolfGTP_decay,0.2,s-1
AC5_GaolfGTP_ATP_decay,0.2,s-1
-AC5_Ca_GaolfGTP_kon,200.0,nM-1*s-1
+AC5_Ca_GaolfGTP_kon,200.0,uM-1*s-1
AC5_Ca_GaolfGTP_koff,0.1,s-1
-AC5_Ca_GaolfGTP_ATP_kon,0.55,nM-1*s-1
+AC5_Ca_GaolfGTP_ATP_kon,0.55,uM-1*s-1
AC5_Ca_GaolfGTP_ATP_koff,1,s-1
-AC5_CA_ATP_GaolfGTP_kon,200.0,nM-1*s-1
+AC5_CA_ATP_GaolfGTP_kon,200.0,uM-1*s-1
AC5_CA_ATP_GaolfGTP_koff,0.1,s-1
AC5_Ca_GaolfGTP_ATP_to_cAMP,10,s-1
AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,0.022,s-1
AC5_Ca_GaolfGTP_decay,0.2,s-1
AC5_Ca_GaolfGTP_ATP_decay,0.2,s-1
-PDE4_cAMP_kon,10.0,nM-1*s-1
+PDE4_cAMP_kon,10.0,uM-1*s-1
PDE4_cAMP_koff,1,s-1
PDE4_cAMP_to_AMP,2,s-1
-PDE10_2cAMP_kon,0.001,nM-1*s-1
+PDE10_2cAMP_kon,0.001,uM-1*s-1
PDE10_2cAMP_koff,9,s-1
-PDE10_cAMP_kon,100.0,nM-1*s-1
+PDE10_cAMP_kon,100.0,uM-1*s-1
PDE10_cAMP_koff,2,s-1
-PDE10_2cAMP_cAMP_kon,130.0,nM-1*s-1
+PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1
PDE10_2cAMP_cAMP_koff,2,s-1
PDE10_cAMP_decay,3,s-1
PDE10_2cAMP_cAMP_decay,10,s-1
-PKA_cAMP2_kon,0.25999999999999995,nM-1*s-1
+PKA_cAMP2_kon,0.25999999999999995,uM-1*s-1
PKA_cAMP2_koff,1,s-1
-PKA_cAMP4_kon,0.34600000000000003,nM-1*s-1
+PKA_cAMP4_kon,0.34600000000000003,uM-1*s-1
PKA_cAMP4_koff,1,s-1
-PKA_activation,10000.0,nM-1*s-1
+PKA_activation,10000.0,uM-1*s-1
PKA_activation_reverse,0.01,s-1
diff --git a/src/lib/pathways/Gs_reactions.csv b/src/lib/pathways/Gs_reactions.csv
index ba93913..af9bc90 100644
--- a/src/lib/pathways/Gs_reactions.csv
+++ b/src/lib/pathways/Gs_reactions.csv
@@ -1,38 +1,38 @@
-Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(nM*s)),Reverse default (1/s)
-1,D1R + DA <-> D1RDA,RL_kon,RL_koff,0.005,5
-3,D1RDA + Golf <-> D1RDAGolf,RL_Golf_kon,RL_Golf_koff,0.003,5
-9,D1RDAGolf -> Gbgolf + D1RDA + GaolfGTP,,RL_Golf_decay,,15
+Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(uM*s)),Reverse default (1/s)
+1,R + L <-> RL,RL_kon,RL_koff,5.0,5
+3,RL + Golf <-> RLGolf,RL_Golf_kon,RL_Golf_koff,3.0,5
+9,RLGolf -> Gbgolf + RL + GaolfGTP,,RL_Golf_decay,,15
10,GaolfGTP -> GaolfGDP,,GaolfGTP_decay,,30
11,GaolfGDP + Gbgolf -> Golf,,Golf_formation,,100
-15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,0.2,0.1
-16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,0.001,0.9
-17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,0.2,0.1
-18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,0.00105,1
+15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,200.0,0.1
+16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,1.0,0.9
+17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,200.0,0.1
+18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,1.05,1
19,[AC5GaolfGTP*ATP] -> cAMP + AC5GaolfGTP,,cAMP_formation,,20
20,cAMP + AC5GaolfGTP -> [AC5GaolfGTP*ATP],,cAMP_reverse,,0.084
-21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1
+21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1
22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1
23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004
-24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1
+24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1
25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5
26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015
-27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_koff,AC5_GaolfGTP_ATP_a_koff,0.2,0.1
+27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_kon,AC5_GaolfGTP_ATP_a_koff,200.0,0.1
28,AC5GaolfGTP -> AC5 + GaolfGDP,,AC5_GaolfGTP_decay,,0.2
29,[AC5GaolfGTP*ATP] -> [AC5*ATP] + GaolfGDP,,AC5_GaolfGTP_ATP_decay,,0.2
-30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9
-31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.00055,1
-32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,0.2,0.1
+30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9
+31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.55,1
+32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,200.0,0.1
33,[AC5CaGaolfGTP*ATP] -> cAMP + AC5CaGaolfGTP,,AC5_Ca_GaolfGTP_ATP_to_cAMP,,10
34,cAMP + AC5CaGaolfGTP -> [AC5CaGaolfGTP*ATP],,AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,,0.022
35,AC5CaGaolfGTP -> AC5Ca + GaolfGDP,,AC5_Ca_GaolfGTP_decay,,0.2
36,[AC5CaGaolfGTP*ATP] -> [AC5Ca*ATP] + GaolfGDP,,AC5_Ca_GaolfGTP_ATP_decay,,0.2
-73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,0.01,1
+73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,10.0,1
74,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2
-75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9
-76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2
-77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2
+75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9
+76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2
+77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2
78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3
79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10
-80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1
-81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1
-82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.01
+80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1
+81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1
+82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.01
--
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