Updated annotations

c/annotations.md

@@ -4,19 +4,24 @@
 
 - `time`, (input) the time variable.
 - `pace`, (input) a dimensionless pacing signal, set by the simulator.
-- `diffusion_current`, (input) a current flowing from cell to cell, set by the simulator.
 - `membrane_potential`, the membrane potential.
-- `stimulus_current`, a current injected with an electrode to pace the cell.
 - `membrane_capacitance`, the modelled cell's capacitance.
+- `membrane_current`, the current through the outer membrane, not including stimulus or gap junctions.
+- `stimulus_current`, a current injected with an electrode to pace the cell.
+- `diffusion_current`, (input) a current flowing from cell to cell, set by the simulator.
 
 - `I_CaL`, the L-type calcium current (all species and compartments combined).
 - `g_CaL`, a variable that can be scaled up and down to scale `I_CaL`.
 - `I_Kr`, the rapid delayed rectifier potassium current.
 - `g_Kr`, a variable that can be scaled up or down to scale `I_Kr`.
 
+- `Ca_i`, the bulk cytosolic calcium concentration
+- `K_o`, the external (bulk, buffer, not cleft) potassium concentration
+
 ## Model meta properties
 
-- `name`, a short model name.
+- `name`, a short model name, ideally unique.
 - `mmt_authors`, the authors of the mmt file (not the model equations).
 - `version`, a free-form version, used to distinguish between similarly named files.
 - `desc`, a description of the model, ideally with references.
+- `display_name`, a longer name with capitalisation etc. for display in figures.

c/bai-2018.mmt

@@ -117,7 +117,7 @@ Vsr = 1094 [um^3]
 Cm = 185 [pF]
     in [pF]
     desc: Cell capacitance
-    label cell_capacitance
+    label membrane_capacitance
 
 #
 # Physical constants

c/ellinwood-2017.mmt

@@ -557,7 +557,7 @@ ICaL_K = ibark * d * f * (fjn_CaL * (1 - fCa_jn) + cell.fsl_CaL * (1 - fCa_sl))
     in [A/F]
 # Permeability
 scaling = 1
-    label I_CaL_scaling
+    label g_CaL
 PCa = scaling * (1 + 0.5 * ISO) * (1 - 0.5 * AF) * 2.7e-4 [L/F/ms]
     in [L/F/ms]
 PNa = scaling * (1 + 0.5 * ISO) * (1 - 0.5 * AF) * 0.75e-8 [L/F/ms]

c/grandi-2010.mmt

@@ -442,7 +442,7 @@ use ion.K_i, ion.K_o
 use cell.fjn_CaL, cell.fsl_CaL
 ICaL = ICaL_Ca + ICaL_Na + ICaL_K
     in [A/F]
-    label ICaL
+    label I_CaL
 ICaL_Ca = ICaL_Ca_jn + ICaL_Ca_sl
     in [A/F]
 ICaL_Ca_jn = fjn_CaL * ibarca_jn * d * f * (1 - fCa_jn) * Q
@@ -459,7 +459,7 @@ ICaL_K = ibark * d * f * (fjn_CaL * (1 - fCa_jn) + cell.fsl_CaL * (1 - fCa_sl))
     in [A/F]
 # Permeability
 scale = 1
-    label gCaL
+    label g_CaL
 PCa = scale * 2.7e-4 [L/F/ms]
     in [L/F/ms]
 PNa = scale * 0.75e-8 [L/F/ms]

c/grandi-2011.mmt

@@ -246,7 +246,6 @@ dot(m) = (inf - m) / tau
     inf = 1 / (1 + exp(-(56.86 [mV] + V) / 9.03 [mV]))^2
     tau = 0.1292 [ms] * exp(-((V + 45.79 [mV]) / 15.54 [mV])^2) + 0.06487 [ms] * exp(-((V - 4.823 [mV]) / 51.12 [mV])^2)
         in [ms]
-    label ina_m
 dot(h) = (inf - h) / tau
     a = if(V >= -40 [mV], 0 [1/ms],
             0.057 [1/ms] * exp(-(V + 80 [mV]) / 6.8 [mV]))
@@ -258,7 +257,6 @@ dot(h) = (inf - h) / tau
     tau = 1 / (a + b)
         in [ms]
     inf = 1 / (1 + exp((V + 71.55 [mV]) / 7.43 [mV]))^2
-        label ina_h_inf
 dot(j) = (inf - j) / tau
     a = if(V >= -40 [mV], 0 [1/ms], (
                 (-2.5428e4 [1/mV/ms] * exp(0.2444 [1/mV] * V) - 6.948e-6 [1/mV/ms] * exp(-0.04391 [1/mV] * V))
@@ -272,7 +270,6 @@ dot(j) = (inf - j) / tau
     tau = 1 / (a + b)
         in [ms]
     inf = 1 / (1 + exp((V + 71.55 [mV]) / 7.43 [mV]))^2
-        label ina_j_inf
 
 #
 # Late sodium current
@@ -503,7 +500,7 @@ ICaL_K = ibark * d * f * (fjn_CaL * (1 - fCa_jn) + cell.fsl_CaL * (1 - fCa_sl))
     in [A/F]
 # Permeability
 scaling = 1
-    label I_CaL_scaling
+    label g_CaL
 PCa = scaling * (1 + 0.5 * ISO) * (1 - 0.5 * AF) * 2.7e-4 [L/F/ms]
     in [L/F/ms]
 PNa = scaling * (1 + 0.5 * ISO) * (1 - 0.5 * AF) * 0.75e-8 [L/F/ms]

c/iyer-2004.mmt

@@ -847,7 +847,7 @@ use extra.Cao, extra.Ko
 # Total current
 ICaL = ICa + ICaK
     in [A/F]
-    label ICaL
+    label I_CaL
 # Calcium component
 ICa = ICamax * y * O
     in [A/F]
@@ -858,7 +858,7 @@ ICaK = PKprime * O * y * VFFRT * (Ki * exp(VFRT) - Ko) / (exp(VFRT) - 1)
     in [A/F]
 # Permeability
 Pscale = 7
-    label gCaL
+    label g_CaL
 PCa = Pscale * 0.0002469 [L/F/s]
     in [L/F/s]
 PK = Pscale * 4.574e-7 [L/F/s]

c/koivumaki-2011.mmt

@@ -136,12 +136,10 @@ amplitude = 2 * -2943 [pA]
 use membrane.V
 use phys.FRT, phys.F
 dot(m) = (inf - m) / tau
-    label ina_m
     inf = 1 / (1 + exp((V + 27.12 [mV]) / -8.21 [mV]))
     tau = 0.000042 [s] * exp(-((V + 25.57 [mV]) / 28.8 [mV])^2) + 0.000024 [s]
         in [s]
 h_inf = 1 / (1 + exp((V + 63.6 [mV]) / 5.3 [mV]))
-    label ina_h12_inf
 dot(h1) = (h_inf - h1) / tau
     tau = 0.03 [s] / (1 + exp((V + 35.1 [mV]) / 3.2 [mV])) + 0.0003 [s]
         in [s]

c/ohara-2011.mmt

@@ -486,7 +486,7 @@ ICaLK = g * PK * PhiK
     desc: K-component of L-type calcium current
 ICaL_tot = ICaLCa + ICaLK + ICaLNa
     in [A/F]
-    label ICaL
+    label I_CaL
 
 #
 # IKr: Rapid delayed rectifier potassium current

c/ohara-cipa-v1-2017.mmt

@@ -475,7 +475,7 @@ PhiK = if(abs(vf) < 1e-6,
     in [mC/L]
 PCa_base = 0.0001 [L/F/ms]
     in [L/F/ms]
-    label gCaL
+    label g_CaL
 PCa = PCa_base * piecewise(cell.mode == 0, 1, cell.mode == 1, 1.2, 2.5) * 1.007
     in [L/F/ms]
 PNa = 0.00125 * PCa
@@ -499,7 +499,7 @@ ICaLK = g * PK * PhiK
     desc: K-component of L-type calcium current
 ICaL_tot = ICaLCa + ICaLK + ICaLNa
     in [A/F]
-    label ICaL
+    label I_CaL
 
 #
 # IKr: Rapid delayed rectifier potassium current

c/priebe-1998.mmt

@@ -178,10 +178,10 @@ dot(j) = alpha * (1 - j) - beta * j
 use membrane.V
 i_Ca = g_Ca_max * d * f * f_Ca * (V - rev.E_Ca)
     in [A/F]
-    label ICaL
+    label I_CaL
 g_Ca_max = 0.064 [mS/uF]
     in [mS/uF]
-    label gCaL
+    label g_CaL
 Km_Ca = 0.0006 [mM]
     in [mM]
 dot(d) = alpha * (1 - d) - beta * d

c/tentusscher-2004.mmt

@@ -12,7 +12,7 @@ desc: """
     This implementation is based on the CellML version on PMR by
     Catherine Lloyd [2], but with substantial rewrites and including the
     unit fixes described in [3].
-    
+
     The stimulus current was set to 0.5ms and approximately twice the threshold
     for depolarisation.
 
@@ -25,7 +25,7 @@ desc: """
 
     [3] Clerx, M., Barral, Y., Agrawal, A. & Mirams, G. R. (2020)
         TNNP unit fixes
-        https://models.cellml.org/workspace/604/file/de5a4e600b57c8b9b0bd477695648c82351bc6dd/TNNP_unit_fixes.pdf   
+        https://models.cellml.org/workspace/604/file/de5a4e600b57c8b9b0bd477695648c82351bc6dd/TNNP_unit_fixes.pdf
 
     """
 # Initial values (ordered as in the original code)
@@ -260,10 +260,10 @@ use phys.FRT, phys.FFRT
 use extra.Cao, calcium.Cai
 ICaL = gCaL * d * f * fCa * 4 * V * FFRT * (Cai * exp(2 * V * FRT) - 0.341 * Cao) / (exp(2 * V * FRT) - 1)
     in [A/F]
-    label ICaL
+    label I_CaL
 gCaL = 0.175 [L/F/s]
     in [L/F/s]
-    label gCaL
+    label g_CaL
 dot(d) = (inf - d) / tau
     inf = 1 / (1 + exp((-5 [mV] - V) / 7.5 [mV]))
     tau = 1 [ms] * (alpha * beta + gamma)

c/tentusscher-2006.mmt

@@ -32,7 +32,7 @@ desc: """
 
     [4] Clerx, M., Barral, Y., Agrawal, A. & Mirams, G. R. (2020)
         TNNP unit fixes
-        https://models.cellml.org/workspace/604/file/de5a4e600b57c8b9b0bd477695648c82351bc6dd/TNNP_unit_fixes.pdf   
+        https://models.cellml.org/workspace/604/file/de5a4e600b57c8b9b0bd477695648c82351bc6dd/TNNP_unit_fixes.pdf
 
     """
 # Initial values (ordered as in the original code)
@@ -289,10 +289,10 @@ use phys.FRT, phys.FFRT
 use extra.Cao, calcium.Cai, calcium.CaSS
 ICaL = gCaL * d * f * f2 * fCaSS * 4 * (V - 15 [mV]) * FFRT * (0.25 * CaSS * exp(2 * (V - 15 [mV]) * FRT) - Cao) / (exp(2 * (V - 15 [mV]) * FRT) - 1)
     in [A/F]
-    label ICaL
+    label I_CaL
 gCaL = 0.0398 [L/F/s]
     in [L/F/s]
-    label gCaL
+    label g_CaL
 dot(d) = (inf - d) / tau
     inf = 1 / (1 + exp((-8 [mV] - V) / 7.5 [mV]))
     tau = 1 [ms] * (alpha * beta + gamma)

c/trovato-2020.mmt

@@ -382,7 +382,7 @@ ICaLK = g * PK * PhiK
     desc: K-component of L-type calcium current
 ICaL_tot = ICaLCa + ICaLK + ICaLNa
     in [A/F]
-    label ICaL
+    label I_CaL
 
 #
 # ICaT: T-type calcium current

c/voigt-2013.mmt

@@ -243,7 +243,6 @@ use membrane.V
 gNa = 23 [mS/uF]
     in [mS/uF]
 dot(m) = (inf - m) / tau
-    label ina_m
     alpha = if(V == -47.13 [mV], 3.2 [1/ms], 0.32 [1/mV/ms] * (V + 47.13 [mV]) / (1 - exp(-0.1 [1/mV] * (V + 47.13 [mV]))))
         in [1/ms]
     beta = 0.08 [1/ms] * exp(-V / 11 [mV])
@@ -257,7 +256,6 @@ dot(h) = (inf - h) / tau
     beta = if(V < -40 [mV], 3.56 [1/ms] * exp(0.079 [1/mV] * V) + 310000 [1/ms] * exp(0.35 [1/mV] * V), 1 / (0.13 [ms] * (1 + exp((V + 10.66 [mV]) / -11.1 [mV]))))
         in [1/ms]
     inf = alpha / (alpha + beta)
-        label ina_h_inf
     tau = 1/ (alpha + beta)
         in [ms]
 dot(j) = (inf - j) / tau
@@ -266,7 +264,6 @@ dot(j) = (inf - j) / tau
     beta = if(V < -40 [mV], 0.1212 [1/ms] * exp(-0.01052 [1/mV] * V) / (1+ exp(-0.1378 [1/mV] * (V + 40.14 [mV]))), 0.3 [1/ms] * exp(-2.535e-07 [1/mV] * V) / (1 + exp(-0.1 [1/mV] * (V + 32[mV]))))
         in [1/ms]
     inf = alpha / (alpha + beta)
-        label ina_j_inf
     tau = 1/ (alpha + beta)
         in [ms]
 INa_jn = junc.Fjn * gNa * m^3 * h * j * (V - nernst.ENa_jn)
@@ -519,7 +516,7 @@ IClB = gClB * (membrane.V - nernst.ECl)
 use membrane.V
 use phys.F, phys.FRT, phys.Q
 scaling = 1
-    label I_CaL_scaling
+    label g_CaL
 pNa = scaling * (1 - 0.5 * cell.AF) * 0.75e-8 [cm/s]
     in [cm/s]
 pCa = scaling * (1 - 0.5 * cell.AF) * 2.7e-4 [cm/s]