Set display_name for all models

myokit · Sep 4, 2024 · e832505 · e832505
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diff --git a/.github/workflows/syntax-test.yml b/.github/workflows/syntax-test.yml
@@ -16,10 +16,10 @@ jobs:
     if: github.event.pull_request.draft == false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Configure Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
           cache: 'pip'

diff --git a/c/aguilar-2017.mmt b/c/aguilar-2017.mmt
@@ -2,6 +2,7 @@
 name: aguilar-2017
 version: 20240904
 mmt_authors: Michael Clerx
+display_name: Aguilar et al., 2017
 desc: """
     Model of the human atrial action potential by Aguilar et al. [1], based on
     the model by Courtemanche et al. [2] and including the IKACh current

diff --git a/c/akwaboah-2021-corrected.mmt b/c/akwaboah-2021-corrected.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: akwaboah-2021-corrected
-version: 20240325
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Akwaboah et al., 2021
 desc: """
     Model of the hiPSC AP by Akwaboah et al [1], with corrections.
 

diff --git a/c/akwaboah-2021-original.mmt b/c/akwaboah-2021-original.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: akwaboah-2021-original
-version: 20240323
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Akwaboah et al., 2021 (uncorrected)
 desc: """
     Model of the hiPSC AP by Akwaboah et al [1], matching the published code.
 

diff --git a/c/bartolucci-2020.mmt b/c/bartolucci-2020.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: bartolucci-2020
-version: 20240816
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Bartolucci et al., 2020
 desc: """
     The 2020 "BPS" model of the human ventricular AP by Bartolucci et al. [1].
 

diff --git a/c/beeler-1977.mmt b/c/beeler-1977.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: beeler-1977
-version: 20230202
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Beeler & Reuter 1977
 desc: """
     The 1977 model of the AP in mammalian ventricular myocardial fibers by
     Beeler and Reuter [1].

diff --git a/c/carro-2011.mmt b/c/carro-2011.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: carro-2011
-version: 20240903
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Carro et al., 2011
 desc: """
     The 2011 model of the human ventricular AP by Carro et al. [1], based
     on the model by Grandi et al. [2].

diff --git a/c/courtemanche-1998.mmt b/c/courtemanche-1998.mmt
@@ -2,6 +2,7 @@
 name: courtemanche-1998
 version: 20240904
 mmt_authors: Michael Clerx
+display_name: Courtemanche et al., 1998
 desc: """
     Model of the human atrial action potential by Courtemanche et al. [1].
 

diff --git a/c/decker-2009.mmt b/c/decker-2009.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: decker-2009
-version: 20230202
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Decker et al., 2009
 desc: """
     The 2009 model of the canine (left) ventricular AP by Decker et al. [1].
 

diff --git a/c/ellinwood-2017.mmt b/c/ellinwood-2017.mmt
@@ -2,6 +2,7 @@
 name: ellinwood-2017
 version: 20240904
 mmt_authors: Michael Clerx
+display_name: Ellinwood et al., 2017
 desc: """
     The 2017 model of the human atrial AP by Ellinwood et al. [1, 2].
     Based on the adaptation of the Grandi model [3] by Morotti et al. [4].

diff --git a/c/gokhale-2017-23.mmt b/c/gokhale-2017-23.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: gokhale-2017-23
-version: 20230503
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Gokhale et al., 2017 (23C)
 desc: """
     The 2017 model of the ex293 AP by Gokhale et al. [1], 23 degrees C version.
 

diff --git a/c/gokhale-2017-35.mmt b/c/gokhale-2017-35.mmt
@@ -1,19 +1,20 @@
 [[model]]
-name: gokhale-2017-23
-version: 20230503
+name: gokhale-2017-35
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Gokhale et al., 2017 (35C)
 desc: """
     The 2017 model of the ex293 AP by Gokhale et al. [1], 35 degrees C version.
 
     The Nav1.5 and Kir2.1 currents in the 23C model are based on the data from
     [2], while endogeneous INa and IK were fit to [3] and [4] respectively.
     All currents in the 35 degrees model were temperature-shifted, sometimes
-    using literature data on temperature effects, sometimes by fitting to 
+    using literature data on temperature effects, sometimes by fitting to
     tissue data (including conduction velocity).
-        
+
     The formulation of the Nav1.5 current is based on the model by Lindblad et
     al. [5], the endogenous INa is a class Hodgkin-Huxley m^3*h form, and the
-    endogenous IK current formulation is based on the IKs equations in [6].    
+    endogenous IK current formulation is based on the IKs equations in [6].
 
     This implementation is based on the equations given in the paper and
     supplement [1]. To avoid overshadowing the sodium current, the stimulus
@@ -24,7 +25,7 @@ desc: """
     units for conductances were changed from [mS/cm^2] to [nS/pF] (thereby
     removing the assumption that the specific membrane capacity is exactly
     1 uF/cm^2).
-    
+
     The implementation was verified by recreating parts of figures 1 and 2,
     which could partly be achieved (some information on monodomain parameters
     and the exact stimulus and voltage-clamp protocols is missing). In
@@ -36,21 +37,21 @@ desc: """
         Variability for Paired Computational-Experimental Studies. PLOS
         Computational Biology. 13(1): e1005342.
         https://doi.org/10.1371/journal.pcbi.1005342
-        
+
     [2] Kirkton, R. D., and Bursac, N. (2011) Engineering biosynthetic
         excitable tissues from unexcitable cells for electrophysiological and
         cell therapy studies. Nature communications 2:300
         https://doi.org/10.1038/ncomms1302
-        
-    [3] He, B., and Soderlund, D. M. (2017) Human embryonic kidney (HEK293) 
-        cells express endogenous voltage-gated sodium currents and Nav1.7 
+
+    [3] He, B., and Soderlund, D. M. (2017) Human embryonic kidney (HEK293)
+        cells express endogenous voltage-gated sodium currents and Nav1.7
         sodium channels. Neuroscience Letters 469:268-272.
         http://doi.org/10.1016/j.neulet.2009.12.012
 
     [4] Yu, S. P., and Kerchner, G. A. (1998) Endogenous voltage-gated
         potassium channels in human embryonic kidney (HEK293) cells. Journal of
         Neuroscience Research, 52:612-617.
-        
+
     [5] Lindblad, D.S., Murphey, C.R., Clark, J.W., and Giles, W.G. (1996) A
         model of the action potential and underlying membrane currents in a
         rabbit atrial cell. American Journal of Physiology, 271, H1666-H1691.
@@ -225,7 +226,7 @@ use membrane.V, rev.EK
 dot(b) = (inf - b) / tau
     inf = 1 / (1 + exp((V + 24.96 [mV]) / -36.58 [mV]))
     tau = 0.584 [ms]
-        in [ms]    
+        in [ms]
 g = 0.1332 [nS/pF]
     in [nS/pF]
 IKwt = g * b^2 * (V - EK)

diff --git a/c/grandi-2010.mmt b/c/grandi-2010.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: grandi-2010
-version: 20240903
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Grandi et al., 2010
 desc: """
     The 2010 model of the human ventricular AP by Grandi et al. [1].
 

diff --git a/c/grandi-2011.mmt b/c/grandi-2011.mmt
@@ -1,15 +1,16 @@
 [[model]]
 name: grandi-2011
-version: 20240903
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Grandi-Pandit-Voigt et al., 2011
 desc: """
     The 2011 model of the human atrial AP by Grandi, Pandit, Voigt et al. [1].
 
     Note that there is a 2010 model of the ventricular AP by the same (first)
     first author [2].
 
     This implementation is based on the original Matlab code provided on the
-    Grandi lab website [3]. It was checked against the original code 
+    Grandi lab website [3]. It was checked against the original code
     numerically by comparing the calculated derivatives.
 
     The stimulus was set to 0.5 ms and approximately twice the threshold value

diff --git a/c/iyer-2004.mmt b/c/iyer-2004.mmt
@@ -2,6 +2,7 @@
 name: iyer-2004
 version: 20240904
 mmt_authors: Michael Clerx
+display_name: Iyer et al., 2004
 desc: """
     The 2004 model of the human left-ventricular AP by Iyer et al. [1].
 
@@ -12,7 +13,7 @@ desc: """
     The formulation for ical.y.tau used in this file is the one from the code,
     which differs slightly from the version in the paper (which is used in the
     updated CellML file).
-    
+
     The stimulus was set to 0.5ms and approximately twice the minimum level for
     depolarisation.
 

diff --git a/c/kernik-2019.mmt b/c/kernik-2019.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: kernik-2019
-version: 20230202
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Kernik et al., 2019
 desc: """
     The 2019 model of induced pluripotent stem-cell derived cardiomyocyte AP by
     Kernik et al. [1].

diff --git a/c/koivumaki-2011.mmt b/c/koivumaki-2011.mmt
@@ -1,9 +1,10 @@
 [[model]]
 name: koivumaki-2011
-version: 20240903
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Koivumäki et al., 2011
 desc: """
-    The 2011 model of the human atrial AP by Koivumaki et al. [1], based on the
+    The 2011 model of the human atrial AP by Koivumäki et al. [1], based on the
     earlier model by Nygren et al. [2].
 
     The stimulus was set to 0.5 ms and approximately twice the threshold for
@@ -14,7 +15,7 @@ desc: """
     calculated derivatives. The code can be run to produce an AP similar to
     that seen in the original paper.
 
-    [1] Koivumaki, J. T, Korhonen, T., & Tavi P. (2011). Impact of Sarcoplasmic
+    [1] Koivumäki, J. T, Korhonen, T., & Tavi P. (2011). Impact of Sarcoplasmic
         Reticulum Calcium Release on Calcium Dynamics and Action Potential
         Morphology in Human Atrial Myocytes: A Computational Study. PLOS
         Computational Biology, 7(1), e1001067.

diff --git a/c/livshitz-2007.mmt b/c/livshitz-2007.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: livshitz-2007
-version: 20230202
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Livshitz & Rudy 2007
 desc: """
     The 2007 update by Livshitz & Rudy [1] of the canine ventricular AP model
     by Hund & Rudy [2].

diff --git a/c/maleckar-2009.mmt b/c/maleckar-2009.mmt
@@ -2,6 +2,7 @@
 name: maleckar-2009
 version: 20240904
 mmt_authors: Michael Clerx
+display_name: Maleckar et al., 2009
 desc: """
     Model of the human atrial action potential by Maleckar et al. [1], based on
     the Nygren et al. [2]. The model contains an IKACh current which is

diff --git a/c/ni-2017.mmt b/c/ni-2017.mmt
@@ -2,6 +2,7 @@
 name: ni-2017
 version: 20240904
 mmt_authors: Michael Clerx
+display_name: Ni et al., 2017
 desc: """
     The 2017 model of the human atrial AP by Ni et al. [1].
 

diff --git a/c/noble-1962.mmt b/c/noble-1962.mmt
@@ -1,11 +1,12 @@
 [[model]]
 name: noble-1962
-version: 20230202
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Noble, 1962
 desc: """
     The 1962 model of the AP in Purkinje fibers by Denis Noble [1].
 
-    Adapted from  CellML version.
+    Adapted from the CellML version by Catherine LLoyd.
 
     References :
 
@@ -14,44 +15,8 @@ desc: """
         of Physiology, 160(2), 317-352.
         https://doi.org/10.1113/jphysiol.1962.sp006849
 
-    Original CellML metadata follows below:
-    ---------------------------------------
+    [2] https://models.physiomeproject.org/e/2a6
 
-    Noble Purkinje Fibre Model 1962
-    Catherine Lloyd
-    Auckland Bioengineering Institute, The University of Auckland
-
-    Model Status
-    This CellML model runs in COR, JSim and OpenCell to recreate the published
-    results. The units have been checked and they are consistent.
-
-    Model Structure
-
-    In 1962, Denis Noble published one of the first mathematical models of a
-    cardiac cell.  By adapting the equations of the original Hodgkin-Huxley
-    squid axon model (1952), Noble described the long lasting action and
-    pace-maker potentials of the Purkinje fibres of the heart.  The
-    potassium-current equations differ from those of Hodgkin and Huxley in that
-    the potassium ions are assumed to flow through two types of channel in the
-    membrane.  By contrast, the sodium current equations are very similar to
-    those of Hodgkin and Huxley. The main failure of the Noble (1962) model is
-    that it only includes one voltage gated inward current, INa.  Calcium
-    currents had not yet been discovered, but there was a clue in the model
-    that something was missing.  The only way the model could be made to work
-    was to greatly extend the voltage range of the sodium current by reducing
-    the voltage dependence of the sodium activation process.  In effect the
-    sodium current was made to serve the function of both the sodium and the
-    calcium channels as far as the plateau is concerned.  There was a clear
-    experimental prediction: either sodium channels in the heart are
-    quantitatively different from those in neurons, or other inward
-    current-carrying channels must exist.  Both predictions are correct.
-
-    The original paper reference is cited below:
-
-    A Modification of the Hodgkin-Huxley Equations Applicable to Purkinje Fibre
-    Action and Pacemaker Potentials, Noble, D. 1962
-    Journal of Physiology, 160, 317-352.
-    PubMed ID: 14480151
     """
 # Initial values
 membrane.V = -87.0

diff --git a/c/nygren-1998.mmt b/c/nygren-1998.mmt
@@ -2,6 +2,7 @@
 name: nygren-1998
 version: 20240904
 mmt_authors: Michael Clerx
+display_name: Nygren et al., 1998
 desc: """
     Model of the human atrial action potential by Nygren et al. [1, 2], based
     in part on the earlier rabbit atrial model by Lindblad et al. [3].

diff --git a/c/ohara-cipa-v1-2017.mmt b/c/ohara-cipa-v1-2017.mmt
@@ -2,7 +2,7 @@
 name: dutta-2017
 version: 20240904
 mmt_authors: Michael Clerx
-display_name: O'Hara-CiPA-v1, 2017
+display_name: Dutta et al., 2017
 desc: """
     The 2017 "CiPA v1" update [1, 2, 3] of the O'Hara et al. model of the human
     ventricular AP [4].

diff --git a/c/paci-2013-ventricular-vs.mmt b/c/paci-2013-ventricular-vs.mmt
@@ -1,7 +1,8 @@
 [[model]]
 name: paci-2013-vs
-version: 20230202
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Paci et al., 2013 (ventricular)
 desc: """
     The 2013 model of the hiPSC AP by Paci et al. [1], ventricular version, but
     with the original units of volts and seconds.

diff --git a/c/priebe-1998.mmt b/c/priebe-1998.mmt
@@ -1,12 +1,13 @@
 [[model]]
 name: priebe-1998
-version: 20240903
+version: 20240904
 mmt_authors: Michael Clerx
+display_name: Priebe & Beuckelmann, 1998
 desc: """
     The 1998 model of the human ventricular AP by Priebe and Beuckelmann [1].
 
     Adapted from the CellML implementation by Catherline Lloyd [2].
-    
+
     The stimulus duration was set to 0.5ms, and the amplitude was set to
     approximately twice the minimum needed to elicit three successive APs.
 

diff --git a/c/sampson-2010.mmt b/c/sampson-2010.mmt
@@ -2,6 +2,7 @@
 name: sampson-2010
 version: 20240904
 mmt_authors: Michael Clerx
+display_name: Sampson et al., 2024
 desc: """
     The 2010 model of the human Purkinje cell AP by Sampson et al. [1].