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MichaelClerxMichaelClerx
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Merge pull request #12 from CardiacModelling/10-meta-in-cellml
Added meta data to CellML files.
2 parents 773095b + 3f70a09 commit 43b9d7d

19 files changed

Lines changed: 588 additions & 78 deletions

‎models-cellml-v1/vc-level-0.cellml‎

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<?xml version='1.0' encoding='UTF-8'?>
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<!--
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Model of a voltage-clamp experiment [1-6].
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This is the full version of the model, including a 2-pole stimulus filter,
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a 6-pole and 4-pole Bessel output filter, a finite amplifier speed and fast
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capacitance cancellation.
8+
9+
[1] Lei, C. L., Clark, A. P., Clerx, M., Wei, S., Bloothooft, M., De Boer,
10+
T., Christini, D. J., Krogh-Madsen, T., & Mirams, G. R. (2025)
11+
Resolving Artifacts in Voltage-Clamp Experiments with Computational
12+
Modeling: An Application to Fast Sodium Current Recordings. Advanced
13+
Science.
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https://doi.org/10.1002/advs.202500691
15+
16+
[2] Lei, C. L., Clerx, M., Whittaker, D. G., Gavaghan, D. J., De Boer, T.
17+
P., & Mirams, G. R. (2020) Accounting for variability in ion current
18+
recordings using a mathematical model of artefacts in voltage-clamp
19+
experiments. Phil. Trans. R. Soc. A. 378: 20190348
20+
https://doi.org/10.1098/rsta.2019.0348
21+
22+
[3] Abrasheva, V. O., Kovalenko, S. G., Slotvitsky, M., Romanova, S. A.,
23+
Aitova, A. A., Frolova, S., Tsvelaya, V., & Syunyaev, R. A. (2024)
24+
Human sodium current voltage-dependence at physiological temperature
25+
measured by coupling a patch-clamp experiment to a mathematical model.
26+
J. Physiol., 602: 633-661.
27+
https://doi.org/10.1113/JP285162
28+
29+
[4] Weerakoon, P., Culurciello, E., Klemic, K. G., & Sigworth, F. J. (2009)
30+
An Integrated Patch-Clamp Potentiostat With Electrode Compensation.
31+
IEEE Trans. Biomed. Circ. 3-2: 117-125
32+
https://doi.org/10.1109/TBCAS.2008.2005419
33+
34+
[5] Sigworth, F. J. (1995) Electronic design of the patch clamp.
35+
In: Single-channel recording (1995): 95-127.
36+
https://doi.org/10.1007/978-1-4419-1229-9_4
37+
38+
[6] Clerx, M. (2026) Voltage-clamp model tutorial.
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https://github.com/CardiacModelling/VoltageClampModel
40+
-->
241
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" name="voltage_clamp_model_level_0">
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<units name="A_per_F">
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<unit units="gram" multiplier="1000"/>

‎models-cellml-v1/vc-level-1.cellml‎

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<?xml version='1.0' encoding='UTF-8'?>
2+
<!--
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"Level 1" simplified model of a voltage-clamp experiment [1-6].
4+
5+
Simplifications:
6+
7+
- L1: Output filters replaced by a single filter. All filters implemented
8+
as first order.
9+
10+
[1] Lei, C. L., Clark, A. P., Clerx, M., Wei, S., Bloothooft, M., De Boer,
11+
T., Christini, D. J., Krogh-Madsen, T., & Mirams, G. R. (2025)
12+
Resolving Artifacts in Voltage-Clamp Experiments with Computational
13+
Modeling: An Application to Fast Sodium Current Recordings. Advanced
14+
Science.
15+
https://doi.org/10.1002/advs.202500691
16+
17+
[2] Lei, C. L., Clerx, M., Whittaker, D. G., Gavaghan, D. J., De Boer, T.
18+
P., & Mirams, G. R. (2020) Accounting for variability in ion current
19+
recordings using a mathematical model of artefacts in voltage-clamp
20+
experiments. Phil. Trans. R. Soc. A. 378: 20190348
21+
https://doi.org/10.1098/rsta.2019.0348
22+
23+
[3] Abrasheva, V. O., Kovalenko, S. G., Slotvitsky, M., Romanova, S. A.,
24+
Aitova, A. A., Frolova, S., Tsvelaya, V., & Syunyaev, R. A. (2024)
25+
Human sodium current voltage-dependence at physiological temperature
26+
measured by coupling a patch-clamp experiment to a mathematical model.
27+
J. Physiol., 602: 633-661.
28+
https://doi.org/10.1113/JP285162
29+
30+
[4] Weerakoon, P., Culurciello, E., Klemic, K. G., & Sigworth, F. J. (2009)
31+
An Integrated Patch-Clamp Potentiostat With Electrode Compensation.
32+
IEEE Trans. Biomed. Circ. 3-2: 117-125
33+
https://doi.org/10.1109/TBCAS.2008.2005419
34+
35+
[5] Sigworth, F. J. (1995) Electronic design of the patch clamp.
36+
In: Single-channel recording (1995): 95-127.
37+
https://doi.org/10.1007/978-1-4419-1229-9_4
38+
39+
[6] Clerx, M. (2026) Voltage-clamp model tutorial.
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https://github.com/CardiacModelling/VoltageClampModel
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-->
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<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" name="voltage_clamp_model_level_1">
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<units name="A_per_F">
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<unit units="gram" multiplier="1000"/>

‎models-cellml-v1/vc-level-2.cellml‎

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<?xml version='1.0' encoding='UTF-8'?>
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<!--
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"Level 2" simplified model of a voltage-clamp experiment [1-6].
4+
5+
Simplifications:
6+
7+
- L1: Output filters replaced by a single filter. All filters implemented
8+
as first order.
9+
- L2: Idealised op-amp, without stray capacitance Cf.
10+
11+
[1] Lei, C. L., Clark, A. P., Clerx, M., Wei, S., Bloothooft, M., De Boer,
12+
T., Christini, D. J., Krogh-Madsen, T., & Mirams, G. R. (2025)
13+
Resolving Artifacts in Voltage-Clamp Experiments with Computational
14+
Modeling: An Application to Fast Sodium Current Recordings. Advanced
15+
Science.
16+
https://doi.org/10.1002/advs.202500691
17+
18+
[2] Lei, C. L., Clerx, M., Whittaker, D. G., Gavaghan, D. J., De Boer, T.
19+
P., & Mirams, G. R. (2020) Accounting for variability in ion current
20+
recordings using a mathematical model of artefacts in voltage-clamp
21+
experiments. Phil. Trans. R. Soc. A. 378: 20190348
22+
https://doi.org/10.1098/rsta.2019.0348
23+
24+
[3] Abrasheva, V. O., Kovalenko, S. G., Slotvitsky, M., Romanova, S. A.,
25+
Aitova, A. A., Frolova, S., Tsvelaya, V., & Syunyaev, R. A. (2024)
26+
Human sodium current voltage-dependence at physiological temperature
27+
measured by coupling a patch-clamp experiment to a mathematical model.
28+
J. Physiol., 602: 633-661.
29+
https://doi.org/10.1113/JP285162
30+
31+
[4] Weerakoon, P., Culurciello, E., Klemic, K. G., & Sigworth, F. J. (2009)
32+
An Integrated Patch-Clamp Potentiostat With Electrode Compensation.
33+
IEEE Trans. Biomed. Circ. 3-2: 117-125
34+
https://doi.org/10.1109/TBCAS.2008.2005419
35+
36+
[5] Sigworth, F. J. (1995) Electronic design of the patch clamp.
37+
In: Single-channel recording (1995): 95-127.
38+
https://doi.org/10.1007/978-1-4419-1229-9_4
39+
40+
[6] Clerx, M. (2026) Voltage-clamp model tutorial.
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https://github.com/CardiacModelling/VoltageClampModel
42+
-->
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<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" name="voltage_clamp_model_level_2">
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<units name="A_per_F">
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<unit units="gram" multiplier="1000"/>

‎models-cellml-v1/vc-level-3.cellml‎

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<?xml version='1.0' encoding='UTF-8'?>
2+
<!--
3+
"Level 3" simplified model of a voltage-clamp experiment [1-6].
4+
5+
Simplifications:
6+
7+
- L1: Output filters replaced by a single filter. All filters implemented
8+
as first order.
9+
- L2: Idealised op-amp, without stray capacitance Cf.
10+
- L3: Removed fast capacitative current and its cancellation.
11+
12+
[1] Lei, C. L., Clark, A. P., Clerx, M., Wei, S., Bloothooft, M., De Boer,
13+
T., Christini, D. J., Krogh-Madsen, T., & Mirams, G. R. (2025)
14+
Resolving Artifacts in Voltage-Clamp Experiments with Computational
15+
Modeling: An Application to Fast Sodium Current Recordings. Advanced
16+
Science.
17+
https://doi.org/10.1002/advs.202500691
18+
19+
[2] Lei, C. L., Clerx, M., Whittaker, D. G., Gavaghan, D. J., De Boer, T.
20+
P., & Mirams, G. R. (2020) Accounting for variability in ion current
21+
recordings using a mathematical model of artefacts in voltage-clamp
22+
experiments. Phil. Trans. R. Soc. A. 378: 20190348
23+
https://doi.org/10.1098/rsta.2019.0348
24+
25+
[3] Abrasheva, V. O., Kovalenko, S. G., Slotvitsky, M., Romanova, S. A.,
26+
Aitova, A. A., Frolova, S., Tsvelaya, V., & Syunyaev, R. A. (2024)
27+
Human sodium current voltage-dependence at physiological temperature
28+
measured by coupling a patch-clamp experiment to a mathematical model.
29+
J. Physiol., 602: 633-661.
30+
https://doi.org/10.1113/JP285162
31+
32+
[4] Weerakoon, P., Culurciello, E., Klemic, K. G., & Sigworth, F. J. (2009)
33+
An Integrated Patch-Clamp Potentiostat With Electrode Compensation.
34+
IEEE Trans. Biomed. Circ. 3-2: 117-125
35+
https://doi.org/10.1109/TBCAS.2008.2005419
36+
37+
[5] Sigworth, F. J. (1995) Electronic design of the patch clamp.
38+
In: Single-channel recording (1995): 95-127.
39+
https://doi.org/10.1007/978-1-4419-1229-9_4
40+
41+
[6] Clerx, M. (2026) Voltage-clamp model tutorial.
42+
https://github.com/CardiacModelling/VoltageClampModel
43+
-->
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<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" name="voltage_clamp_model_level_3">
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<units name="GOhm">
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<unit units="gram" multiplier="1000000000000"/>

‎models-cellml-v1/vc-level-4.cellml‎

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<?xml version='1.0' encoding='UTF-8'?>
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<!--
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"Level 4" simplified model of a voltage-clamp experiment [1-6].
4+
5+
Simplifications:
6+
7+
- L2: Idealised op-amp, without stray capacitance Cf.
8+
- L3: Removed fast capacitative current and its cancellation.
9+
- L4: All filters removed.
10+
11+
[1] Lei, C. L., Clark, A. P., Clerx, M., Wei, S., Bloothooft, M., De Boer,
12+
T., Christini, D. J., Krogh-Madsen, T., & Mirams, G. R. (2025)
13+
Resolving Artifacts in Voltage-Clamp Experiments with Computational
14+
Modeling: An Application to Fast Sodium Current Recordings. Advanced
15+
Science.
16+
https://doi.org/10.1002/advs.202500691
17+
18+
[2] Lei, C. L., Clerx, M., Whittaker, D. G., Gavaghan, D. J., De Boer, T.
19+
P., & Mirams, G. R. (2020) Accounting for variability in ion current
20+
recordings using a mathematical model of artefacts in voltage-clamp
21+
experiments. Phil. Trans. R. Soc. A. 378: 20190348
22+
https://doi.org/10.1098/rsta.2019.0348
23+
24+
[3] Abrasheva, V. O., Kovalenko, S. G., Slotvitsky, M., Romanova, S. A.,
25+
Aitova, A. A., Frolova, S., Tsvelaya, V., & Syunyaev, R. A. (2024)
26+
Human sodium current voltage-dependence at physiological temperature
27+
measured by coupling a patch-clamp experiment to a mathematical model.
28+
J. Physiol., 602: 633-661.
29+
https://doi.org/10.1113/JP285162
30+
31+
[4] Weerakoon, P., Culurciello, E., Klemic, K. G., & Sigworth, F. J. (2009)
32+
An Integrated Patch-Clamp Potentiostat With Electrode Compensation.
33+
IEEE Trans. Biomed. Circ. 3-2: 117-125
34+
https://doi.org/10.1109/TBCAS.2008.2005419
35+
36+
[5] Sigworth, F. J. (1995) Electronic design of the patch clamp.
37+
In: Single-channel recording (1995): 95-127.
38+
https://doi.org/10.1007/978-1-4419-1229-9_4
39+
40+
[6] Clerx, M. (2026) Voltage-clamp model tutorial.
41+
https://github.com/CardiacModelling/VoltageClampModel
42+
-->
243
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" name="voltage_clamp_model_level_4">
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<units name="GOhm">
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<unit units="gram" multiplier="1000000000000"/>

‎models-cellml-v1/vc-level-5.cellml‎

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<?xml version='1.0' encoding='UTF-8'?>
2+
<!--
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"Level 5" simplified model of a voltage-clamp experiment [1-6].
4+
5+
This version assumes perfect slow capacitance cancellation.
6+
7+
Simplifications:
8+
9+
- L2: Idealised op-amp, without stray capacitance Cf.
10+
- L3: Removed fast capacitative current and its cancellation.
11+
- L4: All filters removed.
12+
- L5: Removed charging current and its cancellation.
13+
14+
[1] Lei, C. L., Clark, A. P., Clerx, M., Wei, S., Bloothooft, M., De Boer,
15+
T., Christini, D. J., Krogh-Madsen, T., & Mirams, G. R. (2025)
16+
Resolving Artifacts in Voltage-Clamp Experiments with Computational
17+
Modeling: An Application to Fast Sodium Current Recordings. Advanced
18+
Science.
19+
https://doi.org/10.1002/advs.202500691
20+
21+
[2] Lei, C. L., Clerx, M., Whittaker, D. G., Gavaghan, D. J., De Boer, T.
22+
P., & Mirams, G. R. (2020) Accounting for variability in ion current
23+
recordings using a mathematical model of artefacts in voltage-clamp
24+
experiments. Phil. Trans. R. Soc. A. 378: 20190348
25+
https://doi.org/10.1098/rsta.2019.0348
26+
27+
[3] Abrasheva, V. O., Kovalenko, S. G., Slotvitsky, M., Romanova, S. A.,
28+
Aitova, A. A., Frolova, S., Tsvelaya, V., & Syunyaev, R. A. (2024)
29+
Human sodium current voltage-dependence at physiological temperature
30+
measured by coupling a patch-clamp experiment to a mathematical model.
31+
J. Physiol., 602: 633-661.
32+
https://doi.org/10.1113/JP285162
33+
34+
[4] Weerakoon, P., Culurciello, E., Klemic, K. G., & Sigworth, F. J. (2009)
35+
An Integrated Patch-Clamp Potentiostat With Electrode Compensation.
36+
IEEE Trans. Biomed. Circ. 3-2: 117-125
37+
https://doi.org/10.1109/TBCAS.2008.2005419
38+
39+
[5] Sigworth, F. J. (1995) Electronic design of the patch clamp.
40+
In: Single-channel recording (1995): 95-127.
41+
https://doi.org/10.1007/978-1-4419-1229-9_4
42+
43+
[6] Clerx, M. (2026) Voltage-clamp model tutorial.
44+
https://github.com/CardiacModelling/VoltageClampModel
45+
-->
246
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" name="voltage_clamp_model_level_5">
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<units name="GOhm">
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<unit units="gram" multiplier="1000000000000"/>

‎models-cellml-v2/vc-level-0.cellml‎

Lines changed: 39 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,43 @@
11
<?xml version='1.0' encoding='UTF-8'?>
2+
<!--
3+
Model of a voltage-clamp experiment [1-6].
4+
5+
This is the full version of the model, including a 2-pole stimulus filter,
6+
a 6-pole and 4-pole Bessel output filter, a finite amplifier speed and fast
7+
capacitance cancellation.
8+
9+
[1] Lei, C. L., Clark, A. P., Clerx, M., Wei, S., Bloothooft, M., De Boer,
10+
T., Christini, D. J., Krogh-Madsen, T., & Mirams, G. R. (2025)
11+
Resolving Artifacts in Voltage-Clamp Experiments with Computational
12+
Modeling: An Application to Fast Sodium Current Recordings. Advanced
13+
Science.
14+
https://doi.org/10.1002/advs.202500691
15+
16+
[2] Lei, C. L., Clerx, M., Whittaker, D. G., Gavaghan, D. J., De Boer, T.
17+
P., & Mirams, G. R. (2020) Accounting for variability in ion current
18+
recordings using a mathematical model of artefacts in voltage-clamp
19+
experiments. Phil. Trans. R. Soc. A. 378: 20190348
20+
https://doi.org/10.1098/rsta.2019.0348
21+
22+
[3] Abrasheva, V. O., Kovalenko, S. G., Slotvitsky, M., Romanova, S. A.,
23+
Aitova, A. A., Frolova, S., Tsvelaya, V., & Syunyaev, R. A. (2024)
24+
Human sodium current voltage-dependence at physiological temperature
25+
measured by coupling a patch-clamp experiment to a mathematical model.
26+
J. Physiol., 602: 633-661.
27+
https://doi.org/10.1113/JP285162
28+
29+
[4] Weerakoon, P., Culurciello, E., Klemic, K. G., & Sigworth, F. J. (2009)
30+
An Integrated Patch-Clamp Potentiostat With Electrode Compensation.
31+
IEEE Trans. Biomed. Circ. 3-2: 117-125
32+
https://doi.org/10.1109/TBCAS.2008.2005419
33+
34+
[5] Sigworth, F. J. (1995) Electronic design of the patch clamp.
35+
In: Single-channel recording (1995): 95-127.
36+
https://doi.org/10.1007/978-1-4419-1229-9_4
37+
38+
[6] Clerx, M. (2026) Voltage-clamp model tutorial.
39+
https://github.com/CardiacModelling/VoltageClampModel
40+
-->
241
<model xmlns="http://www.cellml.org/cellml/2.0#" xmlns:cellml="http://www.cellml.org/cellml/2.0#" name="voltage_clamp_model_level_0">
342
<units name="A_per_F">
443
<unit units="gram" multiplier="1000"/>

‎models-cellml-v2/vc-level-1.cellml‎

Lines changed: 40 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,44 @@
11
<?xml version='1.0' encoding='UTF-8'?>
2+
<!--
3+
"Level 1" simplified model of a voltage-clamp experiment [1-6].
4+
5+
Simplifications:
6+
7+
- L1: Output filters replaced by a single filter. All filters implemented
8+
as first order.
9+
10+
[1] Lei, C. L., Clark, A. P., Clerx, M., Wei, S., Bloothooft, M., De Boer,
11+
T., Christini, D. J., Krogh-Madsen, T., & Mirams, G. R. (2025)
12+
Resolving Artifacts in Voltage-Clamp Experiments with Computational
13+
Modeling: An Application to Fast Sodium Current Recordings. Advanced
14+
Science.
15+
https://doi.org/10.1002/advs.202500691
16+
17+
[2] Lei, C. L., Clerx, M., Whittaker, D. G., Gavaghan, D. J., De Boer, T.
18+
P., & Mirams, G. R. (2020) Accounting for variability in ion current
19+
recordings using a mathematical model of artefacts in voltage-clamp
20+
experiments. Phil. Trans. R. Soc. A. 378: 20190348
21+
https://doi.org/10.1098/rsta.2019.0348
22+
23+
[3] Abrasheva, V. O., Kovalenko, S. G., Slotvitsky, M., Romanova, S. A.,
24+
Aitova, A. A., Frolova, S., Tsvelaya, V., & Syunyaev, R. A. (2024)
25+
Human sodium current voltage-dependence at physiological temperature
26+
measured by coupling a patch-clamp experiment to a mathematical model.
27+
J. Physiol., 602: 633-661.
28+
https://doi.org/10.1113/JP285162
29+
30+
[4] Weerakoon, P., Culurciello, E., Klemic, K. G., & Sigworth, F. J. (2009)
31+
An Integrated Patch-Clamp Potentiostat With Electrode Compensation.
32+
IEEE Trans. Biomed. Circ. 3-2: 117-125
33+
https://doi.org/10.1109/TBCAS.2008.2005419
34+
35+
[5] Sigworth, F. J. (1995) Electronic design of the patch clamp.
36+
In: Single-channel recording (1995): 95-127.
37+
https://doi.org/10.1007/978-1-4419-1229-9_4
38+
39+
[6] Clerx, M. (2026) Voltage-clamp model tutorial.
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https://github.com/CardiacModelling/VoltageClampModel
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-->
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<model xmlns="http://www.cellml.org/cellml/2.0#" xmlns:cellml="http://www.cellml.org/cellml/2.0#" name="voltage_clamp_model_level_1">
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<units name="A_per_F">
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<unit units="gram" multiplier="1000"/>

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