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feat: added support for max_sim_steps
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@jonrkarr
jonrkarr committed Sep 22, 2021
1 parent 8079b9b commit 702cba6
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Showing 5 changed files with 210 additions and 48 deletions.
197 changes: 154 additions & 43 deletions biosimulators.json
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Original file line number Diff line number Diff line change
Expand Up @@ -96,12 +96,11 @@
}
],
"references": {
"identifiers": [
{
"namespace": "pypi",
"id": "bionetgen",
"url": "https://pypi.org/project/bionetgen/"
},
"identifiers": [{
"namespace": "pypi",
"id": "bionetgen",
"url": "https://pypi.org/project/bionetgen/"
},
{
"namespace": "pypi",
"id": "biosimulators-bionetgen",
Expand Down Expand Up @@ -178,8 +177,7 @@
"version": null,
"supportedFeatures": []
}],
"modelChangePatterns": [
{
"modelChangePatterns": [{
"name": "Change compartments sizes",
"types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
"target": {
Expand Down Expand Up @@ -263,6 +261,30 @@
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"]
},
{
"id": "output_step_interval",
"name": "Output step interval",
"type": "integer",
"value": null,
"recommendedRange": null,
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000684"
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application"]
},
{
"id": "max_sim_steps",
"name": "Maximum simulation steps",
"type": "integer",
"value": null,
"recommendedRange": null,
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000415"
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"]
},
{
"id": "stop_if",
"name": "Stop condition",
Expand All @@ -280,21 +302,26 @@
"namespace": "SIO",
"id": "SIO_000418"
}],
"outputVariablePatterns": [
{
"outputVariablePatterns": [{
"name": "time",
"symbol": {
"value": "time",
"namespace": "urn:sedml:symbol"
}
"value": "time",
"namespace": "urn:sedml:symbol"
}
},
{
"name": "species concentrations",
"target": {"value": "species.<species_id>.count", "grammar": "BNGL"}
"target": {
"value": "species.<species_id>.count",
"grammar": "BNGL"
}
},
{
"name": "molecule concentrations",
"target": {"value": "molecules.<molecule_pattern>.count", "grammar": "BNGL"}
"target": {
"value": "molecules.<molecule_pattern>.count",
"grammar": "BNGL"
}
}
],
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"],
Expand Down Expand Up @@ -325,8 +352,7 @@
"version": null,
"supportedFeatures": []
}],
"modelChangePatterns": [
{
"modelChangePatterns": [{
"name": "Change compartments sizes",
"types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
"target": {
Expand Down Expand Up @@ -398,6 +424,30 @@
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"]
},
{
"id": "output_step_interval",
"name": "Output step interval",
"type": "integer",
"value": null,
"recommendedRange": null,
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000684"
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application"]
},
{
"id": "max_sim_steps",
"name": "Maximum simulation steps",
"type": "integer",
"value": null,
"recommendedRange": null,
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000415"
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"]
},
{
"id": "stop_if",
"name": "Stop condition",
Expand All @@ -415,21 +465,26 @@
"namespace": "SIO",
"id": "SIO_000418"
}],
"outputVariablePatterns": [
{
"outputVariablePatterns": [{
"name": "time",
"symbol": {
"value": "time",
"namespace": "urn:sedml:symbol"
}
"value": "time",
"namespace": "urn:sedml:symbol"
}
},
{
"name": "species counts",
"target": {"value": "species.<species_id>.count", "grammar": "BNGL"}
"target": {
"value": "species.<species_id>.count",
"grammar": "BNGL"
}
},
{
"name": "molecule counts",
"target": {"value": "molecules.<molecule_pattern>.count", "grammar": "BNGL"}
"target": {
"value": "molecules.<molecule_pattern>.count",
"grammar": "BNGL"
}
}
],
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"],
Expand All @@ -454,8 +509,7 @@
"version": null,
"supportedFeatures": []
}],
"modelChangePatterns": [
{
"modelChangePatterns": [{
"name": "Change compartments sizes",
"types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
"target": {
Expand Down Expand Up @@ -486,7 +540,7 @@
"value": "functions.{ name e.g., `h` or name and arguments e.g., `h(...)` }.expression",
"grammar": "BNGL"
}
}
}
],
"simulationFormats": [{
"namespace": "EDAM",
Expand Down Expand Up @@ -527,6 +581,30 @@
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"]
},
{
"id": "output_step_interval",
"name": "Output step interval",
"type": "integer",
"value": null,
"recommendedRange": null,
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000684"
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application"]
},
{
"id": "max_sim_steps",
"name": "Maximum simulation steps",
"type": "integer",
"value": null,
"recommendedRange": null,
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000415"
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"]
},
{
"id": "stop_if",
"name": "Stop condition",
Expand All @@ -544,21 +622,26 @@
"namespace": "SIO",
"id": "SIO_000418"
}],
"outputVariablePatterns": [
{
"outputVariablePatterns": [{
"name": "time",
"symbol": {
"value": "time",
"namespace": "urn:sedml:symbol"
}
"value": "time",
"namespace": "urn:sedml:symbol"
}
},
{
"name": "species counts",
"target": {"value": "species.<species_id>.count", "grammar": "BNGL"}
"target": {
"value": "species.<species_id>.count",
"grammar": "BNGL"
}
},
{
"name": "molecule counts",
"target": {"value": "molecules.<molecule_pattern>.count", "grammar": "BNGL"}
"target": {
"value": "molecules.<molecule_pattern>.count",
"grammar": "BNGL"
}
}
],
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"],
Expand All @@ -582,8 +665,7 @@
"version": null,
"supportedFeatures": []
}],
"modelChangePatterns": [
{
"modelChangePatterns": [{
"name": "Change compartments sizes",
"types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
"target": {
Expand Down Expand Up @@ -655,6 +737,30 @@
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"]
},
{
"id": "output_step_interval",
"name": "Output step interval",
"type": "integer",
"value": null,
"recommendedRange": null,
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000684"
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application"]
},
{
"id": "max_sim_steps",
"name": "Maximum simulation steps",
"type": "integer",
"value": null,
"recommendedRange": null,
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000415"
},
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"]
},
{
"id": "stop_if",
"name": "Stop condition",
Expand All @@ -672,21 +778,26 @@
"namespace": "SIO",
"id": "SIO_000418"
}],
"outputVariablePatterns": [
{
"outputVariablePatterns": [{
"name": "time",
"symbol": {
"value": "time",
"namespace": "urn:sedml:symbol"
}
"value": "time",
"namespace": "urn:sedml:symbol"
}
},
{
"name": "species counts",
"target": {"value": "species.<species_id>.count", "grammar": "BNGL"}
"target": {
"value": "species.<species_id>.count",
"grammar": "BNGL"
}
},
{
"name": "molecule counts",
"target": {"value": "molecules.<molecule_pattern>.count", "grammar": "BNGL"}
"target": {
"value": "molecules.<molecule_pattern>.count",
"grammar": "BNGL"
}
}
],
"availableSoftwareInterfaceTypes": ["desktop application", "command-line application", "BioSimulators Docker image"],
Expand Down
20 changes: 20 additions & 0 deletions biosimulators_bionetgen/data_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -135,6 +135,11 @@ def is_equal(self, other):
'name': 'relative tolerance',
'type': ValueType.float,
},
'KISAO_0000415': {
'id': 'max_sim_steps',
'name': 'Maximum simulation steps',
'type': ValueType.integer,
},
'KISAO_0000525': {
'id': 'stop_if',
'name': 'stop condition',
Expand All @@ -152,6 +157,11 @@ def is_equal(self, other):
'name': 'random number generator seed',
'type': ValueType.integer,
},
'KISAO_0000415': {
'id': 'max_sim_steps',
'name': 'Maximum simulation steps',
'type': ValueType.integer,
},
'KISAO_0000525': {
'id': 'stop_if',
'name': 'stop condition',
Expand All @@ -169,6 +179,11 @@ def is_equal(self, other):
'name': 'random number generator seed',
'type': ValueType.integer,
},
'KISAO_0000415': {
'id': 'max_sim_steps',
'name': 'Maximum simulation steps',
'type': ValueType.integer,
},
'KISAO_0000525': {
'id': 'stop_if',
'name': 'stop condition',
Expand All @@ -186,6 +201,11 @@ def is_equal(self, other):
'name': 'random number generator seed',
'type': ValueType.integer,
},
'KISAO_0000415': {
'id': 'max_sim_steps',
'name': 'Maximum simulation steps',
'type': ValueType.integer,
},
'KISAO_0000525': {
'id': 'stop_if',
'name': 'stop condition',
Expand Down
4 changes: 2 additions & 2 deletions requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
biosimulators_utils[bngl,logging] >= 0.1.118
kisao
biosimulators_utils[bngl,logging] >= 0.1.124
kisao >= 2.29
pandas

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