feat: completed specifications of algorithm parameters; added BioSimu…

…lators interpretation of SED-ML
biosimulators · Aug 23, 2021 · 9c66775 · 9c66775
1 parent 37694a0
commit 9c66775
Show file tree

Hide file tree

Showing 15 changed files with 4,395 additions and 105 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -14,7 +14,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.14"
+ARG VERSION="0.1.15"
 ARG SIMULATOR_VERSION="2.2.0"
 
 # metadata

diff --git a/biosimulators.json b/biosimulators.json
@@ -333,10 +333,22 @@
  {
  "kisaoId": {
  "namespace": "KISAO",
- "id": "KISAO_0000656"
+ "id": "KISAO_0000671"
  },
- "id": "variable_step_size",
- "name": "Adaptive time steps",
+ "id": "stiff",
+ "name": "Stiff",
+ "type": "boolean",
+ "value": "true",
+ "recommendedRange": null,
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
+ },
+ {
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000670"
+ },
+ "id": "multiple_steps",
+ "name": "Multiple steps",
  "type": "boolean",
  "value": "false",
  "recommendedRange": null,
@@ -381,6 +393,67 @@
  }
  ]
  },
+ {
+ "id": "euler",
+ "name": "Forward Euler method",
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000030"
+ },
+ "modelingFrameworks": [{
+ "namespace": "SBO",
+ "id": "SBO_0000293"
+ }],
+ "modelFormats": [{
+ "namespace": "EDAM",
+ "id": "format_2585",
+ "version": null,
+ "supportedFeatures": []
+ }],
+ "simulationFormats": [{
+ "namespace": "EDAM",
+ "id": "format_3685",
+ "version": null,
+ "supportedFeatures": []
+ }],
+ "archiveFormats": [{
+ "namespace": "EDAM",
+ "id": "format_3686",
+ "version": "1",
+ "supportedFeatures": []
+ }],
+ "parameters": [],
+ "dependentDimensions": [{
+ "namespace": "SIO",
+ "id": "SIO_000418"
+ }],
+ "dependentVariableTargetPatterns": [{
+ "variables": "species concentrations",
+ "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species"
+ },
+ {
+ "variables": "parameter values",
+ "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value"
+ },
+ {
+ "variables": "reaction fluxes",
+ "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction"
+ },
+ {
+ "variables": "compartment sizes",
+ "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment"
+ }
+ ],
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"],
+ "dependencies": [{
+ "name": "libRoadRunner",
+ "version": null,
+ "required": true,
+ "freeNonCommercialLicense": true,
+ "url": "http://libroadrunner.org/"
+ }],
+ "citations": []
+ },
  {
  "id": "runge_kutta_4",
  "name": "Runge-Kutta fourth order method",
@@ -474,33 +547,36 @@
  "parameters": [{
  "kisaoId": {
  "namespace": "KISAO",
- "id": "KISAO_0000656"
+ "id": "KISAO_0000485"
  },
- "name": "Adaptive time steps",
- "type": "boolean",
- "value": "true",
+ "id": "minimum_time_step",
+ "name": "Minimum time step",
+ "type": "float",
+ "value": "1e-12",
  "recommendedRange": null,
  "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
  },
  {
  "kisaoId": {
  "namespace": "KISAO",
- "id": "KISAO_0000485"
+ "id": "KISAO_0000467"
  },
- "name": "Minimum time step",
+ "id": "maximum_time_step",
+ "name": "Maximum time step",
  "type": "float",
- "value": "1e-12",
+ "value": "1.0",
  "recommendedRange": null,
  "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
  },
  {
  "kisaoId": {
  "namespace": "KISAO",
- "id": "KISAO_0000467"
+ "id": "KISAO_0000597"
  },
- "name": "Maximum time step",
+ "id": "epsilon",
+ "name": "Epsilon",
  "type": "float",
- "value": "1.0",
+ "value": "0.000000000001",
  "recommendedRange": null,
  "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
  }
@@ -537,7 +613,7 @@
  "citations": []
  },
  {
- "id": "gillespie_direct_ssa",
+ "id": "gillespie",
  "name": "Gillespie direct method of the Stochastic Simulation Algorithm (SSA)",
  "kisaoId": {
  "namespace": "KISAO",
@@ -584,53 +660,22 @@
  "namespace": "KISAO",
  "id": "KISAO_0000488"
  },
+ "id": "seed",
  "name": "Random number generator seed",
  "type": "integer",
- "value": "0",
- "recommendedRange": null,
- "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
- },
- {
- "kisaoId": {
- "namespace": "KISAO",
- "id": "KISAO_0000656"
- },
- "name": "Adaptive time steps",
- "type": "boolean",
- "value": "true",
- "recommendedRange": null,
- "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
- },
- {
- "kisaoId": {
- "namespace": "KISAO",
- "id": "KISAO_0000332"
- },
- "name": "Initial time step",
- "type": "float",
  "value": null,
  "recommendedRange": null,
  "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
  },
  {
  "kisaoId": {
  "namespace": "KISAO",
- "id": "KISAO_0000485"
+ "id": "KISAO_0000673"
  },
- "name": "Minimum time step",
- "type": "float",
- "value": null,
- "recommendedRange": null,
- "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
- },
- {
- "kisaoId": {
- "namespace": "KISAO",
- "id": "KISAO_0000467"
- },
- "name": "Maximum time step",
- "type": "float",
- "value": null,
+ "id": "nonnegative",
+ "name": "Skip reactions which would result in negative species amounts",
+ "type": "boolean",
+ "value": "false",
  "recommendedRange": null,
  "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
  }
@@ -723,6 +768,7 @@
  "namespace": "KISAO",
  "id": "KISAO_0000209"
  },
+ "id": "relative_tolerance",
  "name": "Relative tolerance",
  "type": "float",
  "value": "1e-12",
@@ -734,6 +780,7 @@
  "namespace": "KISAO",
  "id": "KISAO_0000486"
  },
+ "id": "maximum_iterations",
  "name": "Maximum number of iterations",
  "type": "integer",
  "value": "100",
@@ -745,11 +792,120 @@
  "namespace": "KISAO",
  "id": "KISAO_0000487"
  },
+ "id": "minimum_damping",
  "name": "Minimum damping factor",
  "type": "float",
  "value": "1e-20",
  "recommendedRange": null,
  "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
+ },
+ {
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000674"
+ },
+ "id": "allow_presimulation",
+ "name": "Presimulate",
+ "type": "boolean",
+ "value": "false",
+ "recommendedRange": null,
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
+ },
+ {
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000677"
+ },
+ "id": "presimulation_maximum_steps",
+ "name": "Maximum number of steps for presimulation",
+ "type": "integer",
+ "value": "100",
+ "recommendedRange": null,
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
+ },
+ {
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000680"
+ },
+ "id": "presimulation_time",
+ "name": "Amount of time to presimulate",
+ "type": "float",
+ "value": "100",
+ "recommendedRange": null,
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
+ },
+ {
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000682"
+ },
+ "id": "allow_approx",
+ "name": "Whether to find an approximate solution if an exact solution could not be found",
+ "type": "boolean",
+ "value": "false",
+ "recommendedRange": null,
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
+ },
+ {
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000683"
+ },
+ "id": "approx_tolerance",
+ "name": "Tolerance for finding an approximate solution",
+ "type": "float",
+ "value": "0.000001",
+ "recommendedRange": null,
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
+ },
+ {
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000678"
+ },
+ "id": "approx_maximum_steps",
+ "name": "Maximum number of steps for finding an approximate solution",
+ "type": "integer",
+ "value": "10000",
+ "recommendedRange": null,
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
+ },
+ {
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000679"
+ },
+ "id": "approx_time",
+ "name": "Maximum amount of time to spend finding finding an approximate solution",
+ "type": "float",
+ "value": "10000",
+ "recommendedRange": null,
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
+ },
+ {
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000675"
+ },
+ "id": "broyden_method",
+ "name": "Broyden method",
+ "type": "integer",
+ "value": "0",
+ "recommendedRange": null,
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
+ },
+ {
+ "kisaoId": {
+ "namespace": "KISAO",
+ "id": "KISAO_0000676"
+ },
+ "id": "linearity",
+ "name": "Degree of linearity of the systen",
+ "type": "integer",
+ "value": "3",
+ "recommendedRange": null,
+ "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
  }
  ],
  "dependentDimensions": [],

diff --git a/biosimulators_tellurium/__init__.py b/biosimulators_tellurium/__init__.py
@@ -7,7 +7,7 @@
 __all__ = [
  '__version__',
  'get_simulator_version',
- # 'exec_sed_task',
+ 'exec_sed_task',
  'exec_sedml_docs_in_combine_archive',
 ]