Access models in BioModels.

Author: joseph-hellerstein

notebooks/evaluating_autoencoders.ipynb

@@ -1037,8 +1037,9 @@
     }
    ],
    "source": [
-    "PCA_RUNNER = ModelRunnerPCA(n_components=2, random_state=42)\n",
-    "CELL_CYCLE_RUNNER_PCA = plotSimulationFit(CELL_CYCLE_DF, offset=20, untrained_runner=PCA_RUNNER)"
+    "url = \"https://www.ebi.ac.uk/biomodels/services/download/get-files/MODEL2004140001/3/Garde2020.xml\"\n",
+    "runner = ModelRunnerUMAP.makeFromSBML(url, selections=['Gp', 'Gi', 'A'], num_epoch=5)\n",
+    "_ = runner.plotSimulationFit(is_plot=IS_PLOT, antimony_model=\"Sequential\")"
    ]
   },
   {

src/autoencodersb/model_runner.py

@@ -302,8 +302,8 @@ def plotSimulationFit(self,
                 plt.show()
 
     @classmethod
-    def makeFromAntimony(cls,
-            antimony_str: str,
+    def makeFromSBML(cls,
+            model_str: str,
             reduced_dimension: int = 2,
             start_time: int = 0,
             end_time: int = 10,
@@ -312,7 +312,7 @@ def makeFromAntimony(cls,
             **runner_kwargs) -> 'ModelRunner':
         """Creates a ModelRunnerUMAP from an Antimony string and fits the model
         Args:
-            antimony_str (str): Antimony string defining the model.
+            model_str (str): Antimony or url string defining the model.
             reduced_dimension (int): The reduced dimension for the UMAP model.
             start_time (int): The start time for the simulation.
             end_time (int): The end time for the simulation.
@@ -325,7 +325,10 @@ def makeFromAntimony(cls,
         Returns:
             ModelRunnerUMAP
         """
-        rr = te.loada(antimony_str)
+        if "http" in model_str:
+            rr = te.loadSBMLModel(model_str)
+        else:
+            rr = te.loada(model_str)
         data_arr = rr.simulate(start_time, end_time, num_point)
         if selections is not None:
             num_input_feature = len(selections)

tests/test_model_runner.py

@@ -76,7 +76,7 @@ def makeFromAntimony(self, cls, num_epoch=5) -> ModelRunner:
         D = 0
         E = 0
         """
-        runner = cls.makeFromAntimony(ant_str, selections=["B", "C", "D"], num_epoch=num_epoch)
+        runner = cls.makeFromSBML(ant_str, selections=["B", "C", "D"], num_epoch=num_epoch)
         self.assertIsInstance(runner, cls)
         self.assertGreater(len(runner.train_runner_result.losses), 0)  # type: ignore
         return runner
@@ -92,6 +92,10 @@ def testPlotSimulationFit(self):
             return
         runner = self.makeFromAntimony(ModelRunnerUMAP, num_epoch=10)
         _ = runner.plotSimulationFit(is_plot=IS_PLOT, antimony_model="Sequential")
+        #
+        url = "https://www.ebi.ac.uk/biomodels/services/download/get-files/MODEL2004140001/3/Garde2020.xml"
+        runner = ModelRunnerUMAP.makeFromSBML(url, selections=['Gp', 'Gi', 'A'], num_epoch=10)
+        _ = runner.plotSimulationFit(is_plot=IS_PLOT, antimony_model="Sequential")
 
 if __name__ == '__main__':
     unittest.main()