work on sensitivity

Author: matthiaskoenig

src/sbmlsim/sensitivity/example/sensitivity_example.py

@@ -121,7 +121,9 @@ def _sensitivity_parameters() -> list[SensitivityParameter]:
     )
 
     sensitivity_path = Path(__file__).parent / "results"
-    console.print(SensitivityParameter.parameters_to_df(sensitivity_parameters))
+    df = SensitivityParameter.parameters_to_df(sensitivity_parameters)
+    df.to_csv(sensitivity_path / "parameters.tsv", sep="\t", index=False)
+    console.print(df)
 
     settings = {
         "cache_results": True,
@@ -166,8 +168,8 @@ def _sensitivity_parameters() -> list[SensitivityParameter]:
     )
 
     sas = [
-        # sa_local,
-        sa_sampling,
+        sa_local,
+        # sa_sampling,
         # sa_sobol,
         # sa_fast,
     ]

src/sbmlsim/sensitivity/example/simple_chain.md

@@ -1,8 +1,5 @@
 # model: simple_chain
-
-Autogenerated ODE System from SBML
-with [sbmlutils](https://github.com/matthiaskoenig/sbmlutils).
-
+Autogenerated ODE System from SBML with [sbmlutils](https://github.com/matthiaskoenig/sbmlutils).
 ```
 time: [-]
 substance: [-]
@@ -13,26 +10,27 @@ length: [-]
 ```
 
 ## Parameters `p`
-
 ```
-k1 = 1.0  # [-]   
-liver = 1.0  # [-]   
+Vli = 1.0  # [-] liver volume  
+k1 = 1.0  # [-] rate S1 ➞ S2 conversion  
+k2 = 1.0  # [-] rate S2 ➞ S3 conversion  
 ```
 
 ## Initial conditions `x0`
-
 ```
-S1 = 1.0  # [-/-] S1 in liver  
-S2 = 0.0  # [-/-] S2 in liver  
+S1 = 1.0  # [-/-] S1 in Vli  
+S2 = 0.0  # [-/-] S2 in Vli  
+S3 = 0.0  # [-/-] S3 in Vli  
 ```
 
 ## ODE system
-
 ```
 # y
-R1 = k1 * S1  # [-/-]   
+R1 = k1 * S1  # [-/-] R1: S1 ➞ S2 conversion  
+R2 = k2 * S2  # [-/-] R2: S2 ➞ S3 conversion  
 
 # odes
-d S1/dt = -R1 / liver  # [-/-/-] S1  
-d S2/dt = R1 / liver  # [-/-/-] S2  
-```
+d S1/dt = -R1 / Vli  # [-/-/-] S1  
+d S2/dt = R1 / Vli - R2 / Vli  # [-/-/-] S2  
+d S3/dt = R2 / Vli  # [-/-/-] S3  
+```

src/sbmlsim/sensitivity/example/simple_chain.py

@@ -77,5 +77,7 @@
         # TODO: antimony & markdown
 
     )
-
+    from sbmlutils.converters import odefac
+    ode_factory = odefac.SBML2ODE.from_file(sbml_file=results.sbml_path)
+    ode_factory.to_markdown(md_file=results.sbml_path.parent / f"{results.sbml_path.stem}.md")
     visualize_sbml(sbml_path=results.sbml_path)

src/sbmlsim/sensitivity/example/simple_chain.xml

@@ -29,10 +29,10 @@
             </rdf:Bag>
           </dcterms:creator>
           <dcterms:created rdf:parseType="Resource">
-            <dcterms:W3CDTF>2026-01-26T22:23:01Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2026-01-27T12:24:14Z</dcterms:W3CDTF>
           </dcterms:created>
           <dcterms:modified rdf:parseType="Resource">
-            <dcterms:W3CDTF>2026-01-26T22:23:01Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2026-01-27T12:24:14Z</dcterms:W3CDTF>
           </dcterms:modified>
         </rdf:Description>
       </rdf:RDF>