Smith_BMCSystBiol2013 (#180)

* add draft implementation

* fix time & model id

* fix concentration vs amount

* fix Ins concentration

* fix conc/amount

* fix scaling factors nominal value

* add insulin injection event, add simulation test

* Update MODEL1212210000_Ins_events.xml

* Update MODEL1212210000_Ins_events.xml

* fixup event

* don't use infinite parameter values

* fix test problem

* fix compartment observables

* add indicator functions for different model compositions

* Update experimentalCondition_Smith_BMCSystBiol2013.tsv

* conditionalize k4, kminus4, k_irs1_basal_syn, fix test conditions

* workaround E2F1

* revert to original model to avoid amount/conc snafu

* ???

* remove null obs

* update version

* fix conditions

* fix conditions

* correct tx rate for 2H

* remove debug stuff, add reference

* add E2F1 condition

* parametrize fig2h fixes

* fix readme

* use URLs instead of copying files

* add readme

* added simulated data file

* fixes + visualization table

* reenable linting

.gitignore

@@ -4,3 +4,4 @@
 __pycache__
 *egg-info
 src/python/build
+Benchmark-Models/Smith_BMCSystBiol2013/amici_models/*

Benchmark-Models/Smith_BMCSystBiol2013/README.md

@@ -0,0 +1,29 @@
+# Implementation details of the Smith_BMCSystBiol2013 benchmark problem
+
+## Description
+This benchmark problem was implemented using information from the original publication [[1]], 
+the respective supplementary material as well as the accompanying github repository [[2]]. All
+processing that was necessary to obtain the benchmark problem was performed using the `generate_petab.py`
+script contained in this folder, which provides a detailed description of all processing steps.
+
+## Shortcomings
+The resulting PEtab implementation does not capture all steps of the original work, for example 
+tuning of parameters to obtain stable cycles under certain physiological conditions was omitted 
+as this cannot be faithfully represented in PEtab. However, essential features of the model and 
+training data are captured, so it is fair to claim this actually recapitulates a biological problem.
+
+## Validation
+The implementation was validated by comparing the results to original simulation results using the
+test problem provided in the folder `sim_test`, which uses simulation files provided in the GitHub
+directory [[2]] as "measurements". Results were validated using AMICI, which yielded overall 
+satisfactory agreement (rtol=1e-1/1e-2, atol=1e-3). Only notable differences are in simulations for 
+figure 2H, in species related to SOD2/InR transcription. It looks like transcription rates are off 
+by a factor 0.8 and 0.4 resepectively (can be tested by setting `ATTEMPT_FIX_FIGURE_2H` to `True` 
+in `generate_petab.py`) and translation/degradation rate is off by a factor 0.9 for InR. 
+The source of these discrepancies is unclear and are likely due to undocumented changes to the model
+(some of the other parameters reported in the simulation files also vary, but transcription/translation
+specific rates are not reported as they are implemented as local parameters. So this information is lost.).
+However, the impact on remainder of model seems negligible.
+
+[1]: https://doi.org/10.1186/1752-0509-7-41
+[2]: https://github.com/graham1034/Smith2012_insulin_signalling

Benchmark-Models/Smith_BMCSystBiol2013/Smith_BMCSystBiol2013.yaml

@@ -0,0 +1,13 @@
+parameter_file: parameters_Smith_BMCSystBiol2013.tsv
+format_version: 1
+problems:
+- condition_files:
+  - experimentalCondition_Smith_BMCSystBiol2013.tsv
+  measurement_files:
+  - measurementData_Smith_BMCSystBiol2013.tsv
+  sbml_files:
+  - model_Smith_BMCSystBiol2013.xml
+  observable_files:
+  - observables_Smith_BMCSystBiol2013.tsv
+  visualization_files:
+  - visualizationSpecification_Smith_BMCSystBiol2013.tsv

Benchmark-Models/Smith_BMCSystBiol2013/experimentalCondition_Smith_BMCSystBiol2013.tsv

@@ -0,0 +1,36 @@
+conditionId	extracellular_ROS	Ins	t_ins	indicator_jnk	indicator_foxo	k4	kminus4	k_irs1_basal_syn	E2F1
+figure3B__0_0__0_0	0.0	5.0	240.0	1.0	1.0	0.000333333	0.003	130.0	150.0
+figure3B__60_0__0_0	25000.0	5.0	240.0	1.0	1.0	0.000333333	0.003	130.0	150.0
+figure2C__0_0__500000	0.0	500000.0	15.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2D__0_0__500000	0.0	500000.0	15.0	0.0	0.0	0.000333333	0.003	130.0	
+figure3C__0_0__0_0	0.0	5000.0	960.0	1.0	1.0	0.000333333	0.003	130.0	150.0
+figure3C__5_0__0_0	25000.0	5000.0	960.0	1.0	1.0	0.000333333	0.003	130.0	150.0
+figure3C__10_0__0_0	50000.0	5000.0	960.0	1.0	1.0	0.000333333	0.003	130.0	150.0
+figure3C__20_0__0_0	100000.0	5000.0	960.0	1.0	1.0	0.000333333	0.003	130.0	150.0
+figure3C__50_0__0_0	250000.0	5000.0	960.0	1.0	1.0	0.000333333	0.003	130.0	150.0
+figure2B__0_0__1em14	0.0	0.049965999999999997	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__1_5em11	0.0	74.949	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__2em11	0.0	99.93199999999999	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__3_5em11	0.0	174.881	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__4_5em11	0.0	224.847	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__5em11	0.0	249.83	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__1_3em10	0.0	649.558	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__1_5em10	0.0	749.49	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__2em10	0.0	999.32	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__3_1em10	0.0	1548.9460000000001	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__4em10	0.0	1998.64	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__5em10	0.0	2498.3	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__1em09	0.0	4996.6	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__1_5em09	0.0	7494.9	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__2em09	0.0	9993.2	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__3em09	0.0	14989.8	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__5em09	0.0	24983.0	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__1em08	0.0	49966.0	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__1_5em08	0.0	74949.0	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__3em08	0.0	149898.0	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__5em08	0.0	249830.0	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__1em07	0.0	499660.0	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__3em07	0.0	1498980.0	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure2B__0_0__1em06	0.0	4996600.0	30.0	0.0	0.0	0.000333333	0.003	130.0	
+figure3B__0_0__5_0	0.0	50000.0	240.0	1.0	1.0	0.000333333	0.003	130.0	150.0
+figure3B__60_0__5_0	25000.0	50000.0	240.0	1.0	1.0	0.000333333	0.003	130.0	150.0