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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
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‎.gitignore‎

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__pycache__
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*egg-info
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src/python/build
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Benchmark-Models/Smith_BMCSystBiol2013/amici_models/*

‎Benchmark-Models/Smith_BMCSystBiol2013/README.md‎

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

‎Benchmark-Models/Smith_BMCSystBiol2013/Smith_BMCSystBiol2013.yaml‎

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

‎Benchmark-Models/Smith_BMCSystBiol2013/experimentalCondition_Smith_BMCSystBiol2013.tsv‎

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

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