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v2: Update tutorial
Add a short tutorial for PEtab v2 based on the Boehm model (as done for PEtab v1). Closes #627.
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‎doc/index.rst‎

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:caption: PEtab v1
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PEtab v1 specs <v1/documentation_data_format.rst>
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v1/tutorial/tutorial
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Tutorial <v1/tutorial/tutorial>
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v1/software_support
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:caption: PEtab v2
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PEtab v2 draft <v2/documentation_data_format.rst>
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Tutorial <v2/tutorial/tutorial>
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.. toctree::
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:maxdepth: 2

‎doc/v1/tutorial/tutorial.rst‎

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==============
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PEtab tutorial
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==============
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==================
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PEtab 1.0 tutorial
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==================
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.. _Boehm et al. (2014): https://dx.doi.org/10.1021/pr5006923
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‎doc/v2/tutorial/Boehm_JProteomeRes2014.yaml‎

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format_version: 2.0.0
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model_files:
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model:
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location: model_Boehm_JProteomeRes2014.xml
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language: sbml
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parameter_files:
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- parameters.tsv
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experiment_files:
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- experiments.tsv
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condition_files:
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- experimental_conditions.tsv
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observable_files:
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- observables.tsv
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measurement_files:
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- measurement_data.tsv

‎doc/v2/tutorial/experimental_conditions.tsv‎

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conditionId targetId targetValue
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epo_bolus Epo_concentration 1.25E-07

‎doc/v2/tutorial/experiments.tsv‎

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experimentId time conditionId
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epo_stimulation 0.0 epo_bolus

‎doc/v2/tutorial/gfx/copasi_simulation.png‎

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‎doc/v2/tutorial/gfx/tutorial_data.png‎

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‎doc/v2/tutorial/gfx/tutorial_model.png‎

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‎doc/v2/tutorial/measurement_data.tsv‎

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observableId experimentId measurement time noiseParameters
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pSTAT5A_rel epo_stimulation 7.901072999 0 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 66.36349397 2.5 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 81.17132392 5 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 94.73030806 10 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 95.11648305 15 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 91.44171655 20 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 91.25709923 30 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 93.67229784 40 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 88.75423282 50 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 85.26970322 60 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 81.13239534 80 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 76.13592848 100 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 65.24805913 120 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 42.59965871 160 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 25.15779754 200 sd_pSTAT5A_rel
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pSTAT5A_rel epo_stimulation 15.4301824 240 sd_pSTAT5A_rel
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pSTAT5B_rel epo_stimulation 4.596533343 0 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 29.63454599 2.5 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 46.04380647 5 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 81.97473362 10 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 80.5716093 15 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 79.03571964 20 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 75.67238037 30 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 71.62471986 40 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 69.06286328 50 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 67.14738432 60 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 60.89947629 80 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 54.80925777 100 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 43.98128998 120 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 29.77145816 160 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 20.08901656 200 sd_pSTAT5B_rel
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pSTAT5B_rel epo_stimulation 10.96184517 240 sd_pSTAT5B_rel
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rSTAT5A_rel epo_stimulation 14.72316822 0 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 33.76234229 2.5 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 36.79985129 5 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 49.71760229 10 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 46.9281201 15 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 47.83657456 20 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 46.92872725 30 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 40.59775294 40 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 43.78366389 50 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 44.45738765 60 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 41.32715926 80 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 41.06273321 100 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 39.23583003 120 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 36.61946054 160 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 34.8937144 200 sd_rSTAT5A_rel
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rSTAT5A_rel epo_stimulation 32.21107716 240 sd_rSTAT5A_rel

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