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dweindlLeonardSchmiesteryannikschaelte
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Add tutorial for creating PEtab files (#488)
* Add tutorial for creating PEtab files * Formatting * Table captions * Lists of fields to real lists * Highlight table headers * Formatting * Image to figure * Added tutorial PEtab files * fixed formatting * Fix yaml formatting. Fix filenames. * punct. * update link * Tutorial link to readme * Added COPASI section to tutorial * formatting, update sim section * Fix empty table cells * E * Break overwide table * fixup * update readme 'using petab' * add pdf generation script * fix docs * increase pdf margin Co-authored-by: LeonardSchmiester <leonard.schmiester@helmholtz-muenchen.de> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com>
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‎README.md‎

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## Using PEtab
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If you would like to use PEtab yourself, please have a look at
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[doc/documentation_data_format.rst](doc/documentation_data_format.rst) or at
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the example models provided in the
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[benchmark collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab).
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If you would like to use PEtab yourself, please have a look at:
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* [a PEtab tutorial](https://petab.readthedocs.io/en/latest/tutorial.html)
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going through the individual steps of setting up a parameter estimation
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problem in PEtab, independently of any specific software
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* [the PEtab format reference](https://petab.readthedocs.io/en/stable/documentation_data_format.html)
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* the example models provided in the
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[benchmark collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab).
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* the tutorials provided with each of the softwares supporting PEtab
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To convert your existing parameter estimation problem to the PEtab format, you
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will have to:

‎doc/compile_tutorial.sh‎

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#!/bin/sh
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# Build a pdflatex document from the tutorial
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pandoc tutorial.rst \
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-o tutorial.pdf \
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-V geometry:margin=1.5in -V geometry:a4paper -V fontsize=10pt \
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--toc \
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--pdf-engine pdflatex

‎doc/gfx/copasi_simulation.png‎

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‎doc/gfx/tutorial_data.png‎

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‎doc/gfx/tutorial_model.png‎

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‎doc/index.rst‎

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:caption: Data format
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Data format <documentation_data_format.rst>
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tutorial
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.. toctree::
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:maxdepth: 3

‎doc/tutorial.rst‎

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‎doc/tutorial/Boehm_JProteomeRes2014.yaml‎

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format_version: 1
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parameter_file: parameters.tsv
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problems:
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- condition_files:
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- experimental_conditions.tsv
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measurement_files:
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- measurement_data.tsv
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observable_files:
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- observables.tsv
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sbml_files:
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- model_Boehm_JProteomeRes2014.xml
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visualization_files:
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- visualization_specification.tsv

‎doc/tutorial/experimental_conditions.tsv‎

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conditionId conditionName Epo_concentration
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epo_stimulation condition1 1.25E-07

‎doc/tutorial/measurement_data.tsv‎

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observableId simulationConditionId 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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