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 <[email protected]> Co-authored-by: yannikschaelte <[email protected]>
PEtab-dev · Nov 17, 2020 · 167b61b · 167b61b
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diff --git a/README.md b/README.md
@@ -107,10 +107,15 @@ Legend:
 
 ## Using PEtab
 
-If you would like to use PEtab yourself, please have a look at 
-[doc/documentation_data_format.rst](doc/documentation_data_format.rst) or at
-the example models provided in the 
-[benchmark collection](https:/Benchmarking-Initiative/Benchmark-Models-PEtab).
+If you would like to use PEtab yourself, please have a look at:
+
+* [a PEtab tutorial](https://petab.readthedocs.io/en/latest/tutorial.html)
+ going through the individual steps of setting up a parameter estimation
+ problem in PEtab, independently of any specific software
+* [the PEtab format reference](https://petab.readthedocs.io/en/stable/documentation_data_format.html)
+* the example models provided in the
+ [benchmark collection](https:/Benchmarking-Initiative/Benchmark-Models-PEtab).
+* the tutorials provided with each of the softwares supporting PEtab
 
 To convert your existing parameter estimation problem to the PEtab format, you 
 will have to:

diff --git a/doc/compile_tutorial.sh b/doc/compile_tutorial.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# Build a pdflatex document from the tutorial
+
+pandoc tutorial.rst \
+ -o tutorial.pdf \
+ -V geometry:margin=1.5in -V geometry:a4paper -V fontsize=10pt \
+ --toc \
+ --pdf-engine pdflatex
diff --git a/doc/gfx/copasi_simulation.png b/doc/gfx/copasi_simulation.png
diff --git a/doc/gfx/tutorial_data.png b/doc/gfx/tutorial_data.png
diff --git a/doc/gfx/tutorial_model.png b/doc/gfx/tutorial_model.png
diff --git a/doc/index.rst b/doc/index.rst
@@ -6,6 +6,7 @@
  :caption: Data format
 
  Data format <documentation_data_format.rst>
+ tutorial
 
 .. toctree::
  :maxdepth: 3

diff --git a/doc/tutorial.rst b/doc/tutorial.rst
diff --git a/doc/tutorial/Boehm_JProteomeRes2014.yaml b/doc/tutorial/Boehm_JProteomeRes2014.yaml
@@ -0,0 +1,13 @@
+format_version: 1
+parameter_file: parameters.tsv
+problems:
+ - condition_files:
+ - experimental_conditions.tsv
+ measurement_files:
+ - measurement_data.tsv
+ observable_files:
+ - observables.tsv
+ sbml_files:
+ - model_Boehm_JProteomeRes2014.xml
+ visualization_files:
+ - visualization_specification.tsv
diff --git a/doc/tutorial/experimental_conditions.tsv b/doc/tutorial/experimental_conditions.tsv
@@ -0,0 +1,2 @@
+conditionId conditionName Epo_concentration
+epo_stimulation condition1 1.25E-07
diff --git a/doc/tutorial/measurement_data.tsv b/doc/tutorial/measurement_data.tsv
@@ -0,0 +1,49 @@
+observableId simulationConditionId measurement time noiseParameters
+pSTAT5A_rel epo_stimulation 7.901072999 0 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 66.36349397 2.5 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 81.17132392 5 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 94.73030806 10 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 95.11648305 15 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 91.44171655 20 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 91.25709923 30 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 93.67229784 40 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 88.75423282 50 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 85.26970322 60 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 81.13239534 80 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 76.13592848 100 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 65.24805913 120 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 42.59965871 160 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 25.15779754 200 sd_pSTAT5A_rel
+pSTAT5A_rel epo_stimulation 15.4301824 240 sd_pSTAT5A_rel
+pSTAT5B_rel epo_stimulation 4.596533343 0 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 29.63454599 2.5 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 46.04380647 5 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 81.97473362 10 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 80.5716093 15 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 79.03571964 20 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 75.67238037 30 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 71.62471986 40 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 69.06286328 50 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 67.14738432 60 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 60.89947629 80 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 54.80925777 100 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 43.98128998 120 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 29.77145816 160 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 20.08901656 200 sd_pSTAT5B_rel
+pSTAT5B_rel epo_stimulation 10.96184517 240 sd_pSTAT5B_rel
+rSTAT5A_rel epo_stimulation 14.72316822 0 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 33.76234229 2.5 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 36.79985129 5 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 49.71760229 10 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 46.9281201 15 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 47.83657456 20 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 46.92872725 30 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 40.59775294 40 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 43.78366389 50 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 44.45738765 60 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 41.32715926 80 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 41.06273321 100 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 39.23583003 120 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 36.61946054 160 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 34.8937144 200 sd_rSTAT5A_rel
+rSTAT5A_rel epo_stimulation 32.21107716 240 sd_rSTAT5A_rel