Update tutorial (#489)

* Prettify reaction arrows

* added Erikas comments

* Simons comments

* Highlight URLs in pdf

* chmod +x compile_tutorial.sh

* rewrap, typo

Co-authored-by: LeonardSchmiester <[email protected]>

doc/compile_tutorial.sh

@@ -5,5 +5,6 @@
 pandoc tutorial.rst \
  -o tutorial.pdf \
  -V geometry:margin=1.5in -V geometry:a4paper -V fontsize=10pt \
+ -V urlcolor=cyan \
  --toc \
  --pdf-engine pdflatex

doc/tutorial.rst

@@ -44,15 +44,15 @@ tutorial is available `online <https:/PEtab-dev/PEtab/tree/b50d000a5
  == ========================== =============================================
  ID Reaction Rate law
  == ========================== =============================================
- R1 2 STAT5A -> pApA cyt \* BaF3_Epo \* STAT5A^2 \* k_phos
- R2 STAT5A + STAT5B -> pApB cyt \* BaF3_Epo \* STAT5A \* STAT5B \* k_phos
- R3 2 STAT5B -> pBpB cyt \* BaF3_Epo \* STAT5B^2 \* k_phos
- R4 pApA -> nucpApA cyt \* k_imp_homo \* pApA
- R5 pApB -> nucpApB cyt \* k_imp_hetero \* pApB
- R6 pBpB -> nucpBpB cyt \* k_imp_homo \* pBpB
- R7 nucpApA -> 2 STAT5A nuc \* k_exp_homo \* nucpApA
- R8 nucpApB -> STAT5A + STAT5B nuc \* k_exp_hetero \* nucpApB
- R9 nucpBpB -> 2 STAT5B nuc \* k_exp_homo \* nucpBpB
+ R1 2 STAT5A → pApA  cyt \* BaF3_Epo \* STAT5A^2 \* k_phos
+ R2 STAT5A + STAT5B → pApB  cyt \* BaF3_Epo \* STAT5A \* STAT5B \* k_phos
+ R3 2 STAT5B → pBpB  cyt \* BaF3_Epo \* STAT5B^2 \* k_phos
+ R4 pApA → nucpApA  cyt \* k_imp_homo \* pApA
+ R5 pApB → nucpApB  cyt \* k_imp_hetero \* pApB
+ R6 pBpB → nucpBpB  cyt \* k_imp_homo \* pBpB
+ R7 nucpApA → 2 STAT5A  nuc \* k_exp_homo \* nucpApA
+ R8 nucpApB → STAT5A + STAT5B  nuc \* k_exp_hetero \* nucpApB
+ R9 nucpBpB → 2 STAT5B  nuc \* k_exp_homo \* nucpBpB
  == ========================== =============================================
 
 2. Linking model and measurements
@@ -79,21 +79,22 @@ experimental conditions under which a measurement was performed.
 2.1 Specifying experimental conditions
 --------------------------------------
 
-The measurements were collected under the same experimental condition,
+All measurements were collected under the same experimental condition,
 which is a stimulation with Epo. This is specified in the experimental
 condition PEtab file, a tab-separated values (TSV) file\ [#f1]_,
 by providing a condition identifier and listing all condition-specific
 parameters and their respective values.
 
 In the problem considered here, the relevant parameter is
 ``Epo_concentration`` which we want to set to a value of 1.25E-7, as the
-only condition-specific parameter. In our example we include data from
-only one single experiment, so we would not need to specify it here, but
-could set the value in the model or in the parameter table. However,
-having it would allow us to easily add measurements from other
+only condition-specific parameter. Since in this example we include data from
+only one single experiment, it would not be necessary to specify the condition
+parameter here, but instead the value could have been also set in the model or
+in the parameter table. However, the benefit of specifying it in the condition
+table is, that it allows us to easily add measurements from other
 experiments performed with different Epo concentrations later on.
 
-The condition table would look as follows:
+The condition table looks as follows:
 
 .. table:: Conditions table ``experimental_conditions.tsv``.
 
@@ -189,16 +190,13 @@ file:
  containing any form of STAT5A.
 
 * *noiseFormula* is used to describe the formula for the measurement
- noise. Together with *noiseDistribution*\ it defines the noise model. In
- this example, we assume additive normally distributed measurement noise.
+ noise. Together with *noiseDistribution*, it defines the noise model. In
+ this example, we assume additive, normally distributed measurement noise.
  In this scenario, ``noiseParameter1_{observableId}`` is the standard
  deviation of the measurement noise. Parameters following this naming
  scheme are expected to be overridden in a measurement-specific manner in
  the *noiseParameters* column of the measurement table (see below).
 
-* *observableTransformation* defines the scale in which model observable
- and measurement data are compared. Here, we assume a linear scale. Other
- transformations, such as log10 can also be used.
 
 2.3 Specifying measurements
 ---------------------------