From 13f8504549686029171b2f84b60fbdc1010f4bff Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Fri, 20 Nov 2020 11:33:59 +0100 Subject: [PATCH 1/6] Prettify reaction arrows --- doc/tutorial.rst | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/tutorial.rst b/doc/tutorial.rst index 50f80ebb..ef188287 100644 --- a/doc/tutorial.rst +++ b/doc/tutorial.rst @@ -44,15 +44,15 @@ tutorial is available `online 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 From 1c3c95ad4ca8e1ee5e5f87d1532840472804c2b5 Mon Sep 17 00:00:00 2001 From: LeonardSchmiester Date: Fri, 20 Nov 2020 13:51:10 +0100 Subject: [PATCH 2/6] added Erikas comments --- doc/tutorial.rst | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/doc/tutorial.rst b/doc/tutorial.rst index ef188287..51b76cae 100644 --- a/doc/tutorial.rst +++ b/doc/tutorial.rst @@ -87,10 +87,7 @@ 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 parmameter 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: @@ -189,16 +186,13 @@ 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 + 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 --------------------------- From 2259cb5b589574cce0f029fd2e0b2145a3aa7e3b Mon Sep 17 00:00:00 2001 From: LeonardSchmiester Date: Fri, 20 Nov 2020 14:38:16 +0100 Subject: [PATCH 3/6] Simons comments --- doc/tutorial.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/tutorial.rst b/doc/tutorial.rst index 51b76cae..b51f2a0e 100644 --- a/doc/tutorial.rst +++ b/doc/tutorial.rst @@ -79,7 +79,7 @@ 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 @@ -90,7 +90,7 @@ In the problem considered here, the relevant parameter is 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 parmameter 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``. @@ -187,7 +187,7 @@ file: * *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. + 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 From 0846bf560eb162608a3fbb4f1a98ffe536204632 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Fri, 20 Nov 2020 14:45:01 +0100 Subject: [PATCH 4/6] Highlight URLs in pdf --- doc/compile_tutorial.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/compile_tutorial.sh b/doc/compile_tutorial.sh index e0972310..1d3040f8 100644 --- a/doc/compile_tutorial.sh +++ b/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 From a5806221ecbb11403502e56db7667e51dc50287d Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Fri, 20 Nov 2020 14:45:19 +0100 Subject: [PATCH 5/6] chmod +x compile_tutorial.sh --- doc/compile_tutorial.sh | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 doc/compile_tutorial.sh diff --git a/doc/compile_tutorial.sh b/doc/compile_tutorial.sh old mode 100644 new mode 100755 From c057e07db817eda6d8478ccd9519d640c6705dbf Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Fri, 20 Nov 2020 14:46:59 +0100 Subject: [PATCH 6/6] rewrap, typo --- doc/tutorial.rst | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/doc/tutorial.rst b/doc/tutorial.rst index b51f2a0e..4b4781a8 100644 --- a/doc/tutorial.rst +++ b/doc/tutorial.rst @@ -87,7 +87,11 @@ 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. 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 parmameter table. However, the benefit of specifying it in the condition table is, that it allows 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 looks as follows: