Version 12.0 (#299)

* - Update dimensions and units
- Add R script to get the list of dimensions and units.

* Update copyright

* - Update factsheet

* - Add note about modularization

* Edit README

* AI assited wordings

* Part 2 rework

* - Options

* options

* PK-Sim options

* - Implement reviewer suggestions

* - Hints on separate line

* Typo

* - Addressing reviewer comments

* PK-Sim projects

* - Changed order of chapter - Expression Profiles BB comes first

* protein expression rework

* Revert some automatic changes

* - Fix escaping of links

* Do not escape [

* Update part-3/pk-sim-options.md

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

* Rework Individuals

* - Rework populations

* - Compounds rework

* - Continue compounds definition rework

* Remove "Number of individuals per bins" option until clarified

* - PC methods

* - Binding partners

* BuildingBlocks and not Block

* Typo

* - in vivo should not be in italic

* - Remove "(experimental) for species
- Replace "sex" by "gender"
- No inline hints

* - Fix broken listing in hint

* - Replace "sex" by "gender"
- 100 years old for ICRP

* Added link to "Create Individual Algorithm"

* - Clearance processes

* Active transports

* Renal clearance

* - Particle dissolution

* Compound definition rework

* - Grammatical error fix

* Add link to "Inhibition/Induction" section

* Update part-3/pk-sim-creating-populations.md

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

* Update part-3/pk-sim-creating-populations.md

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

* Update part-3/pk-sim-creating-populations.md

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

* Mixed inhibition

* Complete DDI rework

* Update part-3/pk-sim-compounds-defining-inhibition-induction-processes.md

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

* Update part-3/pk-sim-compounds-defining-inhibition-induction-processes.md

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

* Administratin protocols

* Update part-3/pk-sim-administration-protocols.md

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

* - Start events rework

* Events rework

* Add descirption of supersaturation

* Missing space

* Missing space

* - Add section about extracting individuals from a populaton

* - Start formulations rework

* - Rework of formulations

* Simulations rework

* Remove mentioning of sport events

* - Add description of Use as suspension

* Added "Use as suspension" for table formulations

* - Link to import/edit observed data

* Continue rework

* Finish review

* fixed typo

* - Start modularization concept description

* - Continue on morularization concept

* Add module definition

* - Up to "Passive Transports"

* Described merge behavior for PT

* Modularization concept

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* - First steps rework

* Update part-4/first-steps.md

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

* Update part-4/first-steps.md

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

* Update part-4/first-steps.md

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

* Update part-4/first-steps.md

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

* - Implement reviewers comments

* Add sectin for example workflows

* Added link to modularizatoin concept

* Update part-4/example-workflows.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Addressing reviewer comments

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* Update part-4/modularization-concept.md

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

* - Rework of "building block concepts"
- Moved some parts to "model building components" and "setting up simulation"

* Update part-4/building-block-concepts.md

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

* Update part-4/building-block-concepts.md

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

* Update part-4/building-block-concepts.md

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

* Update part-4/building-block-concepts.md

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

* - Added "Options" setting

* Update part-4/building-block-concepts.md

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

* Update part-4/building-block-concepts.md

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

* Update part-4/setting-up-simulation.md

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

* Update part-4/mobi-options.md

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

* - Spatial Strucutre BB descriptoin as a separate section

* Reviewer comments

* Removed options that are not in mobi

* Update part-4/spatial-structures-bb.md

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

* Update part-4/spatial-structures-bb.md

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

* Update SUMMARY.md

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

* - Molecules BB as separate file

* - Continue with molecules bb rework

* Added hint about scale divisors

* Finish molecules rework

* Moved sections

* Update part-4/modularization-concept.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Reactions rework

* Update part-4/model-building-components.md

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

* Fixed weird sentence

* Added description of some options

* Fixing typos

* Moved reactions to a separate file

* add the file..

* Fixed summary

* pt rework

* remove section with molecule-specific passive transports

* - Remove Active Transports from PAssive transports

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Add exapmle how to add active transport process

* Started writing an example for container criteria

* Typo fix

* - Some changes about the definiton of molecule and container observers.

* Events rework

* Rename section to "Observers Building Block"

* Update part-4/model-building-components.md

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

* Start events description

* - Events rework

* Moved one section to a more appropriate place.

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Fixed path

* Update part-4/model-building-components.md

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

* Typo

* Expanded documentation on container criteria.

* Addressing reviewer comments

* In Parent and In Children descritpion

* - Added link to events-bb in summary
- Moved Events content to a separate file

* Add the events file

* Moved content to a separate file

* Moved "Molecules" and "Observers" to separate files

* IC BB rework

* Addressing reviewers comments

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Add a hint

* - Added info on columns of IC BB

* Addressed reviewers comments

* More reviewers comments

* Update part-4/model-building-components.md

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

* Update part-4/model-building-components.md

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

* Replace equation image by math exp

* Move IC BB content to a separate file

---------

Co-authored-by: Pavel Balazki <[email protected]>
Co-authored-by: Copilot <[email protected]>

Author: 3 people

R/get-dimensions-and-units.R

@@ -0,0 +1,24 @@
+library(ospsuite)
+library(xml2)
+
+# Read xml
+dimensionsXML <- xml2::read_xml(system.file("lib", "OSPSuite.Dimensions.xml", package = "ospsuite"))
+dimensionsList <- as_list(dimensionsXML)
+
+outputString <- paste("Dimension", "Base unit", "Deviating default display unit", sep = " | ")
+outputString <- paste(outputString, "\n", paste("---", "---", "---", sep = " | "), sep = "")
+
+# Iterate through nodes
+for (dimension in dimensionsList$DimensionFactory$Dimensions){
+  name <- attr(dimension, "name")
+  baseUnit <- attr(dimension, "baseUnit")
+  displayUnit <- attr(dimension, "defaultUnit")
+  # If no display unit is specified, use the base unit
+  displayUnit <- displayUnit %||% baseUnit
+
+  outputString <- paste(outputString,
+                        paste(name, baseUnit, displayUnit, sep = " | "),
+                        sep = "\n")
+}
+
+cat(outputString)