Santiago Ospina De Los Ríos · Santiago Ospina De Los Ríos · Santiago Ospina De Los Ríos · Santiago Ospina De Los Ríos · Santiago Ospina De Los Ríos · Santiago Ospina De Los Ríos
--- a/.ci/test
+++ b/.ci/test
@@ -21,7 +21,7 @@ SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 source $SCRIPT_DIR/util

 TEST_SOURCEDIR=${SCRIPT_DIR}/../test
-TUTORIAL_SOURCEDIR=${SCRIPT_DIR}/../doc
+DOCS_SOURCEDIR=${SCRIPT_DIR}/../doc

 print_opts_file() {
  cat "${DUNE_OPTIONS_FILE}"
@@ -74,9 +74,9 @@ eval cmake $RELEASE_CMAKE_FLAGS $TEST_SOURCEDIR
 cmake --build . --target build_system_tests
 ctest -j4 -L "system" --output-on-failure

-echo $GREEN "============================ Tutorial Tests ============================" $RESET
+echo $GREEN "============================ Documentation Tests ============================" $RESET

-BUILD_PATH=/tmp/build-system-tutorials
+BUILD_PATH=/tmp/build-docs-tests
 [[ -d ${BUILD_PATH} ]] && ONFAILURE_MESSAGE+="the folder '${BUILD_PATH}' should not exist prior running this script\n" && exit 1
 mkdir $BUILD_PATH && cd $BUILD_PATH

@@ -84,10 +84,10 @@ if [[ -n "$DUNE_OPTIONS_FILE" ]]; then
  RELEASE_CMAKE_FLAGS="$(. $DUNE_OPTIONS_FILE; eval echo \$CMAKE_FLAGS)"
 fi

-echo "cmake $RELEASE_CMAKE_FLAGS $TUTORIAL_SOURCEDIR"
-eval cmake $RELEASE_CMAKE_FLAGS $TUTORIAL_SOURCEDIR
-cmake --build . --target build_tutorial_tests
-ctest -j4 -L "tutorial" --output-on-failure
+echo "cmake $RELEASE_CMAKE_FLAGS $DOCS_SOURCEDIR"
+eval cmake $RELEASE_CMAKE_FLAGS $DOCS_SOURCEDIR
+cmake --build . --target build_docs_tests
+ctest -j4 -L "docs" --output-on-failure

 cd $SCRIPT_PATH
 trap cleanup EXIT
--- a/.gitattributes
+++ b/.gitattributes
 test/data/** filter=lfs diff=lfs merge=lfs -text
+*.pdf filter=lfs diff=lfs merge=lfs -text
+doc/joss/cardiac_ep.png filter=lfs diff=lfs merge=lfs -text
--- a/.gitignore
+++ b/.gitignore
@@ -23,6 +23,7 @@ doc/docusaurus/build
 # Generated files
 doc/docusaurus/.docusaurus
 doc/docusaurus/.cache-loader
+doc/docusaurus/static/doxygen/

 doc/docusaurus/npm-debug.log*
 doc/docusaurus/yarn-debug.log*
@@ -37,3 +38,7 @@ test/build/
 # editor files
 *.swo
 *.swp
+
+doc/joss/paper.jats
+
+doc/joss/media/
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -25,10 +25,10 @@ variables:
  PACKAGE_REGISTRY: ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/generic/dune-copasi
  MASTER_IMAGE: debian:bookworm
  BASE_IMAGE_VERSION:
-    value: "v2.0.1-git"
+    value: "v2.0.2-git"
    options:
-      - "v2.0.1-git"        # Main dependecy base image
-      - "v2.0.1-git-tmp"    # Temporary (one time testing)
+      - "v2.0.2-git"        # Main dependecy base image
+      - "v2.0.2-git-tmp"    # Temporary (one time testing)
    description: "Key to tag images in the registry. Use '*-tmp' key to try out changes that need to rebild the dependencies image"
  FORCE_REBUILD_BASE_IMAGE:
    value: "false"
@@ -187,7 +187,7 @@ codespell:
  image: ${DEPENDENCIES_IMAGE}
  script:
  - codespell
-    --skip="./doc/docusaurus/yarn.lock,./.git/**/*"
+    --skip="./doc/docusaurus/yarn.lock,./.git/**/*,./doc/joss/paper.bib"
    --ignore-words-list="warn"

 config_format:
@@ -294,7 +294,7 @@ deploy_wasm:debian_emscripten:
 deploy:documentation:
  image: ${DEPENDENCIES_IMAGE}
  variables:
-    <<: *debian_emscripten
+    <<: *debian_base
    GIT_STRATEGY: none
  stage: deploy
  script:
@@ -308,3 +308,36 @@ deploy:documentation:
    - !reference [.deploy_rules, rules]
    - changes:
      - doc/**/*
+
+build:doxygen:
+  <<: *update_version
+  image: ${DEPENDENCIES_IMAGE}
+  variables:
+    <<: *debian_clang
+  stage: build
+  script:
+    - |
+      cd doc/doxygen
+      cmake -S . -B build
+      cmake --build build
+      cd build/html/
+      zip -r doxygen.zip ./*
+  rules:
+    - !reference [.build_rules, rules]
+  artifacts:
+    paths:
+      - doc/doxygen/build/html/doxygen.zip
+
+deploy:doxygen:
+  image: ${DEPENDENCIES_IMAGE}
+  variables:
+    <<: *debian_clang
+  stage: deploy
+  script:
+    - |
+      VERSION=$(./util/version_handler.py --replace-prerelease="git")
+      curl --header "JOB-TOKEN: ${CI_JOB_TOKEN}" --upload-file doc/doxygen/build/html/doxygen.zip "${PACKAGE_REGISTRY}/${VERSION}/dune-copasi-doxygen.zip"
+  dependencies:
+    - build:doxygen
+  rules:
+    - !reference [.deploy_rules, rules]
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -28,12 +28,30 @@ Types of changes

 ## [Unreleased] ([git-diff][Unreleased-diff])

+### Added
+
+ - Add experimental support for moving domains !205
+ - Enable super builds for simpler installation instructions !230
+ - Numerical jacobians !204
+
+### Changed
+
+ - Update ExprTk to 0.0.3 !237
+ - Improve documentation !210 !211 !212 !213 !214 !215 !216 !217 !218 !219 !220 !221 !222 !223 !224 !225 !226 !227 !228
+
+### Fixed
+
+ - Wrong configuration of higher order polynomial degrees !236
+ - Memory leak on the UMFPack solver !235
+ - Outflow derivatives set its prefix incorrectly !229
+ - Improve muParser search with CMake !203 !232
+
 ## [2.0.1] ([git-diff][2.0.1-diff]) - 2024-04-22

 ### Fixed

-* Fix memory errors on Blocked Jacobi !197
-* Remove Muparser invalid assertions !196
+ - Fix memory errors on Blocked Jacobi !197
+ - Remove Muparser invalid assertions !196

 ## [2.0.0] ([git-diff][2.0.0-diff]) - 2024-03-26

@@ -41,22 +59,22 @@ _**Note**: This version is a complete re-write of the library based on a custom

 ### Refactor

-* Allows different parser backends: [muparser](https://beltoforion.de/en/muparser/), [exprtk](https://github.com/ArashPartow/exprtk), and [SymEngine](https://github.com/symengine/symengine) !83
-* Adds constants, (lambda) function, and [random fields](https://github.com/parafields/parafields-core) definitions within the parsers !83
-* Re-implementation of local operator: huge performance improvements !83
-* Adds tensor cross-diffusion, storage, velocity, and external boundary terms !83
-* Allows for volume coupling between compartments !83
-* Splits the subdomain and the compartment concepts. Now compartments with no entities or no components are perfectly possible !83
-* Uses new basis functions from dune-pdelab that allows native usage of multi-domains (branch: features/dune-assembler/main) !83
-* Extends compatibility of tiff images to different bit sizes !83
-* Adds monitoring (info, warning and error) of variables with new generic reduce operators !83
-* Switches logging from dune-logging to [spdlog](https://github.com/gabime/spdlog) !83
-* Designed to be thread-safe, although is not entirely yet implemented !83
-* Adds tracing capabilities with [perfetto](https://perfetto.dev/) !83
-* Allows Selection of between direct and sparse solvers, and matrix free operators !83
-* Allows to print matrix layout in a SVG file !83
-* Unifies the executable for different dimensions and different degrees of freedom layouts !83
-* Improves command line interface !83
+ - Allows different parser backends: [muparser](https://beltoforion.de/en/muparser/), [exprtk](https://github.com/ArashPartow/exprtk), and [SymEngine](https://github.com/symengine/symengine) !83
+ - Adds constants, (lambda) function, and [random fields](https://github.com/parafields/parafields-core) definitions within the parsers !83
+ - Re-implementation of local operator: huge performance improvements !83
+ - Adds tensor cross-diffusion, storage, velocity, and external boundary terms !83
+ - Allows for volume coupling between compartments !83
+ - Splits the subdomain and the compartment concepts. Now compartments with no entities or no components are perfectly possible !83
+ - Uses new basis functions from dune-pdelab that allows native usage of multi-domains (branch: features/dune-assembler/main) !83
+ - Extends compatibility of tiff images to different bit sizes !83
+ - Adds monitoring (info, warning and error) of variables with new generic reduce operators !83
+ - Switches logging from dune-logging to [spdlog](https://github.com/gabime/spdlog) !83
+ - Designed to be thread-safe, although is not entirely yet implemented !83
+ - Adds tracing capabilities with [perfetto](https://perfetto.dev/) !83
+ - Allows Selection of between direct and sparse solvers, and matrix free operators !83
+ - Allows to print matrix layout in a SVG file !83
+ - Unifies the executable for different dimensions and different degrees of freedom layouts !83
+ - Improves command line interface !83

 ### Added
 - Docusaurus now upgrades latest `canary` wasm binary automatically !186
@@ -99,7 +117,7 @@ _**Note**: This version is a complete re-write of the library based on a custom
 - Improve support for Wasm binaries !170 !182
 - Move configuration options to a JSON file and use schema validator on it !174
 - Use Debian Bookworm in the CI !171
- - Conditinally test possion config if ExprTk is available !168
+ - Conditionally test possion config if ExprTk is available !168
 - Use (faster) integer based multi-domain grid !165
 - Simplify CMake usage !161 !162 !163
 - Improve version handler !159
@@ -137,7 +155,7 @@ _**Note**: This version is a complete re-write of the library based on a custom
 - Compile final executable with different parsers !95
 - CMake problems on target installation !94
 - Support for {fmt} >= 9.0.0 !90 !91 !93 !129
- - Docker image now uses `dune-copas` executable instead of `dune-copasi-[sd|md]` !91
+ - Docker image now uses `dune-copasi` executable instead of `dune-copasi-[sd|md]` !91
 - CI jobs now passes since the re-write !89
 - Solver on linear problems was wrongly reused !85
 ### Removed

--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -40,7 +40,7 @@ list(PREPEND CMAKE_MODULE_PATH \"\${dune-copasi_MODULE_PATH}\")
 include(CMakeFindDependencyMacro)
 ")

-foreach(module ${ALL_DEPENDENCIES})
+foreach(module ${DUNE_FOUND_DEPENDENCIES})
  if(${${module}_FOUND})
    set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
 find_dependency(${module} REQUIRED)

--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
 # Contributing

-When contributing to `dune-copasi`, first discuss the change you wish to make via the
+When contributing to DuneCopasi, first discuss the change you wish to make via the
 [issue tracker](https://gitlab.dune-project.org/copasi/dune-copasi/-/issues).
 Try to do this before anything else. This will greately improve both your and
 our experience working together :-). We follow the
@@ -14,14 +14,14 @@ contributing single features can be summarized by following these steps:
   proposal has a major change, create a *meta-task*, which should divide the
   proposal in several tasks. Use a suitable issue template for your proposal.
 2. In the created issue, discuss with others the whole idea of your proposal.
-   This is important because you may get input from someone that know the
-   software on how to do it effectively, and poimting out considerations you may
+   This is important because you may get input from someone who knows the
+   software on how to do it effectively, and pointing out considerations you may
   have missed. It also synchronizes ideas so that changes are more easily
   accepted.
-3. **CODE**: Implement what you proposed :-) in a new branch.
-4. Create a [Merge Request (MR)](https://docs.gitlab.com/ee/gitlab-basics/add-merge-request.html)
+3. **CODE**: Implement what you proposed in a new branch :-)
+4. Create a [Merge Request (MR)](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
   using suitable template. Mark the MR as
-   [*Work In Progress* (WIP)](https://docs.gitlab.com/ee/user/project/merge_requests/work_in_progress_merge_requests.html)
+   [*Draft*](https://docs.gitlab.com/ee/user/project/merge_requests/drafts.html)
   until is sent to review for approval. MR differ from issues in that MR
   discuss *how* to implement the idea rather than the idea itself. A MR is
   filled of technical details that ensure that the *task* idea is fulfilled.
@@ -32,7 +32,7 @@ contributing single features can be summarized by following these steps:
 6. If applicable, create a
   [unit test](https://en.wikipedia.org/wiki/Unit_testing) that proves that your
   implementation has the expected behavior. Ensure that the created test is
-   being run by the [Gitlab CI](https://docs.gitlab.com/ee/ci/pipelines.html).
+   being run by the [Gitlab CI](https://about.gitlab.com/blog/2020/12/10/basics-of-gitlab-ci-updated/).
 7. **TEST**: Once implementation and test are finished, ensure that your MR is
   passing the different [pipelines](https://gitlab.dune-project.org/copasi/dune-copasi/-/tree/master/.ci).
 8. Update the [CHANGELOG](CHANGELOG.md) with changes to the interface. It

--- a/README.md
+++ b/README.md
@@ -2,21 +2,181 @@
 [![Build Status](https://github.com/dune-copasi/dune-copasi/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/dune-copasi/dune-copasi/actions/workflows/ci.yml)
 [![Netlify Status](https://api.netlify.com/api/v1/badges/6fc6d371-87df-49b5-8e72-e1873fa5d54b/deploy-status)](https://app.netlify.com/sites/dune-copasi/deploys)

-# DuneCopasi
+<!-- IMPORTANT: Do not add relative links on this file because this is rendered out of source at https://www.dune-project.org/modules/dune-copasi/ too -->

-**WARNING**: This repository is in an ongoing refactor for version 2.0, check out the releases for stable versions!
+---
+# DuneCopasi: A Multi-Compartment Reaction-Diffusion Simulator

-Solver for reaction-diffusion systems in multiple compartments
+DuneCopasi is a C++ library providing a numerical simulator for systems of reaction-diffusion equations on single and multiple compartments using the **D**istributed and **U**nified **N**umerics **E**nvironment [DUNE](https://www.dune-project.org). It supports multi-threaded computations with continuous finite elements on unstructured grids in 1, 2, and 3 dimensions. An application program is made available as a Docker Image, as a Web Assembly binary, or as a GUI through the [Spatial Model Editor](https://spatial-model-editor.github.io) for the manipulation of spatial models of bio-chemical reactions.

- * Solve a different reaction-diffusion system for each comartment
- * Custom fluxes between compartments
- * Easy to modify configuration file
- * Initial conditions can be a TIFF file and/or math expressions
- * Using the finite element/finite volume method
- * Output in the VTK format
+# Table of Contents

-Get started [here](https://dune-copasi.netlify.app/docs//install_use).
+- [DuneCopasi: A Multi-Compartment Reaction-Diffusion Simulator](#dunecopasi-a-multi-compartment-reaction-diffusion-simulator)
+- [Table of Contents](#table-of-contents)
+- [Overview](#overview)
+  - [Features](#features)
+  - [Capabilities](#capabilities)
+  - [Model Problem](#model-problem)
+- [Getting Started](#getting-started)
+  - [Installation](#installation)
+  - [Basic Commands](#basic-commands)
+  - [Tutorials](#tutorials)
+  - [Configuration Options](#configuration-options)
+- [Contributing](#contributing)
+  - [Reporting Issues](#reporting-issues)
+  - [Contributing Guide](#contributing-guide)
+  - [Folder Structure](#folder-structure)
+- [Additional Information](#additional-information)
+  - [License](#license)
+  - [Acknowledgements](#acknowledgements)

 ---

+# Overview
+
+DuneCopasi bridges the gap between systems biology and scientific computing by providing a robust tool for simulating complex biochemical networks, especially those with spatial dependencies. It is particularly suitable for researchers and engineers in systems biology, computational biology, and related fields, offering capabilities that include advanced handling of multi-compartment reaction-diffusion systems.
+
+## Features
+
+- **Multi-Compartment Reaction-Diffusion Simulation**: Solve systems of PDEs across multiple compartments with configurable parameters.
+- **Continuous Galerkin Method**: Utilize continuous finite elements on unstructured grids in 1D, 2D, and 3D.
+- **Multi-Threaded Computation**: Efficient simulation on modern multi-core processors.
+- **Interoperability**: Designed to work seamlessly with SBML, TIFF files for initial conditions, and systems biology workflows.
+- **Flexible Deployment**: Available as a Docker image, WebAssembly binary, and as a GUI through the Spatial Model Editor.
+
+## Capabilities
+
+- **Configurable Executable**: Single executable with runtime configuration options.
+- **SBML Compatibility**: Supports math parsers compatible with the Systems Biology Markup Language (SBML) for model specifications.
+- **Custom Grid and TIFF Input**: Accepts custom grids and image files for initial conditions.
+- **Advanced Boundary Conditions**: Flexible boundary/transmission conditions for complex biological models.
+- **Cross-Diffusion Support**: Allows species to cross-diffuse across compartments.
+- **Result Comparison**: Built-in tools for comparing simulation results with objective functions.
+- **Random Field Generator**: Generates statistical spatial variations using embedded random field algorithms.
+
+## Model Problem
+
+DuneCopasi solves the following system of partial differential equations (PDEs):
+
+$$
+\begin{aligned}
+  \partial_t (\phi_{ik} u_{ik}) &= \nabla \cdot \vec{\mathcal{j}}_{ik}+\mathcal{R}_{ik}(\mathbf{u})\qquad &\text{in }\Omega_k\subset \mathbb{R}^d,\\
+  u_{ik} &= u^{(0)}_{ik} \qquad &\text{on }\Gamma_k^D\subseteq\partial\Omega_k,\\
+  \vec{\mathcal{j}}_{ik}\cdot \mathbf{n}_k &= \sum_{l\in T_k}\mathcal{T}_{ikl}(\mathbf{u}) \qquad &\text{on }\partial\Omega_k \setminus \Gamma^D_{k},\\
+  \vec{\mathcal{j}}_{ik} &:= \sum_{j\in N_k}\mathsf{D}_{ijk}\nabla u_{jk}\\
+\end{aligned}
+$$
+
+where $i\in N_k$ is the subscript for each mass balance equation in the $k$-th compartment and with $k\in K$, $T_k:=\{l\in K : \Gamma_{kl}\neq\varnothing\}$, $\mathbf{u}_k:=(u_{1k},\ldots,u_{\text{dim}(N_k)k})$, $\mathbf{u} := (\mathbf{u}_1, \ldots, \mathbf{u}_{\text{dim}(K)})$, $\mathbf{n}_k$ the unit outer normal on $\Omega_k$, $\overline{\Omega}:=\bigcup_{k\in K}\overline{\Omega}_k$, and $\Gamma_{kl}$ is $\partial\Omega_k\cap\overline{\Omega}_l$ if $k \neq l$ or $\partial\Omega_k\cap\overline{\Omega}$ otherwise.
+
+
+All of the parameterization for the equations are easily configurable at run-time using the command line or a configuration file. That is, the underlying grid, the partition for each sub-domain $\Omega_k$ on the grid, the reaction operator $\mathcal{R}_{ik}(\mathbf{u})$, the non-linear transmission conditions $\mathcal{T}_{ikl}(\mathbf{u})$ on $\Gamma_{kl}$, the Dirichlet boundary conditions $u^{(0)}_{ik}$ on $\Gamma^D_{k}$, the storage terms $\phi_{ik}$, and the cross-diffusion terms $\mathsf{D}_{ijk}$.
+
+# Getting Started
+
+## Installation
+
+For detailed installation instructions specific to each version, please refer to our comprehensive [online documentation](https://dune-copasi.netlify.app).
+
+## Basic Commands
+
+```
+USAGE: dune-copasi [options]
+
+Numerical simulator for diffusion-reaction systems on single or multiple compartments
+
+Website: <https://dune-copasi.netlify.app>
+
+OPTIONS:
+
+    -h / --help          - Display this help.
+    --help-full          - Display this help with long descriptions.
+    --version            - Display the version of this program.
+    --parser-default     - Display the default parser.
+    --parser-list        - Display the parsers available for this program.
+    --dimension-list     - Display the grid dimensions available for this program.
+    --dump-config        - Dumps configuration in the INI format to stdout.
+    --config=<string>    - Specifies a config file in INI format. See Configuration Options.
+    --{key}={value}      - Overrides key=value sections of the config file. See Configuration Options.
+```
+
+## Tutorials
+
+To help you get started with DuneCopasi, we offer a dedicated [tutorial website](https://dune-copasi.netlify.app/tutorials) featuring step-by-step guides and practical examples. These tutorials are designed to walk you through various aspects of the software.
+
+## Configuration Options
+
+We have a rich set of options to configure many possible settings for our problem model.
+You can find detailed information of each option by invoking the `--help-full` command or by exploring our [online documentation](https://dune-copasi.netlify.app).
+
+# Contributing
+
+## Reporting Issues
+
+If you encounter any issues, please report them on the [issue tracker](https://gitlab.dune-project.org/copasi/dune-copasi/issues) or by contacting us via the email ![Service Desk](https://img.shields.io/badge/dune--copasi%40dune--project.org-informational).
+
+## Contributing Guide
+
+We welcome contributions from the community. Please read our Contributing Guide in `CONTRIBUTING.md` file for details on our code of conduct, and the process for submitting merge requests.
+
+## Folder Structure
+
+The following may help you understand the general structure of this project.
+Below, you can find the folder structure with the most prominent parts of this repository and a short description of their purpose.
+Notice that many of these sub-directories have their own `README.md` file explaining how to use its contents.
+
+```
+.                                          # . Root directory
+├── .ci                                    # ├── Scripts to run during Continuous Integration (CI)
+├── .github                                # ├── GitHub configuration files
+├── .gitlab                                # ├── GitLab configuration files
+├── cmake                                  # ├── CMake scripts and modules
+├── doc                                    # ├── Documentation files
+│   ├── docusaurus                         # │   ├── Files for online documentation
+│   │   ├── docs                           # │   │   ├── Main online documentation files
+│   │   │   ├── assets/ini                 # │   │   │   ├── Configuration examples for online documentation (tested)
+│   │   │   └── assets/config_opts.json    # │   │   │   └── Configuration options database (source of truth for all docs)
+│   │   ├── tutorials                      # │   │   ├── Main online tutorial files
+│   │   │   └── assets/ini                 # │   │   │   └── Configuration examples for online tutorials (tested)
+│   │   └── ...                            # │   │   └── [...]
+│   ├── doxygen                            # │   ├── Configuration files for autogenerated C++ documentation
+│   ├── joss                               # │   ├── Paper submitted to the Journal of Open Source Software
+│   └── man                                # │   └── Documentation for `man`
+├── docker                                 # ├── Docker files for different environments
+├── dune/copasi                            # ├── C++ header files
+│   ├── common                             # │   ├── Common infrastructure
+│   ├── concepts                           # │   ├── Type constrains/requirements
+│   ├── finite_element                     # │   ├── Finite element utilities
+│   ├── grid                               # │   ├── Grids utilities
+│   ├── model                              # │   ├── Simulation logic for a model problem
+│   │   └── diffusion_reaction             # │   │   └── Diffusion-Reaction specifics of the model problem
+│   ├── parser                             # │   ├── Interface and implementation of math parsers
+│   └── solver/istl                        # │   └── Custom linear algebra solvers/preconditioners for dune-istl
+├── npm                                    # ├── WebAssembly package files for NPM
+├── src                                    # ├── Object files and main program (mirrors dune/copasi folder)
+├── test                                   # ├── Testing suite
+│   ├── data                               # │   ├── Custom data used for tests
+│   ├── dune                               # │   ├── Unit tests on specific C++ constructs (mirrors dune/copasi folder)
+│   └── *.ini                              # │   └── Configuration files for system tests
+├── util                                   # ├── Misc utilities to handle the repository
+├── .gitlab-ci.yml                         # ├── GitLab CI configuration file
+├── CHANGELOG.md                           # ├── List of major changes
+├── CMakeFiles.txt                         # ├── Main CMake configuration file
+├── CODE_OF_CONDUCT.md                     # ├── Code of conduct
+├── CONTRIBUTING.md                        # ├── Contribution guilde
+├── Dockerfile                             # ├── Main docker file to build the project
+├── dune-copasi.opts                       # ├── DUNE options file with default CMake options
+├── LICENSE.md                             # ├── BSD 2-Clause License file
+├── README.md                              # ├── Overview documentation of repository
+└── ...                                    # └── [...]
+```
+
+# Additional Information
+
+## License
+
+This project is licensed under the BSD 2-Clause License - see the `LICENSE.md` file for details.
+
+## Acknowledgements
+
 Research funded by the German federal Ministry of Education and Research (BMBF) FKZ 031L0158
--- a/cmake/modules/Findmuparser.cmake
+++ b/cmake/modules/Findmuparser.cmake
@@ -38,14 +38,6 @@ if(muparser_FOUND
    muparser_VERSION_STRING
    "${muparser_version_str}")
  unset(muparser_version_str)
-  add_library(
-    muparser::muparser
-    UNKNOWN
-    IMPORTED)
-  set_target_properties(
-    muparser::muparser
-    PROPERTIES IMPORTED_LOCATION ${muparser_LIBRARY}
-               INTERFACE_INCLUDE_DIRECTORIES ${muparser_INCLUDE_DIR})

  set(muparser_test_path "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/CMakeTmp/muparser_test.cc")
  set(muparser_test_source
@@ -60,21 +52,42 @@ if(muparser_FOUND
  file(WRITE "${muparser_test_path}" "${muparser_test_source}")
  try_compile(COMPILE_RESULT_DYNAMIC "${CMAKE_CURRENT_BINARY_DIR}"
               SOURCES "${muparser_test_path}"
-               LINK_LIBRARIES muparser::muparser)
+               CXX_STANDARD 17
+               LINK_LIBRARIES ${muparser_LIBRARY}
+               CMAKE_FLAGS -DINCLUDE_DIRECTORIES=${muparser_INCLUDE_DIR})

-  if(NOT COMPILE_RESULT_DYNAMIC)
+  if(COMPILE_RESULT_DYNAMIC)
+    add_library(
+      muparser::muparser
+      UNKNOWN
+      IMPORTED)
+    set_target_properties(
+      muparser::muparser
+      PROPERTIES IMPORTED_LOCATION ${muparser_LIBRARY}
+                INTERFACE_INCLUDE_DIRECTORIES ${muparser_INCLUDE_DIR})
+  else()
    file(WRITE "${muparser_test_path}" "${muparser_test_source}")
    try_compile(COMPILE_RESULT_STATIC "${CMAKE_CURRENT_BINARY_DIR}"
                SOURCES "${muparser_test_path}"
                COMPILE_DEFINITIONS -DMUPARSER_STATIC
-                LINK_LIBRARIES muparser::muparser)
+                CXX_STANDARD 17
+                LINK_LIBRARIES ${muparser_LIBRARY}
+                CMAKE_FLAGS -DINCLUDE_DIRECTORIES=${muparser_INCLUDE_DIR})

    if(NOT COMPILE_RESULT_STATIC)
-      message(FATAL_ERROR "A simple muparser test program could not be successfully compiled")
-    endif()
+      # message(FATAL_ERROR "A simple muparser test program could not be successfully compiled")
+      set(muparser_FOUND OFF)
+    else()

-    set_target_properties(
-      muparser::muparser
-      PROPERTIES INTERFACE_COMPILE_DEFINITIONS MUPARSER_STATIC)
+      add_library(
+        muparser::muparser
+        UNKNOWN
+        IMPORTED)
+      set_target_properties(
+        muparser::muparser
+        PROPERTIES IMPORTED_LOCATION ${muparser_LIBRARY}
+                  INTERFACE_INCLUDE_DIRECTORIES ${muparser_INCLUDE_DIR}
+                  INTERFACE_COMPILE_DEFINITIONS MUPARSER_STATIC)
+    endif()
  endif()
 endif()
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -21,25 +21,50 @@ if (TARGET Dune::Copasi::Executable)

  enable_testing()

-  dune_declare_test_label(LABELS tutorial)
+  dune_declare_test_label(LABELS documentation)

-  file(COPY "docusaurus/tutorials/assets/ini" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/tutorials/")
+  file(COPY "docusaurus/docs/assets/ini"      DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/docs/")

  dune_add_test(
-    NAME                tutorial_test
-    LABELS              tutorial
+    NAME                docs_test
+    LABELS              docs
    TARGET              Dune::Copasi::Executable
-    WORKING_DIRECTORY   "${CMAKE_CURRENT_BINARY_DIR}/tutorials/ini/"
+    WORKING_DIRECTORY   "${CMAKE_CURRENT_BINARY_DIR}/docs/ini/"
    CMD_ARGS            --config=test.ini)

+  dune_add_test(
+    NAME                docs_heat
+    LABELS              docs
+    TARGET              Dune::Copasi::Executable
+    WORKING_DIRECTORY   "${CMAKE_CURRENT_BINARY_DIR}/docs/ini/"
+    CMD_ARGS            --config=heat.ini)
+
+    dune_add_test(
+    NAME                docs_volka_terra
+    LABELS              docs
+    TARGET              Dune::Copasi::Executable
+    WORKING_DIRECTORY   "${CMAKE_CURRENT_BINARY_DIR}/docs/ini/"
+    CMD_ARGS            --config=volka_terra.ini)
+
+  dune_add_test(
+    NAME                docs_grey_scott
+    LABELS              docs
+    TARGET              Dune::Copasi::Executable
+    WORKING_DIRECTORY   "${CMAKE_CURRENT_BINARY_DIR}/docs/ini/"
+    CMD_ARGS            --config=grey_scott.ini
+                        --model.time_step_operator.time_end=1.5)
+
+  file(COPY "docusaurus/tutorials/assets/ini" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/tutorials/")
+
  if(ExprTk IN_LIST DUNE_COPASI_PARSER_LIST)
    dune_add_test(
      NAME                tutorial_EP_simulation1
-      LABELS              tutorial
+      LABELS              docs
      TARGET              Dune::Copasi::Executable
      WORKING_DIRECTORY   "${CMAKE_CURRENT_BINARY_DIR}/tutorials/ini/"
-      CMD_ARGS            --config=EP_simulation1.ini
-                          --model.time_step_operator.time_end=10)
+      CMD_ARGS            --config=cardiac_ep_1.ini
+                          --model.time_step_operator.time_end=10
+                          --grid.refinement_level=6)
  endif()

 endif()
--- a/doc/docusaurus/docs/api.mdx
+++ b/doc/docusaurus/docs/api.mdx
@@ -3,8 +3,12 @@ id: api
 title: Application Programming Interface
 description: Application Programming Interface
 sidebar_label: API
+tags:
+  - API
 ---

+import DoxygenButton from '@site/src/components/DoxygenButton'
+
 ### Doxygen Documentation

 The C++ classes are documented in the C++ source code and may be visualized with
@@ -12,3 +16,5 @@ The C++ classes are documented in the C++ source code and may be visualized with
 documentation, build [DuneCopasi from source](install_source) and use the
 `make dune-copasi-doxygen` target in the build directory. For this, you need to
 have `doxygen` on your system.
+
+<DoxygenButton/>
--- a/doc/docusaurus/docs/assets/config_opts.json
+++ b/doc/docusaurus/docs/assets/config_opts.json
@@ -145,6 +145,45 @@
      }
    }
  },
+  "model.jacobian.[type|epsilon]": {
+    ".brief": "General options for the jacobian of the model",
+    ".options": {
+      "type": {
+        ".type": "enum",
+        ".brief": "Evaluation type of the jacobian",
+        ".default": "analytical",
+        ".details": [
+          "This option specifies how to generate the assembled operator that is applied on linear systems.",
+          "If the type is 'analytical', each entry is constructed from the 'model.scalar_field.{var}.jacobian.{dvar}'",
+          "configuration options."
+        ],
+        ".options": {
+          "'analytical'": {
+            ".brief": "Jacobians are computed from analyicial expressions provided within the configuration options",
+            ".details": [
+              "In this case, the sparsity pattern is inferred from the 'model.scalar_field.{var}.jacobian.{dvar}'",
+              "configuration options and its value corresponds to the evaluation of these expressions."
+            ]
+          },
+          "'numeric'": {
+            ".brief": "Jacobians are computed numerically from the primary expressions provided within the configuration options",
+            ".details": [
+              "In this case, the sparsity pattern is inferred from the 'model.scalar_field.{var}.jacobian.{dvar}'",
+              "configuration options and its value corresponds a forward euler evaluation of the",
+              "'model.scalar_field.{var}' expressions. Notice that the 'jacobian' configuration options may not be evaluated at all",
+              "(e.g. 'no_value' is a valid expression) but they still need to be present, otherwise, the pattern will not be created",
+              "correctly and the numerical evaluation will yield an invalid access error."
+            ]
+          }
+        }
+      },
+      "epsilon": {
+        ".type": "float",
+        ".brief": "The discretization step to evaluate jacobians with a numerical type",
+        ".default": "1e-7"
+      }
+    }
+  },
  "model.assembly.[type|partition.type|partition.patches|partition.coloring]": {
    ".brief": "Options for the execution policy on the assembly of residuals and jacobians",
    ".options": {
@@ -199,6 +238,25 @@
    ".brief": "Control data layout of the matrices and vectors. Note that this affects the allowed solvers",
    ".details": "To visualize the resulting layout of a matrix use the `model.time_step_operator.linear_solver.layout.writer.svg.path` option."
  },
+  "model.domain.deformation.[x|y|z].[expression|parser_type]": {
+    ".brief": "Expression options for the deformation of the domain (Experimental)`",
+    ".details": [
+      "The domain deformation expressions may depend on any number of variables `{var}` from the 'scalar_field' section and only works when using numerical jacobians.",
+      "Depending on a variable `{var}` makes the problem non-linear and makes every `{var}` in 'scalar_field' depend on the variables `{var}` used here.",
+      "In practice, this means that the jacobian of every sub-section in `scalar_field.{var}` needs to also explicitly show the dependency on the variables used here.",
+      "The differential equations on the `scalar` section are posed on the deformed domain and conserved over time via the Reynolds Transport Theorem.",
+      "The latter means that the equations are in their conservative form."
+    ],
+    ".options": {
+      "expression": {
+        ".type": "math-expr"
+      },
+      "parser_type": {
+        ".type": "enum",
+        ".default": "<see '--parser-default' option>"
+      }
+    }
+  },
  "model.scalar_field.{var}.[reaction|storage|velocity.[x|y|z]|outflow.{cmp}].jacobian.{wrt}.[expression|parser_type]": {
    ".brief": "Expression options for the jacobian wrt variable `{wrt}` of the scalar field equation in variable `{var}`",
    ".options": {

--- a/doc/docusaurus/docs/assets/ini/grey_scott.ini
+++ b/doc/docusaurus/docs/assets/ini/grey_scott.ini
+#########################################################################
+# GREY-SCOTT EQUATIONS:
+#
+# ∂ₜu = 2·D·∂ₓ∂ₓu + f·(1-u) - u·v²
+# ∂ₜv =   D·∂ₓ∂ₓu - (f+k)·v + u·v²
+#
+# See: https://groups.csail.mit.edu/mac/projects/amorphous/GrayScott/
+#
+#########################################################################
+
+[grid]
+extensions = 1 1
+dimension = 2
+refinement_level = 7
+
+[parser_context.bump]
+type = function
+expression = x, y: 0.5*exp(-100*(x^2 + y^2))
+parser_type = ExprTk
+
+[parser_context.F]
+type = constant
+value = 0.0420
+
+[parser_context.k]
+type = constant
+value = 0.0610
+
+[parser_context.D]
+type = constant
+value = 1e-5
+
+[model]
+order = 1
+parser_type = ExprTk
+
+[model.time_step_operator]
+time_begin = 0
+time_end = 10000
+time_step_initial = 0.1
+time_step_max = 50
+
+[model.time_step_operator.linear_solver]
+type = RestartedGMRes
+preconditioner.type = Jacobi
+
+[model.time_step_operator.nonlinear_solver]
+type = Alexander2
+convergence_condition.relative_tolerance = 1.00000000000000002e-08
+convergence_condition.absolute_tolerance = 0
+
+[model.writer.vtk]
+path = vtk
+
+[compartments]
+compartment.expression = 1
+
+[model.scalar_field.U]
+compartment = compartment
+initial.expression = 0.7
+storage.expression = 1
+reaction.expression = F*(1-U) - U*V^2
+reaction.jacobian.U.expression = -F - V^2
+reaction.jacobian.V.expression = -2*U*V
+cross_diffusion.U.expression = D*2
+
+[model.scalar_field.V]
+compartment = compartment
+initial.expression = bump(0.25-position_x, 0.25-position_y) + bump(0.25-position_x, 0.75-position_y) + bump(0.75-position_x, 0.25-position_y) + bump(0.75-position_x, 0.75-position_y)
+storage.expression = 1
+reaction.expression = -(F+k)*V + U*V^2
+reaction.jacobian.U.expression = V^2
+reaction.jacobian.V.expression = -(F+k) + 2*U*V
+cross_diffusion.V.expression = D
--- a/doc/docusaurus/docs/assets/ini/heat.ini
+++ b/doc/docusaurus/docs/assets/ini/heat.ini
+#########################################################################
+# HEAT EQUATION:
+#
+# ∂ₜu = ∂ₓ(T·∂ₓu) + ∂ᵧ(T·∂ᵧu)
+#
+# where u(x,y,t) is the temperature at a time t on the domain for a
+# thermal conductivity T.
+#
+# See: https://en.wikipedia.org/wiki/Heat_equation
+#
+#########################################################################
+
+[grid]
+# extensions of the grid in x and y directions
+extensions = 1 0.1
+# where the grid left-bottom corner starts
+origin = 0.0 0.0
+# number of cells of the initial grid in x and y directions
+cells = 10 1
+# number of times to refine the grid
+refinement_level = 5
+
+# defines a compartment with the name "domain"
+[compartments.domain]
+expression = 1
+
+# Define a constant with name "T" to use in the equations
+[parser_context.T]
+type = constant
+value = 0.005
+
+# our model is linear because there is no reaction
+[model]
+is_linear = true
+
+##### Definition of the equation to solve function u(x,y,t) ######
+
+# Declares the compartment where this function is defined
+[model.scalar_field.u]
+compartment = domain
+
+# Declares that the equation is transient
+[model.scalar_field.u.storage]
+expression = 1
+
+# Declares the diffusion part on the diffusion-reaction equation
+[model.scalar_field.u.cross_diffusion.u]
+expression = T
+
+[model.scalar_field.u.initial]
+# Declares the value of the function at the initial time: u(x,y,0)
+# Try changing this to be a function of x and y: use "position_x" and "position_y"
+# to represents its values, for example:
+# "expression = position_x^2"
+# represents the case where u(x,y,0) := x^2
+# ...
+# function for u(x,y,0)
+expression = 10
+
+# Declares the diffusion part on the diffusion-reaction equation
+# Here we use the following ExprTk syntax to constraint the left and right parts of
+# the compartment: "condition ? if_true : if_false"
+# the "if_true" part contains the values set on the left and right boundaries
+[model.scalar_field.u.constrain.boundary]
+expression = (position_x <= 0. or position_x >= 1.) ? 0. : no_value
+parser_type = ExprTk
+
+[model.time_step_operator]
+# initial time of the simulation
+time_begin = 0
+# final time of the simulation
+time_end = 10
--- a/doc/docusaurus/tutorials/assets/ini/test.ini
+++ b/doc/docusaurus/tutorials/assets/ini/test.ini
@@ -8,17 +8,10 @@ refinement_level = 5
 type = expression
 expression = 1

-[parser_context]
-diffusion.type = constant
-diffusion.value = 0.005
-
-gauss.type = function
-gauss.expression = x, y, z: exp(-(x^2+y^2+z^2)/(4*diffusion)) / (4*3.14159265359*diffusion)
-
 [model.scalar_field.u]
 compartment = domain
-cross_diffusion.u.expression = diffusion
-initial.expression = gauss(position_x, position_y, position_z)
+cross_diffusion.u.expression = 0.005
+initial.expression = exp(-(position_x^2+position_y^2+position_z^2)/(4*0.005)) / (4*3.14159265359*0.005)
 storage.expression = 1

 [model.time_step_operator]

--- a/doc/docusaurus/docs/assets/ini/volka_terra.ini
+++ b/doc/docusaurus/docs/assets/ini/volka_terra.ini
+#########################################################################
+# VOLKA-TERRA EQUATIONS:
+#
+# ∂ₜu = α·u   - β·u·v
+# ∂ₜv = δ·u·v - γ·v
+#
+# See: https://en.wikipedia.org/wiki/Lotka%E2%80%93Volterra_equations
+#
+# Note that there is not derivative on the positions x or y, so the
+# functions are the same on every point in x and y for a given time t.
+# Hence, we do not refine the grid at all.
+#
+#########################################################################
+
+[grid]
+# extensions of the grid in x and y directions
+extensions = 1 1
+# number of cells of the initial grid in x and y directions
+cells = 1 1
+
+# defines a compartment with the name "domain"
+[compartments.domain]
+expression = 1
+
+# Define constants with name "alpha", "beta", "delta", and "gamma"
+# representing α, β, δ, and γ respectively
+[parser_context.alpha]
+type = constant
+value = 0.666666
+[parser_context.beta]
+type = constant
+value = 1.33333
+[parser_context.delta]
+type = constant
+value = 1
+[parser_context.gamma]
+type = constant
+value = 1
+
+# our model is linear because there is a non-linear reaction part
+[model]
+is_linear = false
+
+##### Definition of the equation to solve function u(x,y,t) ######
+
+# Declares the compartment where this function is defined
+[model.scalar_field.u]
+compartment = domain
+
+# Declares that the equation is transient
+[model.scalar_field.u.storage]
+expression = 1
+
+# Declares the reaction part on the diffusion-reaction equation for equation for u
+[model.scalar_field.u.reaction]
+expression = alpha*u - beta*u*v
+
+# Declares the jacobian of the reaction of u
+[model.scalar_field.u.reaction.jacobian.u]
+# ∂ᵤ(α·u - β·u·v) = α - β·v
+expression = alpha - beta*v
+[model.scalar_field.u.reaction.jacobian.v]
+# ∂ᵥ(α·u - β·u·v) = - β·u
+expression = -beta*u
+
+[model.scalar_field.u.initial]
+# function for u(x,y,0)
+expression = 1
+
+##### Definition of the equation to solve function v(x,y,t) ######
+
+# Declares the compartment where this function is defined
+[model.scalar_field.v]
+compartment = domain
+
+# Declares that the equation is transient
+[model.scalar_field.v.storage]
+expression = 1
+
+# Declares the reaction part on the diffusion-reaction equation for equation for v
+[model.scalar_field.v.reaction]
+expression = delta*u*v - gamma*v
+
+# Declares the jacobian of the reaction of v
+[model.scalar_field.v.reaction.jacobian.u]
+# ∂ᵤ(δ·u·v - γ·v) = δ·v
+expression = delta*v
+[model.scalar_field.v.reaction.jacobian.v]
+# ∂ᵥ(δ·u·v - γ·v) = δ·u - γ
+expression = delta*u-gamma
+
+[model.scalar_field.v.initial]
+# function for v(x,y,0)
+expression = 1
+
+[model.time_step_operator]
+# initial time of the simulation
+time_begin = 0
+# final time of the simulation
+time_end = 20
+# limit the maximum time-step
+time_step_max = 0.25
--- a/doc/docusaurus/docs/config.mdx
+++ b/doc/docusaurus/docs/config.mdx
+---
+id: config
+title: Configuration Options
+description: API & CLI configuration options
+sidebar_label: Configuration Options
+tags:
+  - API
+  - CLI
+---
+
+import DocCardList from '@theme/DocCardList';
+
+In order to configure DuneCopasi, a set of configuration options must be provided.
+When using the [GUI](use_gui), the program will automatically them set up for you. On the other hand, in the
+case of [CLI](use_cli) and [API](use_cli) usage, they need to be manually specified.
+
+In the following documentation pages we will assume that you are working with the [CLI](use_cli).
+The [API](use_cli) essentially consists on the same options sythetized in the
+[`Dune::ParameterTree`](https://www.dune-project.org/doxygen/2.9.1/classDune_1_1ParameterTree.html) C++ object.
+
+<DocCardList/>
--- a/doc/docusaurus/docs/ini_file.mdx
+++ b/doc/docusaurus/docs/ini_file.mdx
@@ -3,46 +3,37 @@ id: ini_file
 title: Config File
 description: Syntax of INI file
 sidebar_label: Config File
+tags:
+  - API
+  - CLI
 ---

 import Tabs from '@theme/Tabs';
 import TabItem from '@theme/TabItem';
+import CodeBlock from '@theme/CodeBlock';

-The [INI format](https://en.wikipedia.org/wiki/INI_file) defines a set of [configuration options](param_tree) to initialize and run the models.
+::::note CLI Usage
+This documentation page is intended for the [Command Line Interface (CLI)](use_cli). If you're new to DuneCopasi, we recommend starting with our [Tutorials](/tutorials).
+::::

-## Format
+To express different [mathematical problems](/math_model) we typically write a configuration file (with `.ini` extension by convention) which entails all the information that is needed for the DuneCopasi solver to construct the problem at hand.
+The configuration file consists of a parameter tree containing the [simulation options](param_tree). The nodes at the top level can be divided in 4 categories:

-The forrmat we use follows the DUNE `ini` file convention. In short, the data is composed of a *key–value pairs* on the form `key = value`.
+| Category | Description  |
+|     ---- | -----------  |
+| `grid`                  | The nodes under the grid header describe the basic properties of the grid. For example the dimension, extension, origin, etc.
+| `parser_context`        | Under this node we are able to define constant and functions that can be used to define the mathematical model.
+| `compartments`          | In this category we define the properties related to division of the problem to multiple compartments.
+| `model`                 | This is the heart of the mathematical problem where we define the reaction terms, diffusion, etc.

-### Comments
-
-Characters followed by hash `#` will be ignored.
-
-```ini title="config.ini"
-# %highlight
-# line comment
-key = value
-```
-
-### Entries
-
-An entry is given by a *key-value pair* and must be entirely contained in one line. Additionally, *keys* must be unique.
+The ini files we use follow the DUNE convention. In short, the data is composed of a key–value pairs on the form ```key = value```. For example, to define a `property` of the category `grid` we write

 ```ini title="config.ini"
-id = value
-# %highlight-error
-id = val
-# error: repeated key 'id'
+grid.property = value
 ```

-### Group
+In essence the ini file is nothing else than a parameter tree of key-value pairs. For convenience one can use sections to avoid rewriting the leading part and provide more structure. This is done by using ``` [section.subsection] ``` syntax. The keys below will now be within the designated subsection. As an example, the three following ini files, are equivalent

-A *key* is a string which may be contained on a common
-group of parameters by preceding the line with the *group name* between
-brackets and/or by preceding the *key* by the *group name* separated by a dot. Notice that
-the two forms may be combined.
-
-As an example, the three following INI files, are equivalent
 <Tabs
  defaultValue="form1"
  values={[
@@ -55,7 +46,7 @@ As an example, the three following INI files, are equivalent
  <TabItem value="form1">

 ```ini title="config.ini"
-# No preceding section
+# No preceding section (everything after a '#' will be ignored)
 section.subsection.first = 1.0
 section.subsection.second = 2.0
 ```
@@ -82,3 +73,39 @@ second = 2.0

  </TabItem>
 </Tabs>
+
+
+:::tip Examples
+
+import HeatINI from '!!raw-loader!./assets/ini/heat.ini';
+import VolkaTerraINI from '!!raw-loader!./assets/ini/volka_terra.ini';
+import GreyScottINI from '!!raw-loader!./assets/ini/grey_scott.ini';
+
+<Tabs
+  groupId="config-examples"
+  defaultValue="heat"
+  values={[
+      {label: 'Heat Eqs', value: 'heat', },
+      {label: 'Volka-Terra Eqs', value: 'volka_terra', },
+      {label: 'Grey-Scott Eqs', value: 'grey_scott', },
+    ]
+  }>
+
+  <TabItem value="heat">
+    <CodeBlock language="ini" title="heat.ini" showLineNumbers>
+      {HeatINI}
+    </CodeBlock>
+  </TabItem>
+  <TabItem value="volka_terra">
+    <CodeBlock language="ini" title="volka_terra.ini" showLineNumbers>
+      {VolkaTerraINI}
+    </CodeBlock>
+  </TabItem>
+  <TabItem value="grey_scott">
+    <CodeBlock language="ini" title="grey_scott.ini" showLineNumbers>
+      {GreyScottINI}
+    </CodeBlock>
+  </TabItem>
+</Tabs>
+
+:::
--- a/doc/docusaurus/docs/input_data.mdx
+++ b/doc/docusaurus/docs/input_data.mdx
@@ -3,6 +3,9 @@ id: input_data
 title: Input Data
 description: List of possible to input data
 sidebar_label: Input Data
+tags:
+  - API
+  - CLI
 ---

 import ConfigOptsJSON from './assets/config_opts.json';
@@ -10,6 +13,10 @@ import Markdown from 'react-markdown';

 export const JoinDetailsArray = (a) => {return Array.isArray(a) ? a.join('\n') : a}

+::::note CLI Usage
+This documentation page is intended for the [Command Line Interface (CLI)](use_cli). If you're new to DuneCopasi, we recommend starting with our [Tutorials](/tutorials).
+::::
+
 Several input data files in the `dune-copasi` program are possible:

 ### Config Options (INI Format)
@@ -85,4 +92,4 @@ Notice how `position_x` and `position_y` are assigned on each grid cell to deter
 If the resulting function `{tkn}` is evaluated outside the domain of the `tiff` image, the
 arguments will be [clamped](https://en.wikipedia.org/wiki/Clamping_(graphics)) to
 the nearest valid point in the domain.
-:::
\ No newline at end of file
+:::
--- a/doc/docusaurus/docs/install.mdx
+++ b/doc/docusaurus/docs/install.mdx
+---
+id: install
+title: Installation Options
+description: What are the installation options?
+sidebar_label: Install
+tags:
+  - Docker
+  - Debian
+  - GUI
+  - API
+  - CLI
+---
+
+import DocCardList from '@theme/DocCardList';
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
+import {useCurrentSidebarCategory} from '@docusaurus/theme-common';
+import React, { useState } from 'react';
+
+:::tip CLI on the Web Browser
+If you're interested in exploring and using the [Command Line Interface (CLI)](use_cli) without installation, you're in luck! The [Web Browser executable](try) allows you to interact with the CLI directly from any device. No setup required—just open your browser and start experimenting!
+:::
+
+
+## Tailored Recommendations
+
+Getting started with DuneCopasi might seem daunting due to its wide range of options.
+However, by making selections below, you'll receive tailored recommendations that fit your needs and use case.
+
+export const Checklist = ({ title, options, selectedOptions, setSelectedOptions }) => {
+  const handleCardClick = (value) => {
+    setSelectedOptions((prev) =>
+      prev.includes(value) ? prev.filter((item) => item !== value) : [...prev, value]
+    );
+  };
+
+  return (
+    <div className="container">
+      <div className="card-description-container">
+        <h4 className="card-title">{title}</h4>
+      </div>
+      <div className="card-list">
+        {options.map(({ value, label }) => (
+          <div
+            key={value}
+            className={`card-container ${selectedOptions.includes(value) ? 'selected' : ''}`}
+            onClick={() => handleCardClick(value)}
+          >
+            <input
+              type="checkbox"
+              value={value}
+              checked={selectedOptions.includes(value)}
+              onChange={() => handleCardClick(value)}
+              style={{ display: 'none' }}
+            />
+            <div className="card-style">
+              <div className="card-body">
+                <h4 className="card-title">{label}</h4>
+              </div>
+            </div>
+          </div>
+        ))}
+      </div>
+    </div>
+  );
+};
+
+export const FilterDocCardList = ({ ids }) => (
+  <DocCardList
+    items={useCurrentSidebarCategory().items.filter(
+      item => !ids || ids.length === 0 || ids.includes(item.docId)
+    )}
+  />
+);
+
+export const getRecommendations = (os, usage, user) => {
+  const recommendations = [];
+
+  if (usage.includes('GUI')) {
+    recommendations.push('install_binary');
+  }
+
+  if (usage.includes('CLI')) {
+    recommendations.push('install_docker');
+    if (os.includes('Linux') && user.includes('user')) {
+      recommendations.push('install_package');
+    }
+  }
+  if (usage.includes('API')) {
+    recommendations.push('install_docker');
+    if (os.includes('Linux') || os.includes('macOS')) {
+      recommendations.push('install_source');
+    }
+  }
+
+  if (user.includes('dev')) {
+    recommendations.push('install_docker');
+    if (os.includes('Linux') || os.includes('macOS')) {
+      recommendations.push('install_source');
+    }
+  }
+
+  if (recommendations.length === 0) {
+    recommendations.push('install_binary');
+  }
+
+  return recommendations;
+};
+
+export function TailoredRecommendation() {
+  const [osSelection, setOsSelection] = useState([]);
+  const [usageSelection, setUsageSelection] = useState([]);
+  const [userSelection, setUserSelection] = useState([]);
+
+  const osOptions = [
+    { value: 'Windows', label: 'Windows' },
+    { value: 'macOS', label: 'macOS' },
+    { value: 'Linux', label: 'Linux' },
+  ];
+
+  const usageOptions = [
+    { value: 'GUI', label: 'Graphical User Interface' },
+    { value: 'CLI', label: 'Command Line Interface' },
+    { value: 'API', label: 'Application Public Interface' },
+  ];
+
+  const userOptions = [
+    { value: 'user', label: 'Simulate Models' },
+    { value: 'dev', label: 'Develop New Features' },
+  ];
+
+  const recommendations = getRecommendations(osSelection, usageSelection, userSelection);
+
+  return (
+    <div>
+      <Checklist
+        title="I want to use the"
+        options={usageOptions}
+        selectedOptions={usageSelection}
+        setSelectedOptions={setUsageSelection}
+      />
+      <Checklist
+        title="My Operating System is"
+        options={osOptions}
+        selectedOptions={osSelection}
+        setSelectedOptions={setOsSelection}
+      />
+      <Checklist
+        title="I want to"
+        options={userOptions}
+        selectedOptions={userSelection}
+        setSelectedOptions={setUserSelection}
+      />
+
+      <div className="recommendation-container">
+        <h3 className="recommendation-title">Recommendations:</h3>
+        {recommendations.length > 0 && (
+          <FilterDocCardList ids={recommendations} />
+        )}
+      </div>
+    </div>
+  );
+}
+
+<TailoredRecommendation />
+
+
+
+## Installation Guides by Category
+
+Explore the installation options organized by different categories:
+
+### By usage interface
+
+<Tabs className="unique-tabs">
+  <TabItem value="GUI" label="Graphical User Interface">
+    <FilterDocCardList ids = {['install_binary']}/>
+  </TabItem>
+  <TabItem value="CLI" label="Command Line Interface" default>
+    <FilterDocCardList ids = {['install_docker', 'install_package', 'install_source']}/>
+  </TabItem>
+  <TabItem value="API" label="Application User Interface">
+    <FilterDocCardList ids = {['install_docker', 'install_source']}/>
+  </TabItem>
+</Tabs>
+
+### By operating system
+
+<Tabs className="unique-tabs">
+  <TabItem value="Windows" label="Windows">
+    <FilterDocCardList ids = {['install_binary', 'install_docker']}/>
+  </TabItem>
+  <TabItem value="macOS" label="macOS" default>
+    <FilterDocCardList ids = {['install_docker', 'install_source']}/>
+  </TabItem>
+  <TabItem value="Debian" label="Linux (Debian 11)">
+    <FilterDocCardList ids = {['install_package', 'install_docker', 'install_source']}/>
+  </TabItem>
+  <TabItem value="Linux" label="Linux (Other)">
+    <FilterDocCardList ids = {['install_docker', 'install_source']}/>
+  </TabItem>
+</Tabs>