8  Selection of tools

8.1 Scientific publishing

The following tools might be of interest for creating scientific content with embedded code.

• Jupytext documentation
• Jupyter Book
• Weave.jl - Scientific Reports Using Julia
• Franklin - Building static websites in Julia
• Pluto.jl - interactive Julia programming environment
• Quarto

8.2 Scientific web apps

Some practical tools for creating web applications for scientific applications:

• Gradio
• Panel
• Streamlit
• Trame
• Voilà

8.3 API and databases

Python:

• FastAPI
• Pydantic
• TinyDB

Rust (frameworks):

• Actix
• Axum
• Rocket

Rust databases:

• redb
• ReefDB
• sled

8.4 Graphics

• Fiji

• gnuplot

• Graphviz

8.5 Geometry

• blender: the most powerful 3D (in the general sense) open source modeling tool; allows geometries to be exported to STL, which is compatible with most meshing software.

• FreeCAD: contrarily to blender, this is the most mature open source modeling tool in the technical sense. It supports both 3D conception and detailed drawing, among other features.

• cadquery: a simple parametric geometry tool.

• Salome: not just grometry, but also a large meshing toolbox provided by EDF.

8.6 Meshing

• gmsh: the to-go meshing tool for 2D geometries and visualization of many formats of 3D meshes; before trying to produce reliable structured meshes and geometry in 3D some ninja skills need to be developed. Its own scripting language makes parametric meshing easy.

• MeshLab: allows to manipulate triangulated grids generated in CAD; helpful for preparing patches for use with #OpenFOAM/snappyHexMesh.

8.7 Rendering

• ParaView: the de facto post-processing tool for many fields of application.

• trame: rendering results in web-applications.

8.8 Simulation

• Cantera

• CasADi

• DualSPHysics

• DWSIM

• Elmer: multiphysics FEM toolkit (see dedicated topic); download it here

• FreeFem++

• LAMMPS

• MFiX

• OpenFOAM: general purpose FVM CFD toolkit (see dedicated topic).

• OpenModelica

• RadCal

• SU2

• TRUST Platform: the basis for TrioCFD code by CEA.

8.9 Productivity

Obsidian is the de facto solution for note-taking and second brain management, but it is not free for commercial ends and that has become a problem for my intended work use. Looking for alternatives for this tool which is my main productivity setting, I came across the following packages. Testing was done with I want it to be the same mindset and if after a few minutes I was not convinced by the application, it was automatically discarded. In summary, I liked both Joplin and Zettlr but will pursue the use of the latter only as Joplin does not meet by criteria. StandardNotes is a false open-source package and logseq is still too raw for any production setting.

Software	Pros	Cons
laurent22/joplin	Rich interface with many features; excellent tool if you are not seeking version control as a target. Available as portable executable.	Counterintuitive interface and files are not directly stored as .md; file system synchronization requires and absolute path. After closing the executable, a process was kept alive.
logseq/logseq	Available as portable executable.	Poor UI at first sight. Fast but dumb in the sense it will only support one file with a given title, what is incompatible with my way of organizing directories. Pages are not organized as in the folder view.
standardnotes/app	Interface is cleaner/less cluttered than Joplin. Available as portable executable.	Stopped using it as received the first notification that smart tags require a paid plan. Also only plain text files are supported in free mode.
Zettlr/Zettlr	Support to YAML frontmatter. UI gets better as you open files. Integration to BibTeX.	Poor UI at first sight. Not available as portable executable; but installation can be done in any user folder, what is also fine. It took a long time to import my existing second brain and sometimes it glitches/has some lags.

8.10 Other

• protobuf: for parsing #OpenFOAM dictionaries from Python.