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The docs are more like a collection of ideas now, we should give it a clear tutorial structure.
My idea for the structure is as follows:
Introduction, what does COBREXA solve and what it does not solve
Totally primitive example ((down)load 1 model and do 1 FBA)
Section with tutorials
Model loading and conversion
Running FBA, FVA and sampling on small models
Running FVA on HPCs
Modifying and saving the models (Serialize, "export" through conversion to JSON/MAT and saving.)
Section with advanced tutorials
Using modifications to scan for many model properties at once (this still needs to be implemented, but it's hopefully 50LOC :D )
Using a custom model structure
Writing own reconstructions and modifications and running them on HPC
Using the extra information in StdModel to screen through many model variants, e.g. knockouts or something (I guess some of the original tutorials may sink in here)
Examples (aka backing notebooks)
Loading and saving
Simple FBA and FVA
Sampling and seeing the results
Parallel FVA
Knockouts
Custom models
Function documentation (REFERENCE, this should correspond to the structure in src/ as much as possible. I'd still separate it into some roughly consistent functions ordered by kinda bottom-up structure)
Types
IO
Analysis functions
Sampling
Modifications and reconstruction functions
Utils+misc
Feel free to edit/suggest.
The text was updated successfully, but these errors were encountered:
The docs are more like a collection of ideas now, we should give it a clear tutorial structure.
My idea for the structure is as follows:
Feel free to edit/suggest.
The text was updated successfully, but these errors were encountered: