jonrkarr
commented
4 years ago - Added README to the examples directory
- Renamed metabolic example subdirectories
- Added provenance to metabolism example files
- Grouped the metabolic models in docs.html, re-titled the examples, and noted that they are discussed in the supplementary materials
Hi Jonathan,
On the website ("Download additional examples"), in
Metabolomics: Khodayari & Maranas kinetic model of Escherichia coli metabolism Metabolomics: Gerosa thermodynamic model of Escherichia coli metabolism
I would replace "Metabolomics" by "Metabolic models". Also it could be marked more clearly that these are the examples discussed in the paper SI. Maybe you could group them together, like the SBtab files, and add this info in the header line, like "Metabolic models (see [OUR PAPER REFERENCE])"
In the github repository https://github.com/KarrLab/obj_tables/tree/master/examples/ the directory names
metabolic_kinetics metabolic_merged metabolic_reactions metabolic_thermodynamics
are not fully self-explaining, and in the subdirectories (and data files) there is no clear reference to the original papers, nor to our paper.
If it's easily possible, I would put these four subdirectories together in a subdirectory, with a README.md files briefly explaining how they were retrieved and modified. Ideally, there should also be a bit of provenance information in the data files themselves (at least a link pointing back to the github directory where this information can be found).
Thank you!
Best, Wolf