Import common-name metabolites in model creation (step 4)

[JoshLoecker]

Movivation

Adding reactions to MADRID can be tedious, because specific reaction names are required.

It would be beneficial to be able to include a common name (i.e., L-glutamine, glutamic acid, etc.) instead of the reaction name currently required by MADRID's model creation step (i.e., EX_gln_L[e])

Using web scraping or an API access for the Human Metabolome Database, it should be possible to obtain reaction information for common-name metabolites

Input

Input would come from a list of common metabolite names

Output

The output would be the reaction listed in HMDB, and saved to an output file. This file can be merged with the default file included in MADRID (i.e., bcell_boundary_rxns.csv).

[JoshLoecker]

Started in branch https://github.com/HelikarLab/MADRID/tree/feature/issue_90

[JoshLoecker]

This has been reworked to include a more readable input list, such as follows

Reaction	Abbreviation	Compartment	Minimum Reaction Rate	Maximum Reaction Rate
Exchange	glc_D	Extracellular	-100	1000
Demand	15HPETATP	Cytosol	-1	1000
Sink	met_L	Internal Membranes	-1000	1