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The BiGG Models website server
http://bigg.ucsd.edu
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Model usage notes #163

Open zakandrewking opened 9 years ago

zakandrewking commented 9 years ago

It would be great to add notes on how to use the model. For example, the iJO1366 paper says this:

By default, the core biomass reaction is set as the objective to be maximized. Certain reactions are by default constrained to carry zero flux to avoid unrealistic behaviors. These reactions are CAT, DHPTDNR, DHPTDNRN, FHL (formate hydrogen lyase), SPODM, SPODMpp, SUCASPtpp, SUCFUMtpp, SUCMALtpp, and SUCTARTtpp.

This could be added with another flat file (preference file).

draeger commented 9 years ago

This is an excellent idea. However, why using additional flat files when we have a database? The description column in the model table would perfectly suitable for this. However, the following query doesn't currently yield meaningful descriptions:

SELECT bigg_id, description FROM model;

The result is something like this:

bigg_id description
iJO1366 iJO1366
iAF1260 iAF1260
iMM904 iMM904
iSB619 iSB619
RECON1 RECON1

Wouldn't it be better to write this usage information in the description? Or, if this is not desired, add another column to the model table?