I used cobrapy to calculate the maximum ehtanol yield from glucose using the iMM904 yeast model.
The results were correct, but the reactions do not map to the escher map in some cases. See cell 19 here:
A good example is the HEX1 reaction on the canvas which is zero since the model
uses the GLUK reaction for what is essentially the same reaction. Do I have to delete these reactions in the model
or can I make escher show the correct reaction?
Message: Invalid type. Expected String but got Integer. Schema path: https://escher.github.io/escher/jsonschema/1-0-0#/items/1/properties/reactions/patternProperties/[0-9]+/properties/segments/patternProperties/[0-9]+/patternProperties/(from|to)_node_id/type
to_node_idshould be strings, not integers
notesproperty for genes referring to
original_bigg_ids. escher.github.io doesn't complain about it even though it is not a valid map according to https://github.com/zakandrewking/escher/blob/master/jsonschema/1-0-0. Then I figured that quite a lot of these maps exist on GitHub https://github.com/search?q=original_bigg_ids&type=Code Does anyone know how this came about? Is this maybe the result of some kind of automatic conversion? Should the schema be relaxed maybe to to allow additional properties at https://github.com/zakandrewking/escher/blob/master/jsonschema/1-0-0#L96?