I want to run simulations of various metabolic pathways – the project could end up becoming quite large, and having a machine readable chart would make thing a lot easier. Does anyone know if there is a machine readable file of Dr. Gerhard Michal's famous metabolic pathways chart?

  • $\begingroup$ Can you think of any format you would like this map to be in? $\endgroup$ – Remi.b Apr 6 '16 at 0:59
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    $\begingroup$ If yes, you could maybe email ROCHE directly to ask. I am not so familiar with the standard methods used in numerical simulation of metabolic pathway to know whether there is such thing as a standard format for this kind of data. $\endgroup$ – Remi.b Apr 6 '16 at 1:03
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    $\begingroup$ Can you give more details about the sort of simulations you want to run? $\endgroup$ – curious_cat Apr 6 '16 at 18:58

Roche's Biochemical Pathways works as a big png image and just put labels on the map. But you could try to extract data using queries like http://biochemical-pathways.com/pol/fts/query?query=Glutarate It seems to be legal as it's not prohibited.

Escher is a good pathway visualization tool where you can save map in JSON or SVG.

Another choice is VMH (Virtual Metabolic Human) - the virtual metabolic human database provides literature-derived information on human metabolism, gut microbial metabolism, nutrition, and diseases.

Reactome has two layer map - first layer is biological interactions, second layer is pathways.


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