2. Escher, COBRA, and COBRApy

Escher can be used as an independent application, but it draws heavily on the information in COBRA models. A COBRA model is a collection of all the reactions, metabolites, and genes known to exist in an organism. (In the literature, these are generally called genome-scale models (GEMs), but we refer to them as COBRA models here to emphasize that Escher interoperates with models that are exported from COBRApy.)

By loading a COBRA model into the Escher interface, you have access to every reaction and metabolite in that model. You also have the gene reaction rules for the reactions in the network, which allow you to connect gene data to reactions and metabolites.

COBRApy is a software package for COBRA modeling written in Python. The Escher Python package uses COBRApy package for reading and writing COBRA models.

2.1. Maps and models

In Escher, you will see references to maps and models.

A map contains the reactions and metabolites that you see in the Escher builder, including their locations, text annotations, and the canvas.

A model (a COBRA model) contains reactions and metabolites that you have not drawn yet. Thus, you can load a COBRA model when you want to draw new reactions on the map.

2.2. What is JSON and why do we use it?

Both Escher maps and COBRA models are stored as JSON files. JSON is a useful, plain-text format for storing nested data structures. We use JSON much like the SBML community uses XML. You may notice that SBML files have a .xml extension, and Escher maps and COBRA models have a .json extension.

You can use Python to explore a JSON file like this:

import json

with open('map.json', 'r') as f:
    map_object = json.load(f)

print map_object[0]
print map_object[1]['reactions'].values()[0]

2.3. Escher, SBML, and SBGN

A tool has been developed for converting Escher maps to SBML Layout and SBGN, and it will be released soon.

COBRA models can be converted to SBML using COBRApy.